The general webchat topics addressed by the Dana-Farber doctors are listed below. For your convenience, we also provided the approximate video start time associated with each discussion topic. The entire video runs 49 minutes and 20 seconds.
Various types/subtypes of ovarian cancer and treatment differences. [1:40 minutes]
CA-125 and other ovarian cancer biomarkers. [5:10 minutes]
Areas of ongoing ovarian cancer research. [9:28 minutes]
Ovarian cancer treatment alternatives to standard of care chemotherapy. [13:55 minutes]
PARP Inhibitors & Immunotherapy. [15:03 minutes]
Mechanisms to reverse platinum drug resistance. [17:15 minutes]
Correlation between ovarian cancer and HPV (Human papillomavirus). [19:30 minutes]
The use of clinical trials for the treatment of ovarian cancer. [19:43 minutes]
Stage 1 ovarian cancer prognosis. [21:47 minutes]
Gene mutations related to hereditary ovarian cancer risk. [22:55 minutes]
Treatment options for platinum drug refractory/resistant ovarian cancer. [25:27 minutes]
Treatment of BRCA gene-mutated ovarian cancer patients. [27:50 minutes]
Ovarian cancer prevention. [30:18 minutes]
Promising treatments for ovarian clear cell cancer. [31:43 minutes]
Proper nutrition during and after ovarian cancer treatment. [33:47 minutes]
Symptoms associated with an ovarian cancer recurrence. [35:06 minutes]
Ovarian neuroendocrine cancer. [36:16 minutes]
Small-cell ovarian cancer. [39:22 minutes]
Origin of ovarian cancer. [42:41 minutes]
Treatment options for isolated or limited recurrent ovarian cancer tumors/lesions. [45:26 minutes]
Closing: Most Exciting Ovarian Cancer Developments. [47:07 minutes]
A preliminary report from the Caris Registry™ demonstrated significantly longer post-profiling survival in patients with ovarian, Fallopian tube or primary peritoneal cancer who were given treatments that their tumor profile showed were likely to benefit.
The preliminary report from the Caris Registry™ demonstrated significantly longer post-profiling survival in patients with ovarian, Fallopian tube, or primary peritoneal cancer who were given treatments that their tumor profile showed were likely to benefit them, as compared with patients who were treated with drugs that profiling suggested would be less effective. Data revealed that patients whose treatment was guided by tumor profiling had a 46% lower risk of death (Hazard Ratio = 0.54, p value = 0.0018).
The comprehensive tumor profiling service used in the study measures a broad range of cancer “biomarkers” (proteins, genes or other molecules that affect how cancer cells grow, multiply and respond to therapies) and interprets the results to identify treatments most likely to be of benefit and help eliminate those that are less likely to benefit the patient. The results allow oncologists to better determine appropriate treatments for each patient, based on the individual makeup of their cancer rather than the site of the tumor.
Data from earlier studies show that comprehensive tumor profiling consistently identifies biomarkers linked to specific treatments in over 90% of patients, and that clinicians change their intended treatment decision based on profiling results in over 80% of cases. Across a range of cancer types, tumor profiling-guided treatment has been shown to benefit patients and improve outcomes when compared to unguided treatment. The ESGO data demonstrate that for many ovarian cancer patients who have run out of options, comprehensive tumor profiling consistently offers oncologists actionable insights to help choose a patient’s next treatment and can improve patient outcomes.
“The data presented at ESGO this year further support the use of comprehensive tumor profiling. It offers new options to patients whose cancers are difficult to treat or rare, or who have exhausted standard treatment options. I’m extremely excited to see this breadth of research on a global platform and I am hopeful that profiling will be rapidly adopted in clinical practice in Europe.”
“In order to improve the outlook for women with ovarian cancer, we need to know much more about types of tumors, and tumor profiling is becoming paramount in this area. We are hugely impressed that Caris is investing in research to provide information on ovarian tumors and we hope that this potentially leads to a breakthrough in treatment which may subsequently impact survivorship.”
Andreas Voss, VP of Medical & Clinical Affairs, Caris Life Sciences
Andreas Voss, Vice President, Medical and Clinical Affairs, Caris Life Sciences said:
“Comprehensive tumor profiling is a hot topic this year. It is becoming increasingly clear that the best approach to tumor profiling is to use a variety of methods to test for mutations, gene expression levels, and protein biomarkers. These combined analyses provide a comprehensive report and actionable treatment options for oncologists. Caris Molecular Intelligence™ remains the world’s most advanced commercial tumor profiling service – we are proud to be working with leading oncologists worldwide to bring the benefits of tumor profiling to cancer patients.”
Caris Molecular Intelligence™ is not yet formally reimbursed across Europe but it is available to purchase in all European markets. Individual insurance companies, clinics and organizations in some countries have agreed to reimburse the service on application. Caris Life Sciences is dedicated to working to ensure the service is reimbursed across Europe.
About Caris Life Sciences and Caris Molecular Intelligence™
Caris Life Sciences is a leading biosciences company focused on fulfilling the promise of precision medicine. Caris Molecular Intelligence™, the industry’s first and largest tumor profiling service, provides oncologists with the most potentially clinically actionable treatment options available to personalize care today. Using a variety of advanced and clinically validated technologies, which assess relevant biological changes in each patient’s tumor, Caris Molecular Intelligence correlates biomarker data generated from a tumor with biomarker/drug associations derived from the cancer clinical literature. The company is also developing a series of blood tests based on its proprietary Carisome® TOP™ platform, a revolutionary blood-based testing technology for diagnosis, prognosis, and theranosis of cancer and other complex diseases. Headquartered in Irving, Texas, Caris Life Sciences offers services throughout Europe, the U.S., Australia, and other international markets. To learn more, please visit http://www.carislifesciences.eu.
Andrea Sloan, a 7-year survivor of stage 3c ovarian cancer, is seeking a “compassionate use” exemption from pharmaceutical company BioMarin to save her life. Sloan is scheduled to start treatment at the M.D. Anderson Cancer Center on September 5 and would like to obtain access to the “PARP 1/2 inhibitor” drug known as “BMN 673” by that time. A robust grassroots campaign in support of Sloan has emerged on social media and Change.org in an effort to get an affirmative response from BioMarin.
Andrea Sloan, a 7-year, stage 3c survivor of ovarian cancer, is seeking a “compassionate use” investigational cancer drug exemption from pharmaceutical company BioMarin to save her life. Sloan, the executive director of a non-profit that advocates for survivors of domestic violence and abuse, now finds herself forced to publicly advocate for herself in a last chance effort to get the cancer treatment she needs.
Drugs that are being tested but have not yet been approved by the U.S. Food and Drug Administration (FDA) are called “investigational drugs.” These drugs are generally available only to people who are taking part in a clinical trial. The FDA “Expanded Access” protocol — sometimes referred to as a “compassionate use” exemption — involves the use of an investigational drug outside of a clinical trial to treat a patient with a serious or immediately life-threatening disease or condition, who has no comparable or satisfactory alternative treatment options.
FDA regulations allow access to investigational drugs for treatment purposes on a case-by-case basis for an individual patient, or for intermediate-size groups of patients with similar treatment needs who otherwise do not qualify to participate in a clinical trial. Before an investigational drug can qualify for compassionate use, the patient’s physician, the FDA, and the drug manufacturer must approve such use.
Unfortunately, drug manufacturers may not always be willing or able to provide access to a drug outside of their clinical trials. By law, drug companies are not required to make their drug available through the FDA expanded access protocol, or to make more of a drug for that purpose.
Andrea Sloan, a 7-year survivor of stage 3c ovarian cancer, is seeking a compassionate use exemption from pharmaceutical company BioMarin to save her life. Sloan is scheduled to start treatment at the University of Texas M.D. Anderson Cancer Center on September 5, and she would like to obtain access to the “PARP 1/2 inhibitor” drug known as “BMN 673” by that time. A robust grassroots campaign in support of Sloan has emerged on social media and Change.org in an effort to get an affirmative response from BioMarin.
“BioMarin’s BMN 673 offers me the best chance at a long life,” said Sloan. “My doctors and the FDA agree that I am an excellent candidate for this drug and meet the criteria for compassionate use exemption. However, BioMarin’s lack of a policy on compassionate use is preventing me from gaining access to the drug I need to save my life. I respectfully implore them to reconsider and make the ethical decision to help me.” [Emphasis added]
Sloan has endured two full rounds of chemotherapy, five surgeries, and a stem cell transplant. While her cancer remains responsive to treatment, her bone marrow can no longer tolerate traditional therapies. Her world-class oncology team at M.D. Anderson believes that BioMarin’s PARP inhibitor BMN 673, which is currently being tested in a phase I solid tumor clinical trial, is the best option for Sloan’s BRCA-1 gene-mutated form of ovarian cancer.
Unfortunately, Sloan hit a barrier in gaining access to BMN 673. Further enrollment of ovarian cancer patients in the phase I solid tumor trial is now closed, and the publicly announced portion of the trial that will be entering phase III testing is only open to BRCA gene-mutated breast (but not ovarian) cancer patients. Therefore, Sloan is left with the compassionate use exemption as her only option to access the drug she needs to fight her cancer. Based on FDA requirements, Sloan qualifies for the compassionate use exemption. Data emerging from the phase I BMN 673 study suggest that the drug is a safe and effective treatment option for patients with BRCA gene-mutated ovarian cancer.
Moreover, on August 16, 2013, BioMarin announced that its medical study abstract, entitled “PARP inhibition with BMN 673 in ovarian and breast cancer patients with deleterious mutations of BRCA1 and BRCA2,” has been selected as a “late breaking” abstract by the 17th ECCO — 38th ESMO — 32nd ESTRO European Cancer Congress, which will be held from September 27 through October 1, 2013 in Amsterdam, The Netherlands. BioMarin’s oral presentation at the European Cancer Congress (scheduled for September 29, 2013) will include data presented from 28 ovarian cancer patients with deleterious germline (inherited) BRCA gene mutations, including 17 patients from the phase I BMN 673 trial dose escalation cohort (range 100 µg to 1100 µg) and 11 patients from the dose expansion cohort. Presumably, the most recent ovarian cancer patient data to be presented at the European Cancer Congress will expand upon the positive data presented by the company at the 2013 Annual Meeting of the American Society of Clinical Oncology, which indicate that positive RECIST (“Response Evaluation Criteria in Solid Tumors“) and/or CA-125 ovarian cancer patient responses occurred at BMN 673 drug doses ≥ 100 µg/d in 11 out of 17 (64%) BRCA gene-mutated ovarian and peritoneal cancer patients. The positive RECIST medical imaging findings and the CA-125 blood test results highlight the promising effectiveness of BMN 673, albeit among a small group of ovarian cancer patients.
BMN 673 is a targeted therapy designed to disrupt the tumor without traditional chemotherapy drug side effects, thereby making it an optimal treatment for Sloan.
Despite Sloan’s best efforts, she has been unable to convince BioMarin to allow compassionate use of BMN 673. BioMarin, according to Sloan, has not been cooperative, merely citing their lack of a policy on the issue. Sloan, the executive director of a non-profit that advocates for survivors of domestic violence and abuse, now finds herself forced to publicly advocate for herself in a last chance effort to save her life. Sloan is committed to advocating for meaningful reform on this topic and hopes BioMarin will lead by example in starting a national dialogue.
If you would like to help Andrea Sloan obtain compassionate use of BMN 673, please click on this picture and sign her petition at Change.org.
For those interested in supporting Andrea Sloan, please sign her petition on Change.org that urges BioMarin to grant her a compassionate use investigational cancer drug exemption for BMN 673. Also, you can follow Andrea on Twitter at @andi_sloan.
Yesterday, BioMarin issued a statement to KXAN, an Austin, Texas local affilate of NBC, in response to a in-depth news story that KXAN aired tonight regarding Andrea Sloan’s dire situation. Effectively, BioMarin rejected Andrea Sloan’s request for compassionate use of BMN 673, although its statement was worded as a general drug “expanded access” policy explanation.
BioMarin acknowledged that it allowed preapproved expanded access to one of its investigational drugs which completed phase III clinical testing last year. In terms of general guidelines for its expanded access programs, the company stated:
“We implement these [expanded access] programs when we have sufficient scientific evidence to support both the safety and the efficacy of a product for an indication. Additionally, we implement these programs only when we can ensure that access will be provided equitably, ensuring that the process is appropriately blinded, and when we are confident that the expanded access will not inhibit our clinical trial plans or clinical trials for a disease generally.”
In terms of Andrea Sloan’s specific case, BioMarin stated that it does not comment on the status of individual patients. Apparently in a refusal to grant expanded access to any preapproved patient who requests compassionate use of BMN 673 prior to completion of phase III drug testing, the company stated:
“… However, we note that, although the current data [for BMN 673] that we have looks promising, there is no data at this point to support anything beyond dosing and some preliminary safety. It is too early to know if the experimental therapy is safe or effective, or will even prolong life, until we conduct the appropriate Phase 3 trials. The data that we have is from an ongoing early stage clinical trial, and it is the first trial that we have ever done with this therapy in humans.”
Accordingly, it appears that BioMarin’s current expanded access policy for its investigational drugs, such as BMN 673, will only extend to drugs that have already completed phase III clinical trial testing.
Ovarian Cancer Survivor Andrea Sloan Seeks Compassionate Use Exemption From BioMarin to Save Her Life, Press Release, Digital Journal, August 29, 2013.
BioMarin Provides BMN 673 Program Update, BioMarin Pharmaceutical Inc, Press Release, July 25, 2013.
An Aurora A/angiogenic kinase inhibitor named “ENMD-2076” demonstrated anti-cancer activity in recurrent, platinum-resistant epithelial ovarian cancer patients, including three patients with a difficult-to-treat subtype of the disease referred to as “clear cell carcinoma.”
An Aurora A/angiogenic kinase inhibitor named “ENMD-2076” demonstrated anti-cancer activity in recurrent, platinum-resistant epithelial ovarian cancer patients, including three patients with a difficult-to-treat subtype of the disease referred to as “clear cell carcinoma.” The trial drug results were reported in connection with a phase II clinical trial testing of ENMD-2076. The findings associated with ENMD-2076 were published in the January 2013 edition of the European Journal of Cancer.
ENMD-2076 is an orally-active, Aurora A/angiogenic kinase inhibitor with a unique kinase selectivity profile and multiple mechanisms of action. ENMD-2076 has been shown to inhibit a distinct profile of angiogenic tyrosine kinase targets in addition to the Aurora A kinase. Aurora kinases are key regulators of mitosis (cell division), and are often over-expressed in human cancers. ENMD-2076 also targets the VEGFR, Flt-3 and FGFR3 kinases which have been shown to play important roles in the pathology of several cancers.
The phase II trial was an open-label, single-arm Phase II study of single agent ENMD-2076 taken daily (orally). The study enrolled 64 patients, and the progression-free survival (PFS) rate at 6 months was 22%, with a median time-to-progression of 3.6 months. The median number of prior treatment regimens per patient was two. The most common adverse events were fatigue, hypertension and diarrhea, with the most significant events being hypertension and fatigue. Unfortunately, none of the markers of mitotic index or angiogenesis evaluated in the archival tissue samples obtained were predictive of greater benefit or resistance to ENMD-2076 treatment.
Based on the foregoing results, the clinical investigators concluded that ENMD-2076 possesses anti-cancer activity in recurrent, platinum-resistant ovarian cancer, and they observed toxicities were similar to other protein kinase inhibitors. The clinical investigators also noted that additional studies with ENMD-2076 are warranted, especially in combination with active chemotherapeutic agents in platinum-resistant patients. The investigators added that further work to determine appropriate biomarkers for ENMD-2076 should be incorporated into new clinical studies.
“Epithelial ovarian cancer represents the 4th leading cause of cancer deaths among women in the United States. There is unmet medical needs to develop new drugs with fewer side effects and/or better efficacy to improve the quality and duration of life of the patients, especially those whose cancer is resistant to platinum treatment.
ENMD-2076 is a novel small molecule kinase inhibitor with unique combination of mechanisms of action that involve inhibition of several pathways key to tumor growth and survival including angiogenesis, proliferation, and the cell cycle. Based on pre-clinical and Phase 1 clinical studies of ENMD-2076, we believed that the drug candidate may play a role in fitting some of the unmet medical needs. This Phase 2 trial further demonstrates the anti-cancer activity of ENMD-2076 in yet a difficult to treat patient population of platinum-resistant ovarian cancer with tolerable side effects.”
Notably, Dr. Matulonis also commented on the anti-cancer activity of ENMD-2076 in three ovarian clear cell carcinoma patients as follows:
“ENMD-2076 also showed anti-cancer activities in patients with clear cell carcinoma [CCC], a histological subtype considered as chemo-resistant.Two of three [CCC] patients recruited had longer PFS than the median with one patient in stable disease for over two years. As recent reports suggest VEGF is frequently expressed in clear cell cancers, this subtype might be particularly responsive to therapies that incorporate VEGF inhibition. Further clinical evaluations of ENMD-2076 may therefore be warranted in this patient subset either as a single agent or in combinations.” [emphasis added]
Ken Ren, Ph.D., EntreMed’s Chief Executive Officer, further commented:
“We are very pleased and honored to have this Phase 2 trial data published in such an esteemed journal. This is a further endorsement of the global medical and science community on the clinical and scientific value of ENMD-2076 in ovarian cancer treatment. We truly believe that ENMD-2076 may potentially offer unique and competitive advantages for unmet medical needs in such difficult to treat oncology indications including platinum-resistant and/or clear cell ovarian cancer in improving the patients’ quality and duration of life. We are committed to the global clinical development of ENMD-2076 for cancer patients who might benefit from its therapy. With the support of clinical investigators like Dr. Matulonis, their commitment and dedication, and the support from our long term shareholders, we are confident that we can achieve our goal.”
EntreMed, Inc. is a clinical-stage pharmaceutical company employing a drug development strategy primarily in the United States and China to develop targeted therapeutics for the global market. Its lead compound, ENMD-2076, a selective angiogenic kinase inhibitor, has completed several Phase 1 studies in solid tumors, multiple myeloma, and leukemia, and is currently completing a multi-center Phase 2 study in ovarian cancer. EntreMed, Inc. recently initiated a dual-institutional Phase 2 study of ENMD-2076 in triple-negative breast cancer. Additional information about EntreMed is available on the Company’s web site at www.entremed.com.
ENMD-2076 is an orally-active, Aurora A/angiogenic kinase inhibitor with a unique kinase selectivity profile and multiple mechanisms of action. ENMD-2076 has been shown to inhibit a distinct profile of angiogenic tyrosine kinase targets in addition to the Aurora A kinase. Aurora kinases are key regulators of mitosis (cell division), and are often over-expressed in human cancers. ENMD-2076 also targets the VEGFR, Flt-3 and FGFR3 kinases which have been shown to play important roles in the pathology of several cancers. ENMD-2076 has shown promising activity in Phase 1 clinical trials in solid tumor cancers, leukemia, and multiple myeloma. ENMD-2076 is currently completing a Phase 2 trial for ovarian cancer. EntreMed, Inc. recently initiated a dual-institutional Phase 2 study of ENMD-2076 in triple-negative breast cancer.
ENMD-2076 received orphan drug designation from the United States Food and Drug Administration (FDA) for the treatment of ovarian cancer, multiple myeloma and acute myeloid leukemia (AML). In the United States, the Orphan Drug Act is intended to encourage companies to develop therapies for the treatment of diseases that affect fewer than 200,000 people in this country. Orphan drug designation provides seven years of market exclusivity that begins once ENMD-2076 receives FDA marketing approval. It also provides certain financial incentives that can help support the development of ENMD-2076.
Matulonis UA, Lee J, Lasonde B, et. al. ENMD-2076, an oral inhibitor of angiogenic and proliferation kinases, has activity in recurrent, platinum resistant ovarian cancer. Eur J Cancer. 2013 Jan;49(1):121-31.doi:10.1016/j.ejca.2012.07.020. PubMed PMID: 22921155.
Dana-Farber Cancer Institute’s Ursula A. Matulonis, M.D. Article on EntreMed’s ENMD-2076 Published in the European Journal of Cancer, EntreMed, Inc. Press Release, Sept. 6, 2012.
ENMD-2076 Phase II Ovarian Cancer Clinical Trial Protocol Summary:
A Phase 2 Study of Oral ENMD-2076 Administered to Patients With Platinum Resistant Ovarian Cancer, ClinicalTrials.gov Identifier: NCT01104675 (study ongoing, but not recruiting patients).
An analysis of genomic changes in high grade serous ovarian cancer provides the most comprehensive and integrated view of cancer genes for any cancer type to date. Ovarian serous adenocarcinoma tumors from 489 patients were examined by The Cancer Genome Atlas (TCGA) Research Network and its analyses are reported in the June 30, 2011 issue of Nature.
Histopathological image of ovarian serous adenocarcinoma arising in bilateral ovaries. (Photo: The Cancer Genome Atlas)
An analysis of genomic changes in high grade serous ovarian cancer has provided the most comprehensive and integrated view of cancer genes for any cancer type to date. Ovarian serous adenocarcinoma tumors from 500 patients were examined by The Cancer Genome Atlas (TCGA) Research Network and analyses are reported in the June 30, 2011 issue of Nature. 
To enhance educational learning, we recommend that readers who are less familiar with the topics presented in this article, review the seven appendices provided below, prior to reading the main article text. The topics covered in this article and accompanying appendices are set forth below in the table of contents.
Table of Contents
Introduction – The Cancer Genome Atlas
The Cancer Genome Atlas Analysis of High-Grade Serous Ovarian Cancer
Samples & Clinical Data
Demographics and Histopathology
Overall & Progression‐Free Survival
Surgical Outcome is Associated with Overall Survival, Progression-Free Survival & Platinum Status
Gene Mutation Analysis
Gene Copy Number Analysis
High-Grade Serous Ovarian Cancer Subtypes & Patient Outcome Prediction.
Four HG-OvCa Transcriptional Subtypes Based Upon mRNA Analysis
Three HG-OvCa subtypes Based Upon miRNA Analysis
Four HG-OvCa Subtypes Based Upon Epigentic DNA Promoter Methylation Analysis
Transcriptional Signature Predictive of HG-OvCa Patient Survival
Targeted Therapies Based Upon Common Gene Amplifications
The Road Ahead
Limitations of The “One Target- One Drug” Approach
First Steps on the Road to Personalized Medicine.
Creation of an Ovarian Cancer Molecular Disease Model
Chemotherapy Sensitivity & Resistance Assay Testing: A “Bridge” or Adjunct to the Ovarian Cancer Molecular Disease Model?
About the National Cancer Institute
About the National Human Genome Research Institute
About the National Institutes of Health
Appendix 1- DNA & RNA
Appendix 2 – Genes, Chromosomes & Proteins
Appendix 3 – Specific Types of Gene Mutations
Appendix 4 – Epigenetics & Gene Silencing
Appendix 5 – Cellular/Biological Pathways
Appendix 6 – Targeting DNA Repair Through PARP Inhibition
Appendix 7 – PARP Inhibitors: A New Class of Targeted Therapies
Mutations in the TP53 gene are highly prevalent, occurring in at least 96% of HGS-OvCa samples.
Low prevalence (2% – 6% of samples) but statistically recurrent somatic (i.e., lifetime acquired) mutations were identified in nine additional genes, including NF1, BRCA1, BRCA2, RB1 and CDK12.
Several HGS-OvCa genes that were less commonly mutated, include BRAF, PIK3CA, KRAS, and NRAS. It is believed that these mutations are rare but important drivers in HGS-OvCa.
113 significant focal DNA copy number variations, and DNA promoter methylation events involving 168 genes were identified.
Analyses delineated (i) four mRNA ovarian cancer transcriptional subtypes, (ii) three miRNA subtypes, (iii) four promoter methylation subtypes, and (iv) a transcriptional signature associated with survival duration.
Survival duration did not differ significantly among mRNA transcriptional subtypes. Survival duration differed significantly between miRNA subtypes. Patients identified within the four DNA methylation subtypes differ significantly in overall 5-year survival. Patients whose tumors possessed a gene expression signature associated with poor survival lived for a period that was 23 percent shorter than patients whose tumors did not possess such a signature.
BRCA1 and/or BRCA2 were mutated in 20% of HGS-OvCa tumors, owing to a combination of germline (i.e., inherited) and somatic (i.e., lifetime acquired) gene mutations. Analysis of these tumors confirmed prior observations that patients with mutated BRCA1 and BRCA2 genes have better survival odds than patients without mutations in these genes. Importantly, the researchers determined that the mechanism through which the BRCA1 and BRCA2 genes become defective, also relates to survival. If the BRCA1 or BRCA2 gene is mutated, there is improved survival duration. In contrast, if BRCA1 activity is reduced by methylation, there is no improved survival duration.
Cellular/biological pathway analyses suggested that a primary DNA repair process — called “homologous recombination” — is defective in about half of the HGS-OvCa tumors analysed, thereby suggesting potential use of PARP inhibitors in patients whose tumors possess such defects.
Alterations to the p53, FOXM1, RB, RAS/PI3K, and NOTCH signaling pathways were identified in 87%, 84%, 67%, 45%, and 22%, respectively, of the samples analyzed. Based upon this finding, the TCGA researchers suggested that current and future therapeutic opportunities exist. We provide below potential therapeutic approaches for each deregulated pathway.
22 recurrently amplified genes were identified in at least 10% of the HGS-OvCa samples. The TCGA researchers provided a list of existing experimental and U.S. Food & Drug Administration (FDA)-approved drugs or compounds which could theoretically target the recurrent problematic genes. We added additional experimental and FDA-approved drugs or compounds to the list provided by the TCGA researchers.
The gene mutation spectrum identified in the TCGA study confirms that HGS-OvCa is completely distinct from other epithelial ovarian cancer histological subtypes. For example, clear-cell ovarian cancer tumors possess few TP53 gene mutations but have recurrent ARID1A and PIK3CA gene mutations; endometrioid ovarian cancer tumors possess frequent CTNNB1, ARID1A and PIK3CA mutations, but possess a lower rate of TP53 gene mutations; and mucinous ovarian cancer tumors have prevalent KRAS gene mutations. The differences between epithelial ovarian cancer subtypes represent an opportunity to improve ovarian cancer outcomes through subtype-stratified care.
There are significant limitations to the “one drug-one target” approach to personalized medicine; however, scientific progress is being made through molecular/genomic tumor profile testing used to identify individualized cancer therapy.
The creation and continual refinement of an online ovarian cancer molecular disease model (MDM), similar to the melanoma MDM published recently as part of the Cancer Commons project, should be made a priority based upon the high mortality rate associated with the disease.
Chemotherapy sensitivity and resistance assay (CSRA) technology should be further developed through clinical testing. CSRAs could act as a “bridge” or adjunct to the ovarian cancer molecular disease model.
“This landmark study is producing impressive insights into the biology of this type of cancer. It will significantly empower the cancer research community to make additional discoveries that will help us treat women with this deadly disease. It also illustrates the power of what’s to come from our investment in TCGA.”
— Francis Collins, M.D., Ph.D., Director, National Institutes of Health
Introduction – The Cancer Genome Atlas
Researchers working at a NHGRI-supported large-scale sequencing center. (Photo: The Cancer Genome Atlas)
A NHGRI researcher uses a pipette to prepare DNA for sequencing. (Photo: The Cancer Genome Atlas)
The TCGA is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which are both part of the National Institutes of Health (NIH), U.S. Department of Health and Human Services (HHS). Started in 2006, the mission of the TCGA pilot programs is to map the genomic changes in brain, lung and ovarian cancers, and assess the feasibility of a full-scale effort to systematically explore the entire spectrum of genomic changes involved in every major type of human cancer. The ultimate goal is to create a resource that will be used to develop new strategies for preventing, diagnosing and treating cancer.
Ovarian cancer is the fifth-leading cause of cancer death among women in the United States; in 2011, an estimated 21,990 new cases will be diagnosed and 15,460 deaths will occur.  Most patient deaths (i.e., approximately 70%) occur in those women presenting with advanced-stage, high-gradeserous ovarian cancer. [3-4] The standard treatment for HGS-OvCa is aggressive surgery followed by platinum–taxane chemotherapy (e.g., carboplatin and paclitaxel). After therapy, platinum-resistant cancer recurs in approximately 25% of patients within six months,  and the overall five-year survival probability is 31% . Approximately 13% of HGS-OvCa is attributable to germline (i.e., inherited) mutations in the BRCA 1 or BRCA 2 gene [7-8], and a smaller percentage can be accounted for by other germline mutations. However, most ovarian cancer can be attributed to a growing number of somatic (i.e., lifetime acquired) aberrations.
The lack of successful ovarian cancer treatment strategies led the TCGA researchers to (i) measure comprehensively genomic and epigenomic abnormalities with respect to clinically-annotated HGS-OvCa tumor samples, and (ii) identify molecular abnormalities that influence pathophysiology, affect outcome, and constitute therapeutic targets. Microarray analyses produced high-resolution measurements of mRNA expression, miRNA expression, DNA copy number variations, and DNA promoter methylation for 489 HGS-OvCa tumors. Massive parallel sequencing coupled with hybrid affinity capture [10-11] provided whole-exome DNA sequence information for 316 of these samples. [See Appendices 1 & 2]
“The new knowledge of the genomic changes in ovarian cancer has revealed that the molecular catalysts of this disease are not limited to small changes affecting individual genes. Also important are large structural changes that occur in these cancer genomes. Cancer researchers can use this comprehensive body of information to better understand the biology of ovarian cancer and improve the diagnosis and treatment of this dreaded disease.”
— Harold E. Varmus, M.D, Director, National Cancer Institute; Co-Recipient, 1989 Nobel Prize in Physiology or Medicine for discovery of the cellular origin of retroviral oncogenes.
The Cancer Genome Atlas Analysis of High-Grade Serous Ovarian Cancer
Samples & Clinical Data
In this study, TCGA researchers report the analysis of 489 clinically-annotated stage II-IV, HGS-OvCa tumor samples and corresponding normal DNA. Serous adenocarcinoma is the most prevalent form of ovarian cancer, accounting for approximately 85 percent of all ovarian cancer deaths. TCGA researchers completed whole-exome sequencing, which examines the protein-coding regions of the genome, on an unprecedented 316 tumors. They also completed other genomic characterizations with respect to these tumors and an additional 173 samples. The HGS-OvCa tumor samples were surgically resected before systemic treatment, but all patients received a platinum drug and 94% of patients received a taxane drug. The medianprogression-free survival (PFS) and overall survival (OS) of the cohort are similar to those identified in previously published trials. [12-13] Twenty-five percent of the patients remained free from disease and 45% were alive at the time of last follow-up, whereas 31% experienced disease progression within six months of completing platinum-based therapy. The median follow-up time was 30 months (range, 0–179 months).
1. Demographics and Histopathology
As noted above, the characteristics of the HGS-OvCa cases reflect the general population of women with advanced ovarian cancer. Patients reflected the age at diagnosis, stage, tumor grade and surgical outcome of individuals typically diagnosed with HGS-OvCa. Specifically, the average age of women at diagnosis was 60.2 years; all cases possessed serous histology; 79% of cases were FIGO (International Federation of Gynecology and Obstetrics) stage III (with 73% of those cases designated stage IIIC); 16% of cases were FIGO stage IV; 88% of tumors were grade 3; 72% of patients experienced recurrent disease; and 73% of patients had optimal surgical cytoreduction. “Optimal cytoreduction” was defined as ≤ 1 centimetre (cm) of residual disease remaining after surgery. In addition, 69% of the cases represented platinum-sensitive disease, whereas 21% of cases were platinum-resistant. Generally, platinum status was defined as “resistant” when the platinum free interval was less than six months and the patient had progressed or recurred. Platinum status was defined as “sensitive” when the platinum free interval was six months or greater.
2. Overall & Progression‐Free Survival
Patient age at diagnosis was associated with OS. Platinum status was associated with both PFS and OS. Stage III and optimal surgical cytoreduction cases demonstrated a trend toward improved OS. The median PFS and OS was 16.7 and 43.4 months for FIGO stage III patients, and 14 and 32.9 months for FIGO stage IV patients, respectively (p value (p) = 0.12 for PFS and p = 0.07 for OS). The median PFS and OS was 16.7 and 44.2 months for optimally debulked patients, and 15.4 and 36.2 months, respectively, for suboptimally debulked patients (p = 0.34 for PFS and p = 0.06 for OS). The median OS was 57.9 months for platinum-sensitive patients and 33.2 months for platinum-resistant patients (p =3.5‐19).
In a multivariate analysis, the patient’s age at diagnosis and platinum status were independently associated with OS (hazard ratio (HR) = 1.02, 95% confidence interval (CI):1.00‐1.03; HR = 3.69, 95% CI: 2.60‐5.21, respectively). Stage and platinum status were independently associated with PFS (HR = .80, 95% CI: 0.66‐0.96; HR = 25.6, 95% CI: 15.9‐41.7, respectively).
3. Surgical Outcome is Associated with Overall Survival, Progression-Free Survival & Platinum Status
Many recent studies have demonstrated that patients left with microscopic residual disease after surgical cytoreduction have an improved outcome when compared with other optimally or suboptimally debulked patients. [14-17] Accordingly, the researchers examined the PFS and OS of the TCGA ovarian cancer patients in relation to the size of residual disease after surgical cytoreduction.
Size of residual disease was microscopic in 90 (21%) cases; between 1 and 10mm (i.e., .1 cm to 1 cm) in 223 (52%) cases; between 11 and 20mm (i.e., 1.1 cm to 2cm) in 30 (7%) cases; and more than 20mm (i.e., 2cm) in 89 (20%) cases. TCGA ovarian cancer patients left with microscopic residual disease had improved PFS and OS when compared to patients left with optimal, macroscopic residual disease or suboptimal residual disease. The median PFS was 21.8 months for patients with microscopic residual disease, and 15.0 months for patients with more than microscopic residual disease (p = 0.001). The median OS was 57.4 months for patients with microscopic residual disease and 38.1 months for patients with more than microscopic residual disease (p = 3‐4). Microscopic residual disease was found to be independently associated with OS in a multivariate analysis.
An association between surgical cytoreduction and platinum sensitivity has also been previously reported.  Considering the improved PFS and OS identified in patients with microscopic residual disease, the researchers explored the relationship between surgical cytoreduction and platinum sensitivity in the TCGA ovarian cases. They found no association between platinum status and surgical cytoreduction when defined traditionally as “optimal” or “suboptimal” based upon the measurement of macroscopic residual disease. However, when considering microscopic residual disease separately from optimally or suboptimally debulked patients, there was an association between surgical outcome and platinum status. Patients with microscopic residual disease were more likely to be platinum-sensitive than patients with macroscopic residual disease (p = 0.02; p = 0.003, odds ratio = 3.1, 95% CI: 1.44‐6.68). These data suggest that surgical cytoreduction may have a direct impact on the patient’s platinum status. Moreover, logistic regression analyses indicate that microscopic residual disease is independently associated with platinum status (p = 0.005).
Gene Mutation Analysis
Deoxyribonucleic acid (DNA) is the chemical compound that contains the instructions needed to develop and direct the activities of nearly all living organisms. DNA molecules are made of two twisting, paired strands, often referred to as a double helix.
The DNA segments that carry genetic information are called “genes.” [See Appendix 1] The “genome” is the entire set of genetic instructions found in a human cell. [See Appendix 2] The genome consists of 23 pairs of chromosomes. These chromosomes are composed of six billion individual DNA letters. In the English alphabet there are 26 letters: A through Z. In the alphabet of our genes there are four letters: A, C, G and T.
A gene is essentially a sentence made up of the chemical bases — A (adenine), C (cytosine), G (guanine), or T (thymine) — which describes how to make a protein. Any change in the sequence of bases — and therefore in the protein instructions — is called a “mutation.” Just like changing a letter in a word (or a word in a sentence) can change the meaning of the word (or sentence), a mutation can change the instruction contained in the gene. Any changes to those instructions can alter the gene’s meaning and change the protein that is made, or how or when a cell makes that protein.
“Gene expression” is the process by which the information encoded in a gene is used to direct the assembly of a protein. The sequence of the gene is read in groups of three bases. Each group of three bases — referred to as a “codon” — corresponds to one of 20 different amino acids used to build the protein. Gene mutations can (i) result in a protein that cannot carry out its normal function in the cell, (ii) prevent the protein from being made at all, or (iii) cause too much or too little of a normal protein to be made.
A mutation is a change in a DNA sequence. Mutations can result from DNA copying mistakes made during cell division, exposure to ionizing radiation, exposure to chemicals called mutagens, or infection by viruses. Germ line mutations occur in the eggs and sperm and can be passed on to offspring, while somatic mutations occur in body cells and are not passed on.
Gene mutations are broadly divided into two groups — “germline” (i.e., inherited) mutations, and “somatic” (i.e., lifetime acquired) mutations. [See Appendix 3] Gene mutations have varying effects on health, depending on where they occur and whether they alter the function of essential proteins.
The TCGA researchers performed exome capture and sequencing on (i) DNA isolated from 316 HGS-OvCa samples, and (ii) matched normal samples obtained from each individual. On average, 76% of gene coding bases were covered in sufficient depth in both the HGS-OvCa tumor samples and the matched normal samples to allow confident mutation detection. Through application of two algorithms, the researchers identified nine genes that exhibited significant mutations.
Specifically, the TP53 (tumor protein p53) gene was mutated in 303 of 316 HGS-OvCa samples (95.8%), and the BRCA1 (BReast CAncer -1) gene and BRCA2 (BReast CAncer-2) gene possessed germline (inherited) mutations in 9% and 8% of cases, respectively, and exhibited somatic (lifetime acquired) mutations in 3% of cases. The TP53 gene encodes the p53 tumor suppressor protein that normally aids in the prevention of cancer formation. Mutations in the gene disrupt the functionality of the protein, which in turn, contributes to uncontrolled growth of ovarian cancer cells. Mutations in the BRCA1 or BRCA2 gene increase a woman’s lifetime breast and ovarian cancer risk.
The researchers also identified six other statistically recurrent mutated genes: RB1 (retinoblastoma 1), NF1 (neurofibromin 1), FAT3 (FAT tumor suppressor homolog 3), CSMD3 (CUB and Sushi multiple domains 3), GABRA6 (gamma-aminobutyric acid (GABA) A receptor, alpha 6), and CDK12 (cyclin-dependent kinase 12). Five of the nine CDK12 mutations suggested potential loss of function, and four mutations were clustered in its protein kinase domain. According to the researchers, GABRA6 and FAT3 appeared significantly mutated, but such mutations were expressed in HGS-OvCa samples and matching normal fallopian tube tissue. Thus, it is less likely that the GABRA6 and FAT3 gene mutations play a significant role in HGS-OvCa.
Through additional analyses, the TCGA researchers identified several HGS-OvCa genes that were less commonly mutated, including mutations in BRAF (v-raf murine sarcoma viral oncogene homolog B1), PIK3CA (phosphoinositide-3-kinase, catalytic, alpha polypeptide), KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog), and NRAS (neuroblastoma RAS viral (v-ras) oncogene homolog). It is believed that these mutations are rare but important drivers in HGS-OvCa.
Gene Copy Number Analysis
A “chromosome” is an organized package of DNA found in the nucleus of the cell. [See Appendix 2] Humans have 23 pairs of chromosomes–22 pairs of numbered chromosomes, called “autosomes,” and one pair of sex chromosomes, “X “and “Y.” Each parent contributes one chromosome to each pair so that offspring get half of their chromosomes from their mother and half from their father.
“Copy-number variations” (CNVs)—a form of structural variation—are alterations of DNA that result in the cell having an abnormal number of copies of one or more sections of DNA (i.e., genes). CNVs can correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated/amplified (more than the normal number) on certain chromosomes. For example, the chromosome that normally possesses sections in the order of “A-B-C-D” could instead possess sections “A-B-C-C-D” (a duplication of “C”) or “A-B-D” (a deletion of “C”).
The TCGA researchers identified somatic copy number alterations in the 489 HGS-OvCa tumor genomes. The most common gene amplifications encoded CCNE1 (cyclin E1), MYC (v-myc myelocytomatosis viral oncogene homolog ) and MECOM (MDS1 and EVI1 complex locus), each of which was highly amplified in more than 20% of tumors.
Fifty mutations in the form of deletions were also identified by the researchers. The known tumor suppressor genes PTEN (phosphatase and tensin homolog), RB1 and NF1 exhibited deletions in at least 2% of the HGS-OvCa tumors.
High-Grade Serous Ovarian Cancer Subtypes & Patient Outcome Prediction.
The researchers combined expression measurements for 11,864 genes, which were used for various subtype identification and patient outcome predictions. This portion of the HG-OvCa analysis involved four steps which led to the identification of (i) four transcriptional subtypes based on mRNA testing; (ii) three miRNA subtypes, (iii) four DNA promoter methylation subtypes, and (iv) a transcriptional signature that is predictive of HG-OvCa patient survival.
1. Four HGS-OvCa Transcriptional Subtypes Based Upon mRNA Analysis
The mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made. During protein synthesis, a ribosome moves along the mRNA, reads its base sequence, and uses the genetic code to translate each three-base triplet, or codon, into its corresponding amino acid. (Photo: Wikipedia)
RNA is the genetic material that transcribes (i.e., copies) DNA instructions and translates them into proteins. It is RNA’s job to transport the genetic information out of the cell’s nucleus and use it as instructions for building proteins. The “transcriptome” consists of all RNA molecules within our cells, including mRNA, transfer RNA (tRNA), and ribosomal RNA (rRNA). The sequence of RNA mirrors the sequence of the DNA from which it was transcribed or copied. Consequently, by analyzing the entire collection of RNAs (i.e., the transcriptome) in a cell, researchers can determine when and where each gene is turned on or off in our cells and tissues. Unlike DNA, the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time.
As noted above, there are various types of RNA. A major type, called “messenger RNA” or “mRNA,” plays a vital role in making proteins. In this process, mRNA transcribed or copied from genes (which include the protein-coding parts of the genome) is delivered outside the cell nucleus (where DNA is generally stored) to ribosomes, which are molecular machines located in the cell’s cytoplasm (within the cell but outside the nucleus). The ribosomes read, or “translate,” the sequence of the chemical base letters (A, C, G, or T) imprinted in mRNA to assemble protein building blocks (called “amino acids“) into proteins. Accordingly, each mRNA is “transcribed” (copied) from a gene and then “translated” (synthesized) into a specific protein. When the process is uninterrupted, and a protein is produced, the original encoding gene is considered “expressed.”
The mRNA transcriptional analysis of the combined data set identified approximately 1,500 variable genes. Based on the gene expression analysis, the TCGA researchers concluded that at least four robust gene expression subtypes exist in HGS-OvCa. The four HGS-OvCa transcriptional subtypes were identified as “immunoreactive,” “differentiated,” “proliferative” and “mesenchymal” on the basis of gene content in the clusters and observations made in prior studies. 
The immunoreactive subtype was characterized by T-cellchemokineligandsCXCL11 (chemokine (C-X-C motif) ligand 11) and CXCL10 (chemokine (C-X-C motif) ligand 10), and the receptor CXCR3 (chemokine (C-X-C motif) receptor 3).
The proliferative subtype was characterized by (i) high expression of transcription factors — a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA — such as HMGA2 (high mobility group AT-hook 2) and SOX11 (SRY (sex determining region Y)-box 11); (ii) low expression of ovarian tumor markers MUC1 (mucin 1, cell surface associated) and MUC16 (mucin 16, cell surface associated); and (iii) high expression of cell growth proliferation markers such as MCM2 (minichromosome maintenance complex component 2) and PCNA (proliferating cell nuclear antigen).
The differentiated subtype was associated with high expression of MUC16 and MUC1, in tandem with expression of the secretory fallopian tube maker SLPI (secretory leukocyte peptidase inhibitor), thereby suggesting a more mature stage of development.
The mesenchymal subtype was characterized by high expression of HOX genes and markers suggestive of increased stromal components such as myofibroblasts (FAP or fibroblast activation protein, alpha) and microvascular pericytes (ANGPTL2 (angiopoietin-like 2) and ANGPTL1 (angiopoietin-like 1)).
Survival duration did not differ significantly for transcriptional subtypes in the TCGA data set. The proliferative group did exhibit a decrease in the rate of MYC (v-myc myelocytomatosis viral oncogene homolog (avian)) gene amplification and RB1 gene deletion, whereas the immunoreactive subtype showed an increased frequency of MECOM gene amplification.
2. Three HGS-OvCa Subtypes Based Upon miRNA Analysis
Once ignored completely and overlooked in humans until 2001, microRNAs (miRNAs) are encoded in the human genome and can function as natural regulators of global gene expression. miRNAs are a newly-recognized class of small, non-coding RNAs, which have emerged as a central player in controlling cell survival, growth, differentiation, and death. To date, more than 700 human miRNAs have been identified, which are estimated to regulate more than 30% of all human genes.
miRNAs regulate gene expression by binding to complementary protein-related DNA sequences encoded on mRNA. The binding action of miRNA usually results in mRNA translational repression which, in turn, prevents the manufacture or synthesis of the encoded protein. The overall effect produced by miRNAs is the failure of a gene to be expressed, which represents a form of “gene silencing.”
Each miRNA appears to regulate the expression of tens to hundreds of genes, thereby functioning a “master-switch” that regulates and coordinates multiple cellular/biological pathways involving important processes such as embryonic development and immune response, as well as cellular growth and proliferation. Mounting evidence from both basic and clinical studies indicates that miRNAs are expressed in cancer, and different types of cancer have different miRNA expression profiles. The identification of unique miRNA cancer profiles could lead to a novel cancer type (or even subtype)-selective treatment strategy in the future.
The TCGA researchers discovered three miRNA subtypes or clusters in HGS-OvCa, which were identified in the study as “C1,” “C2,” and “C3.”
Notably, miRNA subtype C1 overlapped the mRNA proliferative subtype (discussed above), and miRNA subtype C2 overlapped the mRNA mesenchymal subtype.
Survival duration differed significantly between miRNA subtypes: patients with miRNA subtype C1 tumors survived significantly longer, compared to patients with miRNA subtype C2 or C3.
3. Four HGS-OvCa Subtypes Based Upon Epigentic DNA Promoter Methylation Analysis
A “genome” is the complete set of DNA code or instructions located in the nucleus of each human cell. DNA provides the blueprint instructions for building all proteins. The protein-coding parts of the genome do not make proteins all of the time in each human cell. Instead, different sets of genes are turned on or off in various kinds of cells at different points in time. Differences in the types and amounts of proteins produced determine how cells look, grow and act.
Derived from the Greek word “epi,” the “epigenome” means “above” the genome. The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it and when to do it. In sum, the epigenome influences which genes are active — and which proteins are produced — in a particular cell. The epigenome is what tells your skin cells to behave like skin cells, heart cells like heart cells and so on.
The epigenome marks, which are not part of the DNA itself, can be passed on from cell to cell during cell division, and from one human generation to the next. The epigenome is made up of chemical compounds, some of which come from natural sources like food and others from man-made sources like medicines or pesticides. As it marks the genome with these chemical tags, the epigenome serves as the intersection between the human genome and the environment. The study of the epigenome is referred to as “epigenetics.”
The epigenome marks the human genome in two primary ways, both of which play a role in turning genes off or on.
(Photo: The University of New South Wales)
The first and primary form of epigentic marking is referred to as “DNA methylation,” which directly affects the DNA in the human genome. In this process, chemical tags called “methyl groups” attach to the backbone of the DNA molecule in specific places. The methyl groups turn genes off or on by affecting interactions between DNA and the cell’s protein-making machinery. For example, if a methyl group is added to areas of the DNA where there is a C (cytosine) followed by a G (guanine), the resulting structural changes to the DNA can prevent the DNA from being transcribed (i.e., copied), or translated (i.e., synthesized) into a protein. In this example, DNA methylation causes the “silencing” of certain genes.
There is a class of drugs currently in clinical development which is designed to counteract the effects of DNA methylation. This drug class is generally referred to as “DNA methyltransferase (DNMT) inhibitors” or “hypomethylating agents.” Examples of DNMT inhibitors include SGI-110, decitabine (Dacogen™), and azacitidine (Vidaza®). As of this writing, the latter two drugs are being tested in ovarian cancer and solid tumor clinical trials. The importance of DNMT inhibitors relates to their potential ability to turn tumor suppressor genes back on, which have been silenced previously through DNA methylation.
The second form of epigentic marking is referred to as “histone modification.” Histones are spool-like proteins that enable DNA’s very long molecules to be wound up neatly into chromosomes inside the cell nucleus. A variety of chemical tags can grab the tails of histones, thereby changing how tightly or loosely they package DNA. If the wrapping is tight, a gene may be hidden from the cell’s protein-making machinery, and consequently be switched off. In contrast, if the wrapping is loosened, a gene that was formerly hidden may be turned on.
There is a class of drugs currently in clinical development which are designed to counteract the effects of histone modification. This drug class is generally referred to as “histone deacetylase (HDAC) inhibitors.” Examples of HDAC inhibitors include vorinostat (Zolinza®), entinostat (a/k/a MS-275), panobinostat, belinostat (a/k/a PDX 101), and SB939. Several HDAC inhibitors are being tested in ovarian cancer and solid tumor clinical trials.
In addition to gene deletion and mutation, epigenetic silencing is increasingly recognized as an important form of gene function inactivation with respect to cancer. [20-21] The TCGA researchers believe that identification of epigenetically-silenced genes in a cancer-specific manner is critical to a complete understanding of the molecular alterations which contribute to the creation of cancer. This type of analysis, according to the researchers, can shed light on the early detection, prevention, treatment, and prognosis of the disease.
The researchers reported that increased DNA methylation and reduced tumor expression implicated 168 genes as epigenetically silenced in the HGS-OvCa samples, as compared with the fallopian tube tissue controls.  DNA methylation was correlated with reduced gene expression across all tumor samples. The researchers noted that several genes — AMT (aminomethyltransferase), CCL21 (chemokine (C-C motif) ligand 21), RAB25 (member RAS oncogene family), and SPARCL1 (SPARC-like 1 (hevin)) — showed DNA promoter hypermethylation in the vast majority of tumors. A “gene promoter” is a region of DNA that facilitates the transcription or copying of a particular gene.
According to the researchers, RAB25 is ranked highest among the 168 genes, based on the level of DNA methylation. Unexpectedly, RAB25, previously reported to be amplified and overexpressed in ovarian cancer,  seems to be epigenetically silenced in a subset of HG-OvCa tumors.
SPARCL1 was originally shown to be down-regulated in many epithelium-derived cancers. [24-25] A gene closely related to SPARCL1 (i.e., SPARC (secreted protein, acidic, cysteine-rich (osteonectin)) was previously shown to have tumor-suppressor activity in human ovarian epithelial cells,  and one driver mutation of SPARC was observed in the TCGA study. Loss of SPARCL1 expression was previously shown to be associated with increased proliferation and cell cycle progression,  highlighting its role in tumor formation.
BRCA1 gene silencing via promoter hypermethylation has been reported previously in breast and ovarian cancer,  and recent studies have reported BRCA1 hypermethylation in 10% to 20% of ovarian cancer patients. [32-33; Ref. 31]
The TCGA researchers determined that BRCA1 was hypermethylated and silenced in 56 of 489 (11.5%) of the HGS-OvCa tumors, as reported in previous studies. [Ref. 31]. According to the researchers, the presence of BRCA1 epigenetic silencing was mutually exclusive with all identified BRCA1 and BRCA2 gene mutations. This finding is consistent with a previous population-based study that reported BRCA1 epigenetic silencing only in ovarian cancer patients without a family history associated with a hereditary breast and ovarian cancer syndrome. The findings of the TCGA study, as well as the previous population-based study, suggest that BRCA1 promoter hypermethylation is unlikely to be inherited; rather, it is a lifetime acquired somatic change that leads to BRCA1 inactivation in sporadic ovarian cancers. The researchers also noted that BRCA1 hypermethylated cases are considerably younger and occur more frequently than the BRCA1 somatic gene mutation cases. Accordingly, epigenetic silencing of BRCA1, rather than mutation, could be a more efficient somatic mechanism of gene inactivation.
Based on the totality of the DNA methylation analyses, the researchers identified four HGS-OvCa tumor subtypes referred to as “MC1,” “MC2,” “MC3,” and “MC4,” which were significantly associated with differences in age, BRCA inactivation events, and survival.
The average patient ages in the four DNA methylation clusters are 59.1, 65.8, 57.1, and 62.1, for MC1, MC2, MC3, and MC4, respectively.
The four DNA methylation clusters also differed significantly in their frequencies of BRCA inactivation events, which include BRCA1 and BRCA2 gene mutation, and BRCA1 epigenetic silencing. Altogether, MC1 and MC3 possessed the highest frequencies of BRCA inactivation (46.6% and 44.5%, respectively), while MC2 possessed the lowest frequency (13.2%).
The patients in the four DNA methylation clusters differed significantly in overall 5-year survival (median survival time: MC1 = 48.9 months, MC2 = 35.8 months; MC3 = 40.9 months; MC4 =43.6 months; p=0.04.). After adjusting for age, the researchers determined that MC1 had the best survival and MC3 had a significantly worse survival compared to MC1 (HR = 1.43; p=0.04). MC2 had a marginally significant lower age-adjusted survival (HR = 1.42, p=0.09) compared to MC1.
According to the TCGA researchers, the DNA methylation clusters demonstrated only modest stability, which indicates weak definition with substantial intra-group variations. The researchers note that other clustering methods yielded varying subgroupings of the tumors based on their DNA methylation profiles, and recommend that the DNA methylation cluster memberships should be considered preliminary. Nevertheless, there is a moderate, but statistically significant, overlap between the DNA methylation clusters and gene expression subtypes, thereby suggesting some validity to the subdivisions.
4. Transcriptional Signature Predictive of HGS-OvCa Patient Survival
The TCGA researchers also identified sets of expressed genes that can predict patient survival. A 193-gene transcriptional signature predictive of overall survival was defined using the data set from 215 HGS-OvCa samples. Upon analysis completion, the researchers identified 108 genes that were correlated with poor survival, while 85 genes were correlated with good survival (p = 0.01). Patients whose tumors possessed a gene-expression signature associated with poor survival lived for a period that was 23 percent shorter than patients whose tumors did not possess such a signature.
The researchers validated the predictive power of this gene expression signature on an independent set of 255 HGS-OvCa samples, as well as on three independent expression data sets. Each of the validation samples was assigned a prognostic gene score, reflecting the similarity between its expression profile and the prognostic gene signature. The validation survival analysis of this signature showed statistically significant association with survival in all validation data sets.
Cellular/Biological Pathways Influencing Disease
A cellular/biological pathway is a series of actions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a protein. Pathways can also turn genes on and off. [See Appendix 5]
There are several types of cellular pathways. Some of the most common are involved in metabolism, the regulation of genes, and the transmission of signals. Metabolic pathways make possible the chemical reactions that occur in our bodies. Gene regulation pathways turn genes on and off. Signal transduction pathways move a signal from a cell’s exterior to its interior.
Researchers are learning that cellular pathways are far more complicated than once thought. Most pathways do not start at point A and end at point B. In fact, many pathways have no real boundaries, and they often work together to accomplish tasks. When multiple cellular pathways interact with each other, it is referred to as a “network.”
Several TCGA analyses integrated data obtained from 316 tumors to identify biology that contributes to HGS-OvCa. The researchers analyzed several cellular pathways which are generally altered in various cancer types, including the RAS/PI3K, RB, and p53 signaling pathways, as well as the primary DNA repair pathway which can possess germline (inherited) and somatic (lifetime acquired) alterations in ovarian cancer.
The p53 protein is encoded by the TP53 gene. Often referred to as the “guardian of the genome,” p53 is crucial because it regulates the cell cycle and functions as a tumor suppressor in preventing cancer. The TCGA researchers observed a mutation rate of 96% with respect to the TP53 protein. This finding raises the possibility that TP53 gene mutations in HGS-OvCa are essentially universal. Amplifications of MDM2 (Mdm2 p53 binding protein homolog) and MDM4 (Mdm4 p53 binding protein homolog) were uncommon in the p53 signaling pathway, and only occurred in approximately 4% and 3% of cases, respectively.
2. RB & RAS/PI3K Signaling Pathways
The analyses of the frequency with which known cancer-associated pathways harbored one or more mutations, copy number variations or changes in gene expression revealed that the RB pathway and RAS/PI3K pathway were deregulated or altered in 67% and 45% of cases, respectively.
Cancer researchers are interested in the RB pathway because it is altered consistently in cancer cells and promotes deregulated cell proliferation. In this pathway, the Ink4-family and the RB-family proteins function as tumor suppressors, whereas the D-cyclins, cdk4/cdk6, and E2F promote tumor cell proliferation. Within the RB signaling pathway, the TCGA researchers determined that the alterations affected CDKN2A (cyclin-dependent kinase inhibitor 2A), with 32% of altered samples downregulated or deleted; CCNE1 (cyclin E1), with 20% amplified; CCND1 (cyclin D1), with 4% amplified; CCND2 (cyclin D2), with 15% upregulated; and RB1, with 10% deleted or mutated.
RAS operates in a complex signaling network that regulates many cellular functions such as cell proliferation, differentiation, apoptosis, and senescence. There are two well-known RAS-regulated pathways.
The first pathway consists, in part, of RAS–PI3K (phosphatidylinositol 3-kinases)-PTEN (phosphatase and tensin homolog; tumor suppressor gene)-AKT (protein kinase B)-mTOR(mammalian target of rapamycin)(collectively, the RAS-PI3K-PTEN-AKT-mTOR pathway).
The second pathway consists, in part, of RAS–RAF (Raf kinases)-MEK (a/k/a mitogen activated protein kinase kinase or MAP2K)-ERK (extracellular-signal-regulated kinases; a/k/a MAPK (mitogen-activated protein kinases))(collectively, the RAS-RAF-MEK-ERK pathway).
Within the RAS/PI3K signaling pathway, the alterations affected PTEN (phosphatase & tensin homolog), with 7% of altered samples deleted; PIK3CA with 18% amplified; AKT1 (v-akt murine thymoma viral oncogene homolog 1), with 3% amplified; AKT2 (v-akt murine thymoma viral oncogene homolog 2), with 6% amplified; NF1 (neurofibromin 1), with 12% deleted or mutated; KRAS with 11% amplified; and BRAF with .5% mutated.
3. NOTCH Signaling Pathway
The TCGA researchers performed a search for altered subnetworks in a large protein-to–protein interaction network, which contains genes with significant numbers of mutations and copy number variations. By using HOTNET (an algorithm for finding significantly altered subnetworks within a large gene interaction network), they identified several known pathways, including the NOTCH signaling pathway, which was altered in 22% of HGS-OvCa samples. Among its many functions, the NOTCH signaling pathway is important for cell-to-cell communication, which involves gene regulation mechanisms that control multiple cell differentiation processes during embryonic and adult life.
4. Homologous Recombination DNA Repair Pathway
PARP is a key signaling enzyme involved in triggering the repair of single-strand DNA damage. PARP inhibition has been demonstrated to selectively kill tumor cells lacking components of the homologous recombination (HR) DNA repair pathway while sparing normal cells. Known defects in HR repair include the well-characterized hereditary BRCA1 and BRCA2 mutations in breast and ovarian cancer, as well as nonhereditary BRCA mutations. (Photo Credit: AstraZeneca Oncology)
Approximately 10-15% of ovarian cancers are hereditary, and the majority of these cases are due to germline gene mutations in BRCA1 or BRCA2.  A subset of sporadic ovarian tumors appear to share distinctive DNA-repair defects with BRCA1/BRCA2 germline mutation carriers; a phenomenon broadly described as “BRCAness.” [36-38] DNA-repair defects can be caused by germline or somatic alterations to the primary DNA repair pathway called “homologous recombination” (HR). [See Appendix 6]. The types of HR DNA repair pathway alterations examined by the TCGA researchers included: (i) germline and somatic mutation of BRCA1/BRCA2; (ii) epigenetic silencing of BRCA1 through DNA hypermethylation; (iii) changes to the core set of Fanconi Anemia genes; and (iv) additional genetic changes to other key components of the HR pathway.
Previous published studies reported that cells with a mutated or methylated BRCA1 gene, or mutated BRCA2 gene, possess defective HR and are highly responsive to PARP (poly (ADP-ribose) polymerase) inhibitors. [39-42] [See Appendix 7] Notably, PARP inhibitors proved effective in recent breast and ovarian cancer clinical trials. [43-44; Ref. 40] Moreover, a U.K. research team developed a new assay which predicted that 50% of ovarian cancers would respond to in vitro PARP inhibition.[45-48] Several PARP inhibitors are being tested currently in ovarian cancer and solid tumor clinical trials. [49-50]
The researchers in the TCGA study found that 20% of the HGS-OvCa samples possessed germline or somatic gene mutations in BRCA1 (11%) or BRCA2 (9%). Of the studied samples, 11% of HGS-OvCa tumors lost BRCA1 expression through DNA hypermethylation. Importantly, the presence of epigenetic silencing in BRCA1, in combination with BRCA1 or BRCA2 gene mutations, was mutually exclusive.
The survival analysis performed by researchers regarding the impact of BRCA1 or BRCA2 gene status revealed better overall survival for BRCA1 and BRCA2-mutated HGS-OvCa cases, as compared to non-BRCA gene-mutated cases (median overall survival of 66.5 months vs. 41.9 months). Notably, epigenetically silenced BRCA1 cases experienced survival similar to non-BRCA1 or BRCA2-mutated HGS-OvCa cases (median overall survivals of 41.5 and 41.9 months, respectively, p = 0.69). The researchers believe that BRCA1 is inactivated by mutually exclusive genomic and epigenomic mechanisms; therefore, patient survival appears to depend on the specific mechanism of inactivation.
The genomic alterations in other HR DNA repair pathway-involved genes that could render HG-OvCa cells sensitive to PARP inhibitors discovered in this study include: (i) amplification or mutation of EMSY (chromosome 11 open reading frame 30 or C11orf30) (8%); (ii) deletion or mutation of PTEN (7%); (iii) hypermethylation of RAD51C (RAD51 homolog C) (3%); (iv) mutation of ATM (ataxia telangiectasia mutated) or ATR (ataxia telangiectasia and Rad3 related) (2%); and mutation of Fanconi anemia genes (5%).
The TCGA researchers noted that on an overall basis, the HR DNA repair pathway defects may be present in approximately 50% of all HGS-OvCa cases, thereby providing a rationale for additional clinical trials involving PARP inhibitors, which target HGS-OvCa tumors with these HR-related aberrations.
A comparison between the complete set of BRCA inactivation events to all recurrently altered gene copy number peaks, revealed an unexpectedly low frequency of CCNE1 gene amplification in cases with BRCA inactivation (8% of BRCA gene-altered cases possessed CCNE1 amplification vs. 26% of non-altered BRCA cases). In past studies, overall survival was reported to be lower for patients with CCNE1 amplification, as compared to patients in all other cases. In the TCGA study, a survival disadvantage was not established for CCNE1-amplified cases (p = 0.24) when looking only at BRCA non-altered cases, thereby suggesting that the previously reported CCNE1 survival difference can be explained by the higher survival of BRCA-mutated cases.
The role of the FOXM1 (forkhead box M1) pathway in ovarian cancer has not been established. FOXM1 is a multifunctional transcription factor with three known dominant splice forms, each regulating distinct subsets of genes with a variety of roles in cell proliferation and DNA repair. For example, the FOXM1b isoform regulates a subset of genes that include the DNA repair genes BRCA2 and XRCC1 (X-ray repair complementing defective repair in Chinese hamster cells 1). CHEK2 (CHK2 checkpoint homolog), which is under the indirect control of ATM (ataxia telangiectasia mutated), directly regulates FOXM1’s expression level. The FOXM1c isoform directly regulates several targets with known roles in cell proliferation, including AURKB (aurora kinase B), PLK1 (polo-like kinase 1), CDC25C (cell division cycle 25 homolog C), and BIRC5 (baculoviral IAP repeat containing 5). 
To identify significantly altered pathways through an integrated analysis of both copy number variations and gene expression, the TCGA researchers used a probabilisticgraphical model (referred to as “PARADIGM”) and searched the U.S. National Cancer Institute Pathway Interaction Database (NCI-PID). The PARADIGM computational model incorporates gene copy number changes, gene expression data, and pathway structures to produce an integrated pathway activity (IPA) for every gene, complex, and genetic process present in the pathway database. The TCGA researchers applied PARADIGM to the HGS-OvCa samples and found alterations in many different genes and processes present in pathways contained in the NCI-PID.
Importantly, the researchers determined that the FOXM1 transcription factor network was significantly altered (i.e., activated) in 87% of the HGS-OvCa cases. FOXM1 and its growth proliferation-related target genes, AURKB, CCNB1, BIRC5, CDC25C, and PLK1, were consistently overexpressed but not altered by DNA copy number variations, thereby indicative of transcriptional regulation. Notably, the TP53 gene represses FOXM1 after DNA damage, suggesting that the high rate of TP53 mutation in HGS-OvCa contributes to FOXM1 overexpression. In other data sets, the FOXM1 pathway is significantly activated in tumors relative to adjacent epithelial tissue [54-56] and is associated with HGS-OvCa. 
“Like all cancers, ovarian cancer results from genomic derangements. The efforts of TCGA are confirming that the more we learn about genomic changes in tumor cells, the more we will be able to care for the people affected by cancer.”
— Eric D. Green, M.D., Ph.D., Director, National Human Genome Research Institute
Potential Therapeutic Approaches
The HGS-OvCa mutation spectrum, as identified by the TCGA researchers, indicates that HGS-OvCa is completely distinct from other epithelial ovarian cancer histological subtypes. For example, clear-cell ovarian cancer tumors possess few TP53 mutations but do possess recurrent ARID1A and PIK3CA mutations; endometrioid ovarian cancer tumors have frequent CTNNB1 (catenin (cadherin-associated protein), beta 1, 88kDa), ARID1A, and PIK3CA mutations and a lower rate of TP53 gene mutations; and mucinous ovarian cancer tumors possess prevalent KRAS mutations. [58-61] These differences between ovarian cancer subtypes represents an opportunity to improve ovarian cancer outcomes through subtype-stratified care.
Identification of new therapeutic approaches is a central goal of the TCGA. Overall, the discoveries described above set the stage for approaches to the treatment of HGS-OvCa in which aberrant genes or cellular/biological networks are detected through molecular testing, and targeted with therapies selected to be effective against specific aberrations. Based upon the TCGA study findings, there are three general approaches that could be used to target select HGS-OvCa tumor aberrations: (i) PARP inhibitor use against tumors with HR DNA repair pathway deficiencies; (ii) targeted therapy use against deregulated cellular pathways; and (iii) targeted therapy use against recurrent amplified gene mutations. Each therapeutic approach is addressed below.
PARP Inhibitor Use Against DNA Repair Pathway Defects
Targeting DNA repair through PARP inhibition in BRCA gene-mutated cancer cells. "HR" stands for "homologous recombination," which is the primary cellular DNA repair kit. "DSB" stands for DNA "Double Stand Break." (Photo Credit: AstraZeneca Oncology)
The researchers highlighted the fact that approximately 50% of HGS-OvCa tumors in this study possessed HR DNA repair pathway defects. As noted above, PARP inhibitors could be used in an attempt to take advantage of the primary DNA repair defect observed in half of the HGS-OvCa tumors studied. PARP inhibitors exploit the genetic instability of the tumors and cause the cancer cells to die. [See Appendices 6 & 7] While researchers knew that these drugs could be effective against HGS-OvCa tumors possessing germline (inherited) BRCA1 and BRCA2 gene mutations, this study revealed that 50 percent of HGS-OvCa tumors — including those with HR DNA repair pathway defects — could be responsive to this drug class. [Ref. 49-50]
The key challenges underlying the use of PARP inhibitors include: (i) determination of the extent of DNA repair defects in sporadic ovarian cancers; (ii) development of biomarkers to identify those DNA repair defects and the likelihood of drug response to PARP inhibitors; and (iii) application of this knowledge to identify patients likely to benefit from PARP inhibition therapy.
Targeted Therapies Based Upon Deregulated Cellular/Biological Pathways
The commonly deregulated cellular pathways identified by the TCGA researchers — p53 (87% of samples), RB (67% of samples), RAS/PI3K (45% of samples), FOXM1 (87% of samples), and NOTCH (22% of samples) — also provide current and future opportunities for therapeutic treatment. Unfortunately, the TCGA researchers did not provide specific therapeutic approaches that target the HGS-OvCa deregulated pathways, which were identified in the study. Despite that fact, we thought it would be helpful to address potential treatment approaches for each altered pathway based upon existing preclinical and clinical research.
Considerable energy has been focused on the p53 pathway because nearly all cancers show defects in this system, and over 50% of those cancers have mutations in the TP53 gene. The TCGA researchers observed a 96% mutation rate in the TP53 gene, and related alterations in the associated p53 protein.
To date, there have been several preclinical and clinical therapeutic approaches to treating cancer cells possessing a mutated TP53 gene and impaired p53 protein functionality. These approaches include the following:
(i) restoration of the TP53 gene function through gene therapy;
(ii) generation of an immune system response through vaccination;
(iii) use of inhibitors to target MDM2;
(iv) administration of “cyclotherapy;” and
(v) inhibition of the G2 cell cycle checkpoint. [62-65]
“Gene therapy” is the insertion, alteration, or removal of genes within an individual’s cells for the purpose of treating disease. This technique has already been used in the U.S. (only through clinical trials) and China (through government-approved drugs) in an attempt to correct defective genes such as TP53. The most common form of gene therapy involves the insertion of functional genes into an unspecified genomic location in order to replace a mutated gene.
Gene therapy using an adenovirus vector or "carrier." A new gene is inserted into an adenovirus vector, which is used to introduce the modified DNA into a human cell, thereby allowing the new gene to make a functional protein. (Photo: Wikipedia)
Gendicine™ (a/k/a rAd-p53, SCH-58500, and INGN-201), an adenoviral p53-based gene therapy was approved by the Chinese State Drug and Food Administration in 2003 for the treatment of head and neck cancer, along with radiotherapy. Advexin (a/k/a INGN-201), a p53 tumor suppressor gene therapy agent manufactured by Introgen Therapeutics, Inc., was tested in past U.S. clinical trials. Unfortunately, the U.S. Food and Drug Administration (FDA) refused to approve Advexin in 2008, and shortly thereafter, the company filed for bankruptcy.
As of this writing, Shenzhen SiBiono GeneTech Co., Ltd., the company that apparently owns the rights to the prior U.S. formulations of Gendicine™ (i.e., SCH-58500 and Advexin), is currently conducting several phase IV clinical trials involving the use of Gendicine™ against advanced head and neck tumors.  Despite a review of over 2,500 patients that have received Gendicine™ therapy in China, a definitive report addressing the clinical trial phase IV safety and efficacy of the drug has not been published.  We should note, however, that the early U.S. formulations of Gendicine™ were clinically tested by U.S. companies (i.e., former Schering-Plough, Merck & Co. & former Introgen) in ovarian cancer patients. Those drugs demonstrated anti-cancer activity in ovarian cancer clinical trials involving intraperitoneal administration of the drug used in combination with chemotherapy. [68-71]
Another Chinese p53 gene-based therapy known as “H-101” (brand name: Ocorine; manufactured by Shanghai Sunway Biotech Co., Ltd) was also approved by the Chinese government in 2005.
The second potential therapeutic approach to treating cancer that possesses a TP53 gene mutation involves the use of a vaccine to produce a patient immune system response capable of destroying the mutated cancer cells. Recent advances in our understanding of the regulation of the immune system, based upon detailed analyses of regulatory T cells and the signaling pathways that initiate and restrain the immune response, have revitalized the field of cancer immunology. Vaccines utilizing a p53-derived peptide(s) are currently being tested in ovarian cancer clinical trials.  One of the more advanced p53 vaccines being clinically tested in ovarian cancer is the p53 synthetic long peptide (p53-SLP®) vaccine. To date, the ovarian cancer clinical trials involving the p53 synthetic long peptide (p53-SLP®) vaccine have demonstrated safety and produced a patient immune response. In phase 2 clinical testing, the vaccine produced a low rate (10%) of stable disease; however, a connection could not be made between the clinical response and the vaccine-induced immunity. [73-74]
At this point, it does not appear that p53-SLP®, as a monotherapy, can produce a patient immune response strong enough to create a clinical response in TP53 gene-mutated ovarian cancer. Accordingly, new p53 vaccine approaches (e.g., DNA-based or dendritic cell-delivered) are needed for HGS-OvCa. In the area of small cell lung cancer (SCLC), an adenovirus p53 autologousdendritic cell vaccine (e.g., INGN-225) increased the effectiveness of subsequent chemotherapy.  Specifically, in a phase 1/2 clinical study, 78% of SCLC patients who showed an immune response to the INGN-225 p53 vaccine benefited from subsequent chemotherapy. In contrast, only 33% of vaccinated SCLC patients, who did not experience an immune response, benefited from the same chemotherapy.
The third potential therapeutic approach to treating TP53 gene-mutated cancer involves the use of MDM2 inhibitors. MDM2 can bind to the p53 protein, and degrade its tumor suppressor function. By way of example, JNJ-26854165 and RO5045337 represent two small-molecule MDM2 inhibitors in clinical development. The general concept is to use these inhibitor drugs to suppress MDM2 and restore some p53 protein tumor suppression functionality. [76-78]
There are two caveats associated with potential use of MDM2 inhibitors in HGS-OvCa.
First, many researchers believe that MDM2 inhibitors are not effective against TP53 gene-mutated cancers which do not possess functional p53 protein.  Based upon the results of the TCGA study, there is little doubt that HGS-OvCa is a TP53 gene-mutated cancer which possesses significant p53 protein inactivation or low functionality. Despite that fact, recent preclinical research findings suggest that use of MDM2 inhibitors in TP53 gene-mutated cancer could still be warranted based upon the potential ability of that inhibitor drug class, possibly in combination with a chemotherapeutic agent, to reactivate p73 tumor suppressor protein functionality. [80-82] The TP53 gene family consists of TP53, TP63 and TP73, as well as the associated encoded proteins p53, p63, and p73.
Second, assuming arguendo that MDM2 inhibitors could be effectively used in TP53 gene-mutated HGS-OvCa, the TCGA researchers determined that only 4% of those tumors possessed MDM2 gene amplification, thereby making the gene a potential drug target. Despite the two caveats raised with respect to the use of MDM2 inhibitors against TP53 gene-mutated cancers such as HGS-OvCa, a novel preclinical approach, known as “cyclotherapy,” could nevertheless allow MDM2 inhibitors to play a role in fighting HGS-OvCa.
The fourth potential therapeutic approach to treating TP53 gene-mutated cancer involves administration of so-called “cyclotherapy.” This approach could take advantage of the TP53 gene mutation in HGS-OvCa cancer cells, while protecting normal (non-TP53 gene-mutated) cells from the toxic effect of chemotherapy, as described below. [Ref. 62-64; 83]
The cell cycle is required for cell growth and division into two daughter cells. "Checkpoints" (designated by the red arrows) within each cell cycle phase ensure proper cell division. The function of the G1 and G2 checkpoints is to assess DNA damage, and either repair the damage, or target the cell for destruction through apoptosis (programmed cell death). (Photo: Drexel University College of Medicine)
The “cell cycle” involves a series of events that take place in the human cell which lead to its division and duplication. The cell cycle consists of five phases:
(i) “Gap 0” (G0), a resting phase where the cell leaves the cycle and stops dividing;
(ii) “Gap 1” (G1), in which the cell increases in size, and the “G1 checkpoint” ensures that the cell is is ready for DNA synthesis;
(iii) “Synthesis” (S), in which DNA replication occurs while the “intra-S checkpoint” monitors proper replication in the event of DNA damage or replication stress;
(iv) “Gap 2” (G2), in which the cell continues to grow, and the “G2 checkpoint” ensures that the cell is ready to enter the Mitosis phase and divide; and
(v) “Mitosis” (M), in which cell growth stops and cellular energy is focused on the orderly division of the cell into two daughter cells, while the “metaphase checkpoint” ensures that the cell is ready to complete division.
An important function of the G1 and G2 checkpoints is to assess DNA damage. When damage is found, the checkpoints use a signal mechanism to stall (or arrest) the cell cycle until repairs are made, or alternatively, if repairs cannot be made, to target the cell for destruction via apoptosis (i.e., a form of programmed cell death).
Most active cancer cytotoxic agents preferentially target rapidly dividing cells. Cyclotherapy exploits the difference between the abilities of normal and cancer cells to undergo G1 or G2 checkpoint arrest. In essence, nonstop cycling cancer cells could be killed preferentially through taxane-based chemotherapy,  while normal cells enter a state of reversible cell-cycle checkpoint arrest and subsequently recover with minimal toxic effects. The key to this approach is the identification of major cellular/biological pathways involved in cell-cycle arrest that are altered in cancer cells, but not in normal cells. This requirement seems to be fulfilled by the altered p53 signaling pathway in cancer cells, and therefore, cyclotherapy could be well suited to killing TP53-mutated HGS-OvCa tumor cells.
DNA damage checkpoints within the cell cycle ensure the fidelity of genetic information by arresting cell cycle progression and facilitating DNA repair pathways. If repair is not possible, cell death (or apoptosis) occurs. (Photo: Drexel University College of Medicine)
Pursuant to the cyclotherapy preclinical model, a reversible TP53-dependent G1 cell-cycle arrest is first induced in normal cells bearing no TP53 mutations by a MDM2 inhibitor. HGS-OvCa cells harboring TP53 gene mutations possess a defective G1 checkpoint and continue to cycle despite the presence of a checkpoint-inducing signal created artificially by the MDM2 inhibitor. Next, a mitotic inhibitor (e.g., a taxane drug such as paclitaxel (Taxol)) is introduced while the HGS-OvCa cancer cells continue to divide. In the presence of a mitotic inhibitor, which targets the S phase or M phase of the cell cycle, the HGS-OvCa cancer cells die. In contrast, normal cells with “wild-type” (normal) TP53 gene function are placed in a reversible (p53-dependent) arrest throughout the period of the therapeutic drug treatment, and retain their proliferative capacity after treatment completion.
Proof of concept preclinical studies have determined that cyclotherapy is effective against select non-ovarian TP53-mutated cancers, when combining a MDM2 inhibitor (e.g., nutlin-3a) with paclitaxel (Taxol). These important results stem from the basic biological fact that the mitotic inhibitor class of drugs (which include taxanes) cannot cause mitotic arrest in cells that do not enter the M phase of the cell cycle. Thus, a temporary arrest in the G1 phase produced by the MDM2 inhibitor nutlin-3 treatment, will protect normal cells from the catastrophic mitotic arrest induced by a taxane drug. In preclinical studies, the use of a MDM2 inhibitor has been shown to protect normal cells from mitotic agents such as the aurora kinase inhibitor VX680 , taxanes [Ref. 82-84], and polo-like kinase inhibitors . Most interestingly, nutlin-3 protects mice from PLK1 (polo-like kinase 1) inhibitor–induced neutropenia without abating the anticancer potency of the mitotic inhibitor. [Ref. 86]
In a provocative preclinical study by Apontes et al, the use of rapamycin (a/k/a sirolimus; Rapamune®) and metformin (Glucophage®), in combination with a MDM2 inhibitor, potentiated the killing of TP53-mutated breast cancer cells, while providing additive and longer-term protection to normal cells stimulated into cell cycle arrest by the MDM2 inhibitor. [Ref. 83] Several potential cyclotherapy clinical use implications stem from the findings of Apontes et al. First, the protective agents rapamycin and metformin are already widely used in the clinic, and therefore, the toxicity and pharmacokinetics of these drugs are well-known. The MDM2 inhibitor, nutlin-3a, while not advanced into clinical trials yet, appears to mimick the activity of low concentrations of actinomycin D (a/k/a dactinomycin; Cosmegen®) , a chemotherapy drug with recognized clinical application. Thus, the two additional agents that can be used to protect normal cells under this approach have already been clinically tested. The second observation relates to the anticancer effect of rapamycin and metformin. Notably, while Apontes et. al. demonstrated that rapamycin and metformin seem to provide added protection to normal cells under their approach, those same drug have produced anticancer activity against ovarian cancer in past preclinical studies. The third observation of clinical importance relates to the fact that Apontes et. al. offer specific recommendations on the timing and sequence of administration of these protective agents (i.e., rapamycin and metformin) and mitotic inhibitors in the treatment of TP53-mutated cancer.
Although the promising concept of cyclotherapy appears to work in the lab by using the combination of a MDM2 inhibitor and a taxane drug, the opposite appears to be true for other ovarian cancer drugs such as platinums (e.g., carboplatin and cisplatin) and doxorubicin. [88-89] In fact, MDM2 inhibitors appear to be synergistic with, and increase the power of, these drugs in non-ovarian cancer preclinical studies. Based on the foregoing, it appears that cyclotherapy in platinum-resistant HGS-OvCa patients receiving a single agent “dose dense” taxane drug is theoretically possible. Moreover, the use of cyclotherapy, by administering a MDM2 inhibitor in combination with a platinum drug, could be used in an attempt to reestablish chemosensitivity in platinum-resistant patients, albeit without the protection of normal cells otherwise provided under the general cyclotherapy approach, and with additional toxicity.
The fifth potential therapeutic approach to treating TP53 gene-mutated cancer involves inhibition of the G2 cell cycle checkpoint. [90-92] TP53 is a key regulator of the G1 checkpoint, and according to the TCGA study, is one of the most frequently mutated genes in HGS-OvCa. Due to TP53 gene mutation, HGS-OvCa cancer cells lack the G1 checkpoint, but can retain the G2 checkpoint. As a result, researchers believe that TP53-mutated cells tend to be more dependent on the G2 checkpoint for DNA damage repair. Wee 1 is a tyrosine kinase that can inactivate cdc2 (i.e., human form of cdk1 (cyclin-dependent kinase 1)), and therefore, plays a pivotal role in the G2 DNA damage checkpoint. In theory, the knockout of the G2 checkpoint with a Wee 1 inhibitor could leave TP53-mutated HGS-OvCa cells with significantly impaired options for DNA damage repair. Thus, the administration of DNA damaging chemotherapy in combination with a Wee 1 inhibitor could selectively target TP53-mutated HGS-OvCa cells, while normal cells are ultimately spared albeit with some toxicity.
MK-1775 is a specific and potent inhibitor of Wee-1 and is currently under investigation in a multi-center phase 1 study (ClinicalTrials.gov ID: NCT00648648) as a monotherapy, and in combination with gemcitabine, carboplatin or cisplatin, in patients with advanced solid tumors. The phase 1 study results show good tolerability and promising anti-cancer activity.  In fact, four of six ovarian cancer patients enrolled in the phase 1 study experienced stable disease for four or more months. To view the MK-1775 phase 1 study presentation made at the 2009 American Society of Clinical Oncology (ASCO) annual meeting, click here. It appears that the MK-1775 phase 1 study is still ongoing in the U.S., Canada, and The Netherlands, with a scheduled completion date of July 2012.
As of this writing, there are two separate MK-1775 phase 2 studies underway. [94-95] The first open phase 2 study involves MK-1775 combined with carboplatin in platinum-resistant patients with TP53 gene-mutated epithelial ovarian cancer, who experienced early recurrence (< 3 months), or progression during first line of treatment. The only stated location for this study is The Netherlands Cancer Institute.
The second phase 2 randomized study (announced, but not yet recruiting; study locations unidentified) is evaluating MK-1775 in combination with paclitaxel and carboplatin, versus paclitaxel and carboplatin alone, in platinum-sensitive, TP53-mutated ovarian cancer patients, who progressed after treatment with paclitaxel and carboplatin. For purposes of this phase 2 MK-1775 study, “platinum-sensitivity” is defined as a recurrence that occurs six or more months after first line treatment.
The TCGA researchers discovered that the RB pathway was deregulated or altered in 67% of the HGS-OvCa tumors tested. As noted above, the RB pathway consists of five families of proteins: (i) CDKN2A (cyclin-dependent kinase inhibitor 2A; a/k/a p16Ink4); (ii) D-type cyclins (cyclin protein family — cyclin D1, cyclin D2 and cyclin D3 — is involved in regulating cell cycle progression); (iii) cyclin-dependent protein kinases (cdk4 and cdk6); (iv) RB-family of pocket proteins (RB, p107, and p130); and (v) the E2F-family of transcription factors.  In this pathway, the Ink4-family (CDKN2A) and the RB-family proteins function as tumor suppressors, whereas the D-cyclins, cdk4/cdk6, and several (but not all) E2F transcription factors promote tumor cell proliferation.
Several components of the RB pathway (e.g., CDKN2A, cyclin D1, and RB1) are frequently altered in cancer cells, including the deletion and/or silencing of CDKN2A, the amplification of the cyclin D1, and the mutation of the RB1 gene. In the case of HGS-OvCa, the TCGA researchers discovered that CDKN2A was downregulated or deleted in 32% of altered samples; CCNE1 (cyclin E1) was amplified in 20% of altered samples; CCND1(cyclin D1) was amplified in 4% of altered samples; CCND2 (cyclin D2) was upregulated in 15% of altered samples; and RB1 was deleted or mutated in 10% of altered samples. Thus, components of the RB pathway are rational targets in HGS-OvCa therapy.
There are currently two distinct approaches that are gaining traction in directly targeting the RB pathway. [Ref. 96] The first approach is designed to take advantage of RB pathway deregulation. The second approach is designed to activate the tumor suppression function of the RB pathway. Based on these two general approaches, potential therapeutic strategies that directly target the RB pathway defects include:
(i) the reactivation of CDKN2A expression when that gene is silenced but not mutated;
(ii) the inhibition of cdk4/cdk6 kinase activity; and
(iii) the enhancement of E2F-dependent cell death (apoptosis).
It is well-known that reactivating a compromised tumor suppressor gene such as CDKN2A is a major pharmacological challenge. In terms of the RB pathway, the closest approach to achieving this goal is the use of inhibitors of DNA methylation (DNA methyltransferase (DNMT) inhibitors) and/or histone deacetylases (HDAC inhibitors), which although cytotoxic with potential application against other molecular targets, could also lead to the activation of epigenetically silenced CDKN2A.  DNMT inhibitors that are currently in clinical testing include SGI-110, decitabine (Dacogen™), and azacitidine. Several HDAC inhibitors are also being tested in ovarian cancer and solid tumor clinical trials. 
A second therapeutic strategy involves the use of cyclin-dependent kinase (CDK) inhibitors. [Ref. 96] Specifically, dual inhibition of cdk4 and cdk6 could be used against HGS-OvCa tumors in which the CDKN2A gene is downregulated and the RB1 gene is not deleted. [99-102] Several compounds are currently being tested in clinical trials including flavopiridol (a/k/a alvocidib), R-roscovitine (a/k/a seliciclib and CYC202), UCN-01 (7-hydroxystaurosporine), and BMS-387032 (a/k/a SNS-032). Most of these compounds, however, inhibit multiple cyclin-dependent kinases, with cdk2 being a common target in many drug discovery programs. Despite that fact, several recent preclinical studies suggest that mammalian cells can continue to proliferate in the absence of cdk2/cyclin E activity, possibly attributable to compensation by cdk4 and/or cdk6. [103-105] These preclinical studies suggest that cdk2 could be a less attractive anticancer target than cdk4.
CDK inhibitors that specifically target cdk4 and cdk6 have been developed and appear to be highly selective with no off-target effects based on biochemical and cell-based assays. Of these agents, PD-0332991 is the most broadly deployed in clinical studies. The phase 1 trial of PD-0332991 represented the first targeted use of an agent that specifically attempts to activate the RB pathway.  In keeping with the preclinical data, the PD-0332991 phase 1 trial used RB protein deficiency as an exclusion criterion.  For example, the TCGA researchers found that the RB1 gene is deleted or mutated in 10% of the HGS-OvCa tumors tested. It is likely that HGS-OvCa patients, whose tumors do not possess a RB1 gene due to deletion, would not qualify for PD-0332991 clinical trials. There are several phase 1/2 single-agent or combination PD-0332991 clinical trials in progress. 
In a preclinical study conducted by researchers at the University of California, Los Angeles (UCLA), PD-0332991 was tested against 40 ovarian cancer cell lines. [Ref. 102] The anti-cancer effects of PD-0332991 were observed in all ovarian cancer cell lines, but varied significantly between individual lines. Consistent with past preclinical studies, the UCLA researchers determined that RB gene-proficient cell lines with low p16 protein (encoded by the CDKN2A gene) expression were most responsive to dual cdk4/cdk6 inhibition. In addition, gene copy number variations of CDKN2A, RB, CCNE1, and CCND1 were associated with response to PD-0332991. The UCLA researchers concluded that cdk4/cdk6 inhibition induced G1 cell cycle arrest and enhanced the effects of chemotherapy. Importantly, the UCLA researchers noted that RB gene proficiency with low p16 protein expression was observed in 37% of ovarian cancer patients and was independently associated with poor progression-free survival.
A third potential therapeutic strategy involves harnessing the pro-apoptotic activity of E2F. [Ref. 96] Specifically, there are cellular signaling pathways that can protect cancer cells with deregulated E2F-activity from death. Inhibitors of these pathways, by definition, could be “synthetically lethal” in tandem with the pre-existing disruption of the RB pathway in cancer cells. [109-110] In these preclinical studies, the epidermal growth factor receptor (EGFR; a/k/a HER1) and apoptosis inhibitor 5 (API5, a/k/a AAC11) were required to suppress apoptosis arising from deregulated E2F activity. The studies suggest that EGFR inhibitors (e.g., gefitinib/Iressa®, afatinib, and vandetanib/Zactima®) could have utility in cancer tumors which harbor loss of RB function. Furthermore, API5 is upregulated in a number of tumor cell types, and depletion of API5 mediated cell death of tumor cells. Accordingly, the therapeutic targeting of these “survival” factors could be effective in RB-deficient tumors.
RAS (rat sarcoma) operates in a complex signaling network that regulates many cellular functions such as cell proliferation, differentiation, apoptosis, and senescence. There are two well-known RAS-regulated pathways.
The first RAS signaling pathway cascade consists, in part, of RAS-PI3K-PTEN-AKT-mTOR.
The second RAS signaling pathway cascade consists, in part, of RAS-RAF-MEK-ERK.
Mutated, deleted, and amplified genes in the Ras/Raf/MEK/ERK and Ras/PI3K/PTEN/Akt/mTOR pathways have been detected in HGS-OvCa. (Photo: Chappell WH, et al. Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR inhibitors: rationale and importance to inhibiting these pathways in human health. Oncotarget. 2011 Mar;2(3):135-64; Creative Commons Attribution 3.0 License)
The TCGA researchers discovered that the RAS/PI3K pathways were altered in 45% of the HGS-OvCa samples. There are several classes of therapeutic drugs currently being studied in ovarian and solid tumor clinical trials, which target one or more components of the RAS/PI3K pathways, including RAS (e.g., farnesyltransferase inhibitors (FTI) such as Zarnestra (a/k/a tipifarnib and R115777), and Sarasar (a/k/a lonafarnib)), PI3K , AKT , mTOR , RAF (e.g., sorafenib (Nexavar®)), BRAF , and MEK/ERK .
For example, the TCGA researchers determined that the PIK3CA gene and the KRAS gene were amplified in 18% and 11% of the RAS/PI3K pathway-altered samples tested, respectively. The PTEN tumor suppressor gene was deleted in 7% of the altered samples.
In a phase 1 study conducted by The University of Texas M.D. Anderson Cancer Center, patients with tumors carrying PIK3CA gene mutations and/or PTEN tumor suppressor gene loss were preferentially treated with drugs targeting the PI3K-PTEN-AKT-mTOR pathway. 
The M.D. Anderson researchers reported that the heavily pretreated patients with PIK3CA mutations and/or PTEN loss, and normal (non-mutated) KRAS gene status had a significantly higher partial response (PR) rate (31%) on protocols incorporating PI3K/mTOR inhibitors compared to patients on the same protocols without known PIK3CA gene mutations/PTEN loss (PR = 6%), or patients with PIK3CA mutations and/or PTEN loss and simultaneous KRAS mutations (PR = 6%). Based on these findings, the researchers suggested that screening for PIK3CA mutations, PTEN loss and KRAS mutations is warranted in patients who are treated with PI3K/mTOR inhibitor drugs.
Notably, it appears that ovarian cancer patients with PIK3CA gene mutation or PTEN gene loss could respond to PI3K-AKT-mTOR pathway inhibitors, even if they possess KRAS or BRAF gene mutations. [117-118] Nevertheless, preclinical studies suggest that use of a MEK inhibitor in combination with a PI3K-AKT-mTOR pathway inhibitor could produce the best response in KRAS gene-mutated ovarian cancer tumors. [119-120]
Over the past 25 years, there has been significant progress made in identifying the involvement of the RAS-RAF-MEK-ERK and RAS-PI3K-PTEN-AKT-mTOR pathway cascades in promoting cell growth, regulating apoptosis, and causing chemotherapeutic drug resistance.  There are several pros and cons, however, with respect to targeting one or both RAS signaling pathways.
There are three potential benefits from targeting one or both RAS pathways. First, these pathways are frequently activated in HGS-OvCa and many other human cancers, and therefore, in many cases, targeting one or both RAS pathways will suppress cell growth, in the absence of knowing the precise gene mutation(s) responsible for the cancer. Second, although the biochemical interactions of these pathways are quite complex, researchers possess a great deal of knowledge regarding how these pathways function. Third, several inhibitors that target key components in these pathways (e.g., rapamycin, which targets mTOR) have already undergone extensive evaluation in humans.
There are also three potential obstacles associated with targeting one or both RAS pathways. First, an obvious problem arises from the fact that these pathways control the expression of many downstream molecular and genetic targets (easily in the 1000’s), and therefore, inhibiting these pathways will be detrimental in certain normal cells, unless it is possible to deliver the inhibitor specifically to the cancer cells.
Second, the two RAS pathways discussed above cross regulate (or “crosstalk” to) each other, and affect other cellular pathways including the Wnt/β-cateinin pathway, which is critical for many aspects of cellular growth and differentiation including the epithelial-mesenchymal transition (EMT). In addition, the two RAS pathways also interact with several other pathways, including: (i) the Jak (Janus kinase)/STAT (Signal Transducer and Activator of Transcription) pathway, (ii) the NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) pathway, and (iii) the transforming growth factor-β (TGF-β) pathway, all of which can be directly and indirectly regulated by ERK and AKT phosphorylation (i.e., a process capable of turning enzymes, like kinases, and receptors on or off). The cross-talk between the two RAS pathways, as well as their interaction with other cellular pathways, creates a sort of “Yin-Yang” effect. That is, when one pathway is inhibited by a drug or drug combination, components of the second pathway could be deregulated by, or compensate for, such inhibition.
Third, inhibitors that target one or both RAS pathways are often cytostatic (i.e., stop further cancer growth) but not cytotoxic (i.e., cause cancer regression). In an attempt to solve the third issue, it could be possible to combine the inhibitors used to target these pathways with cytotoxic chemotherapeutic drugs which destroy rapidly growing cancer cells.
The TCGA researchers identified the deregulation or alteration of the FOXM1 signaling pathway in 87% of the HGS-OvCa samples. FOXM1, is a transcription factor that induces the expression of genes involved in cell cycle progression and maintenance of genomic stability. It is generally known that FOXM1 is strongly upregulated in a variety of human solid tumors. Because FOXM1 suppression appears to inhibit cancer proliferation, the identification of anti-cancer drugs or compounds that target FoxM1 could prove beneficial in fighting HGS-OvCa.
For example, past preclinical studies have shown that select antibiotics (e.g., Siomycin A and thiostrepton), as well as proteosome inhibitors (e.g., MG-132, and bortezomib (a/k/a P-341; Velcade®)), inhibit FoxM1 transcriptional activity and expression.[123-125] One team of researchers reported that docetaxel (Taxotere®), alone or in combination with estramustine (Emcyt®), down-regulated the expression of FoxM1 in prostate cancer leading to cell growth inhibition and induction of apoptosis. Another research group determined that genistein (i.e., an isoflavone found in lupin, fava beans, soybeans, kudzu, and psoralea) inhibited pancreatic cell growth, induced apoptosis, and attenuated the activity of FoxM1 and its downstream genes, such as survivin, CDC25a (cell division cycle 25 homolog A ), MMP-9 (atrix metallopeptidase 9), and VEGF (vascular endothelial growth factor).  Similarly, the chemopreventive agent diindolylmethane –an anticarcinogen compound derived from the digestion of indole-3-carbinol found in broccoli, cauliflower, and collard greens — inhibited FoxM1 activation in breast cancer cells, thereby leading to apoptotic cell death. [Ref. 126]
The genes directly affected by FOXM1 activity include CCNB1 (cyclin B1), AURKB (Aurora B), BIRC5 (survivin), PLK1 (polo-like kinase 1), and CDC25B (cell division cycle 25 homolog B). Various preclinical and clinical drugs and compounds are capable of targeting the genes “downstream” from FOXM1. Cyclin B1 could be targeted with CDK inhibitors [128-130]TAK-901 and GSK1070916A are clinical trial drugs designed to target Aurora B. Clinical trial drugs designed to target the polo-like kinase 1 include TAK-960, volasertib (a/k/a BI 6727), and NMS-1286937. YM155 (a/k/a sepantronium bromide) and EZN-3042 are among the clinical trial drugs designed to target survivin. Several vaccines are also in development to target survivin-expressing cancer cells (e.g., survivin peptide vaccine and survivin Sur1M2 peptide vaccine). Drugs and compounds designed to target CDC25B are also in development. 
The NOTCHpathway, with its family of four receptors (Notch-1, -2, -3, -4) and their numerous ligands of the Delta and Jagged/Serrate group, plays an important role in cell fate determination, and organ development during embryonic development. It also carries out cell differentiation and “maintenance” functions during adult life. Because the NOTCH signaling pathway involves ligand-receptor interactions, it can initiate signal transduction –a protein-to-protein interaction between the ligand and cell membrane receptor which runs from cell surface to cell interior — that results in modulation of a set of downstream genes, which mediate the ultimate functions of the pathway. Aberrant activation of the NOTCH signaling pathway could confer a growth advantage to tumor cells.
The TCGA researchers determined that the NOTCH signaling pathway was altered in 22% of the HGS-OvCa samples. Within the pathway, the researchers observed gene amplification in NOTCH 3 (11% of pathway-altered samples), JAG1 (2%), and JAG2 (3%).
This result is consistent with other preclinical studies that found active NOTCH pathway signaling in ovarian cancer. A preclinical study conducted by a team of Johns Hopkins researchers determined that NOTCH pathway activation (i) reprograms HGS-OvCa tumor cells to assume an array of embryonic stem cell markers, and (ii) participates in the development of carboplatin chemoresistance. 
John Hopkins researchers also determined that expression of NOTCH3 activation enhances the expression level of its ligand, Jagged1, a finding that had not been previously reported in cancer cells.  In addition, the Johns Hopkins researchers also demonstrated that the Wnt/β-catenin pathway was essential to Jagged1 expression regulation, indicating that Jagged1 expression is regulated by at least two signaling pathways in ovarian cancer. The Johns Hopkins researchers had determined previously that (i) Jagged-1 is the primary Notch3 ligand in ovarian cancer, and (ii) the Jagged-1/Notch3 interaction constitutes a cell-to-cell communication loop that promotes proliferation and dissemination of ovarian cancer cells within the intraperitoneal cavity.  Notably, Jagged 1 has also been associated with vascular development, but it is unknown whether it promotes angiogenesis in cancer tumors.
The fact that ovarian cancer utilizes dual signaling pathways (NOTCH 3 & Wnt/β-catenin) to control Jagged1 expression indicates the importance of maintaining active Notch signaling in epithelial cancer cells. There are several drugs in clinical development that are designed to act as NOTCH inhibitors, including MK0752 and OMP-59R5.  A recent preclinical study reported that xanthohumol (i.e., the primary flavonoid found in hops, an herb used to make beer) was a potent inhibitor of ovarian cancer cell growth, while noting that it seemed to influence the NOTCH pathway.
It is also possible that gamma-secretase (GS) inhibitors can target the NOTCH signaling pathway. The gamma-secretase complex consists of four known proteins that act as “gatekeepers” to the interior of a cell after signal transduction initiation caused by NOTCH receptor-ligand binding. In concept, if the signal can be blocked, the associated signal activity can also be blocked. GS inhibitors (also generally referred to as “NOTCH inhibitors”) that are being tested in clinical trials include BMS-708163, PF-03084014, and RO4929097.
Based upon the Johns Hopkins finding that the NOTCH and Wnt/β-catenin pathways contribute to Jagged-1 expression, the dual targeting of both pathways could be necessary. The Wnt signaling pathway is a network of proteins associated with embryonic development and cancer, as well as normal human physiological processes. Wnt inhibitors that are being tested in clinical trials include PRI-724 and OMP-18R5.
Targeted Therapies Based Upon Common Gene Amplifications
To identify opportunities for specific targeted treatment, the TCGA researchers searched for existing drugs that might inhibit amplified or overexpressed genes which could play a role in ovarian cancer. The search identified 68 genes that could be targeted by existing FDA-approved or experimental therapeutic drugs or compounds. Within the supplemental information that accompanied the TCGA study, the researchers provided a list of therapeutic inhibitors that already exist for 22 frequently amplified HGS-OvCa genes, which warrant initial or further clinical assessment in HGS-OvCa cases.
Each of the 22 genes identified by the researchers, including MECOM, MAPK1, CCNE1 and KRAS, is amplified in at least 10% of the HGS-OvCa cases.
The 22 frequently amplified HGS-OvCa genes and the corresponding therapeutic inhibitors indentified by TCGA researchers are listed below. Additional drugs/compounds identified by Libby’s H*O*P*E* (LH) are listed within brackets directly below the researcher-provided therapeutic inhibitors.
“The integration of complex genomic data sets enabled us to discover an intricate array of genomic changes and validate one specific change that occurs in the vast majority of all ovarian cancers. Significantly, we have also found new information regarding the role that the BRCA1 and BRCA2 genes play in determining survival.”
— Paul T. Spellman, Ph.D., Lead TCGA HGS-OvCa study author; Prinicipal Scientist, Lawrence Berkeley National Laboratory; and Co-Director, Berkeley Cancer Genome Center.
The Road Ahead
Limitations of The “One Target- One Drug” Approach
Chemotherapy still remains one of the most effective anti-cancer therapies. The effectiveness of chemotherapy, which targets DNA replication and mitosis, is limited by the side effects resulting from killing normal cells that also proliferate.
The discovery of cancer-related molecular abnormities stimulated research to develop targeted therapies aimed at selectively inhibiting the growth of cancer by interfering with specific molecules or signal transduction pathways that are overexpressed (overactive) in cancer cells. It was anticipated that targeted cancer therapies would be more effective than current treatments and less harmful to normal cells.
Unfortunately, the “one-target, one-drug approach” has not held up for most cancer types. This result is not surprising because the target is usually the component of a cell signaling pathway that, while overexpressed in cancer, is also essential for the survival of normal cells. Recent projects, including the TCGA study, have deciphered the genomes of cancer cells and discovered that an array of different genetic mutations can lead to the same cancer in different patients. The long-term goal of these genome studies is the development of “personalized medicine.” That is, each cancer patient would receive the drug or drug combination which is most likely to work based upon his or her genomic and molecular tumor profile.
The complexity of the personalized medicine approach is daunting. Instead of discovering ways to attack one well-defined genetic enemy, researchers are now faced with the prospect of fighting lots of little enemies. Fortunately, this complex view could be simplified by looking at which cellular/biological pathways are disrupted by the genetic mutations. Rather than designing dozens of drugs to target dozens of mutations, drug developers could focus their attentions on just two or three cellular/biological pathways. Patients could then receive the drugs most likely to work for them based upon the pathways affected in their particular tumors.
First Steps on the Road to Personalized Medicine.
Although scientific researchers and medical clinicians are just beginning to understand the complexity of the human genome, epigenome, and cellular pathways, progress is being made. At the 2011 ASCO annual meeting, the M.D. Anderson Cancer Center reported that customizing targeted therapies to the molecular characteristics of a patient’s tumor — instead of using a “one-size-fits-all” approach based upon broad cancer type — could be more effective for some types of cancer. In patients with various forms of end-stage cancer, patients matched with a clinical trial therapy based upon the molecular characteristics of their tumor achieved a 27% response rate, as compared to a 5% response rate in those patients who were not matched with a personalized therapy. 
In September 2008, the Genomics of Drug Sensitivity In Cancer Project was launched with funding from a five-year Wellcome Trust Sanger Institute strategic award. The U.K.–U.S. collaboration harnesses the experience in experimental molecular therapeutics at Massachusetts General Hospital Cancer Center and the expertise in large scale genomics, sequencing, and bioinformatics at the Wellcome Trust Sanger Institute.  In July 2010, the researchers working on the the study identified the responses of 350 cancer samples (including ovarian cancer) to 18 anticancer therapeutics based upon an initial dataset.
The TCGA study also represents a significant step ahead with respect to glioblastoma multiforme (i.e., an aggressive form of brain cancer) and HGS-OvCa. As noted above, the researchers identified existing experimental or FDA-approved drugs which could target frequently amplified genes associated with HGS-OvCa. The TCGA is in the process of collecting samples for many other forms of cancer which will be analyzed in similar fashion to glioblastoma and HGS-OvCa.
Creation of an Ovarian Cancer Molecular Disease Model
There is a long road ahead for ovarian cancer scientific researchers in their attempt to fully understand HGS-OvCa, as well as other subtypes of epithelial ovarian cancer such as clear cell, endometrioid and mucinous. As ovarian cancer researchers and clinicians move ahead, there is a greater need for better application of current ovarian cancer preclinical scientific research to related preclinical drug development, clinical trial testing of developed drugs, and ultimately, patient drug use.
An interesting research and treatment model is being developed in the area of melanoma; it is the creation of a melanoma molecular map to assist clinicians in making personalized therapy treatment decisions. We believe that the general principles underlying the creation of this innovative melanoma treatment model could provide a general roadmap or framework for future ovarian cancer scientific research and personalized therapy.
In this regard, the mission of CollabRx® is to save lives by using information technology (IT) to personalize cancer treatments and accelerate research. The CollabRx® web-based applications and services power Cancer Commons, a family of open-science cancer communities in which physicians, patients, and scientists collaborate on models of cancer subtypes towards the goal of more accurately predicting responses to therapy. These web-based applications allow scientific researchers and clinicians to find tests and therapies, discuss cases and treatment recommendations, report outcomes, analyze data, provide laboratory and analytic services, and ultimately refine the models.
Each molecular disease model (MDM) is supported by scientific and medical experts with respect to a particular form of cancer. These experts are responsible for creating and maintaining a MDM for their designated cancer, which enumerates the known genomic subtypes and molecular pathways, hyperlinked to the latest and most relevant diagnostic tests, treatments, trials, literature, and news. At each point in time, a patient can be treated with the best available experimental therapies for that individual’s tumor molecular subtype. The subtypes and associated therapies are continually refined within the model based upon how individual patients respond. In sum, the MDMs serve as living review articles, which are maintained online and continuously updated by the experts who created them.
In March 2011, the first MDM created by the Cancer Commons project was published.  The information contained in that MDM addresses the treatment of melanoma and is embodied in the “Targeted Therapy Finder — Melanoma” online application. The melanoma MDM consists of a set of “actionable” molecular subtypes and proposed practice guidelines for treating each disease subtype; that is, which therapies (approved or experimental) should be considered by a patient’s oncologist and which are contraindicated. A “molecular subtype of melanoma” is loosely defined as those tumors containing the same set of molecular (primarily genetic) defect(s) and their associated cellular/biological pathways. A subtype is deemed actionable if there is both a CLIA-approved assay to determine whether a given tumor fits that classification, and at least one FDA-approved or experimental targeted therapy with potential effectiveness for that subtype.
Notably, the bold CollabRx®/Cancer Commons initiative is supported by ASCO through a partnership with CollabRx®, which was announced in April 2011. 
We took the liberty of writing to the Cancer Commons initiative to encourage the existing scientific research and medical team to form a team or network of ovarian cancer experts who could oversee the creation of an ovarian cancer MDM. Although the list of all proposed cancer types to be addressed by the Cancer Commons initiative has not been stated, it appears that expert networks in the area of sarcoma, breast cancer and lung cancer have already been formed or will be formed in the near future.
Although there is a great deal of preclinical and clinical research that must be performed in the future with respect to ovarian cancer, the creation of an ovarian cancer MDM should become a priority within the gynecologic scientific and medical community. We urge that community to undertake this important goal, especially given the high mortality rate associated with ovarian cancer.
Chemotherapy Sensitivity & Resistance Assay Testing: A “Bridge” or Adjunct to the Ovarian Cancer Molecular Disease Model?
If we assume arguendo that a future ovarian cancer MDM is warranted, the model development process should incorporate all existing technologies which allow us to transition from the current standard of care treatments to the emerging ovarian cancer MDM. This transition period is attributable to the considerable time that it will take for scientific researchers and clinicians to fully “blueprint” all of the significant molecular and genomic workings of the ovarian cancer cell.
We decided to address this issue after reading an expert commentary published as part of the 2011 ASCO annual meeting Daily News publication. The commentary is entitled, Utility of Chemotherapy Sensitivity and Resistance Assays for Optimizing Treatment for Patients with Solid Tumors.  The commentary was written by Drs. Harold J. Burstein, M.D., Ph.D., and Jaffer A. Ajani, M.D. Dr. Burstein is an Assistant Professor of Medicine at Harvard Medical School, and a medical oncologist in the Breast Oncology Center at the Dana-Farber Cancer Institute. He is also the Chair-Elect of the ASCO Cancer Education Committee. Dr. Ajani is a medical oncologist and Professor of Medicine at the M. D. Anderson Cancer Center. In the commentary, the authors raise several excellent points about the development of personalized medicine and highlight the frustrations experienced along the way by patients and clinicians alike.
The primary focus of the commentary is the future viability of chemotherapy sensitivity and resistance assays (CSRAs), in light of the rapid development of new molecular and genomic profile testing methods. The basic premise of CSRAs involves: (i) procurement of fresh tumor samples (primary or metastatic) and/or malignant effusions (including abdominal ascites fluid) from the cancer patient through primary/secondary surgery or biopsy; (ii) disaggregation of tumor cells from the sample; and (iii) exposure of these tumor cells to one or more therapeutic agents under various in vitro conditions (including 3-D lab culture models). The overarching goal of using a CRSA is to identify a drug or drug combination that will work for a cancer patient with the least amount of toxicity, prior to actual administration of the the drug to the patient.
Older forms of CSRAs measured chemotherapy resistance only; that is, the identification of drugs that are unlikely to benefit the cancer patient. Newer forms of CSRAs also include the measurement of chemotherapy sensitivity; that is, the identification of drugs that are likely to benefit the cancer patient. One of the newest forms of CSRA testing identifies potential cancer patient treatment benefit based upon the measurement of actual cancer cell death (i.e., apoptosis) after in vitro drug(s) application, in lieu of the older measurement involving cancer cell proliferation or growth. The difference is subtle but important.
In regard to CSRAs, Drs. Burstein and Ajani state: “It might be that the era of CSRA is coming to an end.” The reasons provided by the authors are as follows:
The academic oncology community has been reviewing the extent of clinical development of CSRA, as well as their utility in treatment selection and other benefits, such as improving overall survival of those patients treated based on the assay results compared with empiric approaches. ASCO addressed the issue of CSRA utility in 2004 and is updating the guideline in 2011. Each time the subject has been addressed, ASCO commissioned a number of experts to conduct detailed reviews of existing English literature on CSRA and to establish the level of evidence based on randomized trials.
In 2004 ASCO found that, although there were many commercially available CSRA, there was insufficient evidence of benefit to patients; therefore, ASCO did not recommend the use of any CSRA for selection of chemotherapeutic agents for individual patients with cancer outside of clinical trials.
The major setback for CSRA lies in the lack of rigorous clinical testing (i.e., small sample sizes and lack of prospective comparisons) necessary to document patient benefit, and most published studies significantly fall short of this requirement.
The authors further explain that advances in biotechnology provide us with a much deeper understanding of how cancer is organized, how it maintains itself (i.e., tumor-initiating cells with self-renewal potential), and how it acquires several survival advantages under stressful circumstances. Moreover, Drs. Burstein and Ajani emphasize that detailed sequencing of tumor DNA has already provided us with a greater understanding of activating gene mutations, amplifications, deletions, and translocations. These types of functional studies have led to discrimination between genetic “driver” mutations (which push cells towards cancer) and “passenger” mutations (which are a by-product of cancer development). The authors further state that without the advancement of molecular/genomic science, cancer researchers would not have identified drugs like imatinib (Gleevec®) (e.g., for select chronic myeloid leukemias and gastrointestinal stromal tumors), trastuzumab (Herceptin®) (e.g., for HER-2 positive breast cancers), crizonib (e.g., for certain lung cancers), crizonib (PF-02341066 )(e.g., for certain lung cancers), and PLX4032 (vemurafenib) (e.g., for select melanomas) through use of CSRAs.
The authors close the article by pointing out the continued importance of, and need for, prospective, randomized studies when evaluating new technologies (including CRSAs) and drugs.
We agree with many of the points raised in the ASCO expert commentary; however, we believe that new technologies (e.g., modern CRSAs based upon measurement of actual cell death) should not be abandoned or considered a mutually exclusive alternative to molecular and genetic tumor profile analyses. In fact, we believe that the newest forms of CSRAs should be evaluated as a means to steer ovarian cancer patients into potentially beneficial clinical trials, with possible use in combination with molecular/gemonic tumor profile testing. We base our position on several important factors.
First, Drs. Burstein and Ajani support their position with studies that do not address the newest forms of CRSAs. [147-148]
Second, the more recent CRSA studies in the area of ovarian cancer indicate that such testing can be predictive of progression-free and overall survival. [149-154] That fact alone warrants further evaluation of CRSA in ovarian cancer clinical trials.
Third, several ovarian cancer studies suggest CRSAs are capable of increasing patient response rates, and progression-free survival; [155-158] albeit no study has demonstrated an increase in overall survival (with one possible exception[Ref. 156]). One study even reports that CRSAs could decrease recurrent ovarian cancer treatment costs. 
Fourth, past CSRA studies have reported novel drug combination recommendations in the treatment of ovarian cancer. [160-161; Ref. 154, 158]
Fifth, although neither ASCO or the National Comprehensive Cancer Network (NCCN) recommend CRSA use outside of a clinical trial, some NCCN member institutions are utilizing such testing. 
Sixth, a CRSA should be viewed as another medical oncology test (similar to computed tomography (CT) or magnetic resonance imaging (MRI)) which can assist a doctor in making optimal cancer treatment recommendations, as opposed to a drug treatment to be approved or disapproved based solely upon overall survival data.
Seventh, CRSAs enhance our understanding as to the general ability of a drug or drug combination to cause apoptosis in a cancer cell. Simply put, either the drug kills the cancer cell or it does not. Although it is true that many factors come into play within the human body (which are not reproducible through an in vitro 3-D lab culture) and affect cancer cell proliferation or death (e.g., the immune system), it is still helpful to know whether a drug possesses the ability to kill a patient’s tumor cells in vitro prior to use of that drug in the patient’s body.
Eighth, we are not aware of any published studies that suggest CRSAs should not be further tested in clinical trials. In fact, ChemoFx®  and the MiCK apoptosis assay™  were recently evaluated through ovarian and non-ovarian cancer clinical trials.
Ninth, researchers are engaging in preclinical research with the working hypothesis that tandem use of CRSAs and molecular/genomic tumor profiling could enhance our understanding of more targeted cancer treatment. [165-167]
It is true that CSRA testing does not result in the discovery of new drugs, but it should enhance the drug developmental process. Specifically, cancer drug development should be enhanced by assessing the value of CSRAs in combination with molecular genomic techniques. This action should allow better stratification and assignment of patients to clinical trials which are predicted to be of greatest beneﬁt to the individual patient. In turn, such studies may better deﬁne the optimal diagnostic criteria for treatment selection and accelerate the approval of new rationally-designed drugs. These drugs may be effective in small subsets of patients that have developed tumors which possess the requisite molecular drug targets. Accordingly, the integration of CRSAs and molecular genomic diagnostics into the clinical trial design should be a high priority.
It is also true that the use of the most advanced forms of CRSAs in everyday oncology practice remains a controversial topic. [168-169] Nevertheless, we should not allow that fact to stop the clinical evaluation of CRSAs, which could advance basic ovarian cancer scientific knowledge, especially knowing that the road of discovery to personalized medicine will likely be a long one with many obstacles and detours along the way. Stated in the vernacular, let’s not throw the baby out with the bathwater!
About the National Cancer Institute
The National Cancer Institute (NCI) is part of the National Institutes of Health (NIH), which is one of 11 agencies that compose the U.S. Department of Health and Human Services (HHS). The NCI, established under the National Cancer Institute Act of 1937, is the U.S. Government’s principal agency for cancer research and training. The National Cancer Act of 1971 broadened the scope and responsibilities of the NCI and created the National Cancer Program. Over the years, legislative amendments have maintained the NCI authorities and responsibilities and added new information dissemination mandates as well as a requirement to assess the incorporation of state-of-the-art cancer treatments into clinical practice.
NCI takes the lead in coordinating the National Cancer Program, which conducts and supports (i) research, training, and health information dissemination; (ii) programs with respect to the cause, diagnosis, prevention, and treatment of cancer; (iii) programs with respect to rehabilitation from cancer; and (iv) the continuing care of cancer patients and the families of cancer patients.
For more information about cancer, please visit the NCI website at www.cancer.gov or call NCI’s Cancer Information Service at 1-800-4-CANCER (1-800-422-6237).
About the National Human Genome Research Institute
The National Human Genome Research Institute (NHGRI) began as the National Center for Human Genome Research (NCHGR), which was established in 1989 to carry out the role of the NIH in the International Human Genome Project (HGP).
In 1993, NCHGR expanded its role on the NIH campus by establishing the Division of Intramural Research to apply genome technologies to the study of specific diseases. In 1996, the Center for Inherited Disease Research (CIDR) was also established (co-funded by eight NIH institutes and centers) to study the genetic components of complex disorders.
In 1997, the HHS renamed NCHGR as the “National Human Genome Research Institute”, officially elevating it to the status of research institute – one of 27 institutes and centers that make up the NIH.
The National Institutes of Health (NIH), the nation’s medical research agency, includes 27 Institutes and Centers and is a component of the HHS. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research. NIH also investigates the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.
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47/New Assay Test Predicts That 50% of Ovarian Cancers Will Respond To In Vitro PARP Inhibition, by Paul Cacciatore, Libby’s H*O*P*E*™ website, November 11, 2010.
48/10 Exciting Ovarian Cancer Research Topics from 2010 — PARP Inhibitors & BRCA Gene-Mutated Ovarian Cancer (Topic #2 of 10), Episode #2, WORD of HOPE Ovarian Cancer Podcast, April 11, 2011.
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65/Stathis A, et. al. Targeting Wee1-like protein kinase to treat cancer. Drug News Perspect. 2010 Sep;23(7):425-9. Review. PubMed PMID: 20862394.
66/A list of open clinical trials involving Gendicine (a/k/a rAd-p53).
67/Shi J, et. al. An update on gene therapy in China. Curr Opin Mol Ther. 2009 Oct;11(5):547-53. PubMed PMID: 19806503.
68/Wolf JK, et. al. A phase I study of Adp53 (INGN 201; ADVEXIN) for patients with platinum- and paclitaxel-resistant epithelial ovarian cancer. Gynecol Oncol. 2004 Aug;94(2):442-8. PubMed PMID: 15297186.
69/Wen SF, et. al. Assessment of p53 gene transfer and biological activities in a clinical study of adenovirus-p53 gene therapy for recurrent ovarian cancer. Cancer Gene Ther. 2003 Mar;10(3):224-38. PubMed PMID: 12637944.
70/Buller RE, et. al. Long term follow-up of patients with recurrent ovarian cancer after Ad p53 gene replacement with SCH 58500. Cancer Gene Ther. 2002 Jul;9(7):567-72. PubMed PMID: 12082456.
71/Buller RE, et. al. A phase I/II trial of rAd/p53 (SCH 58500) gene replacement in recurrent ovarian cancer. Cancer Gene Ther. 2002 Jul;9(7):553-66. PubMed PMID: 12082455.
72/A list of ovarian cancer clinical trials involving use of a p53 vaccine.
73/Leffers N, et. al. Long-term clinical and immunological effects of p53-SLP® vaccine in patients with ovarian cancer. Int J Cancer. 2011 Feb 16. doi: 10.1002/ijc.25980. [Epub ahead of print] PubMed PMID: 21328579.
74/Leffers N, et. al. Immunization with a P53 synthetic long peptide vaccine induces P53-specific immune responses in ovarian cancer patients, a phase II trial. Int J Cancer. 2009 Nov 1;125(9):2104-13. PubMed PMID: 19621448.
75/Chiappori AA, et. al. INGN-225: a dendritic cell-based p53 vaccine (Ad.p53-DC) in small cell lung cancer: observed association between immune response and enhanced chemotherapy effect. Expert Opin Biol Ther. 2010 Jun;10(6):983-91. PubMed PMID: 20420527.
76/Yuan Y, et. al. Novel targeted therapeutics: inhibitors of MDM2, ALK and PARP. J Hematol Oncol. 2011 Apr 20;4:16. PubMed PMID: 21504625; PubMed Central PMCID: PMC3103487.
77/Millard M, et. al. Small-molecule inhibitors of p53-MDM2 interaction: the 2006-2010 update. Curr Pharm Des. 2011;17(6):536-59. PubMed PMID: 21391905.
78/Kojima K, et. al. The novel tryptamine derivative JNJ-26854165 induces wild-type p53- and E2F1-mediated apoptosis in acute myeloid and lymphoid leukemias. Mol Cancer Ther. 2010 Sep;9(9):2545-57. PubMed PMID: 20736344.
79/Yuan Y, et. al. Novel targeted therapeutics: inhibitors of MDM2, ALK and PARP. J Hematol Oncol. 2011 Apr 20;4:16. PubMed PMID:21504625; PubMed Central PMCID: PMC3103487.
80/Ray RM, et. al. Mdm2 inhibition induces apoptosis in p53 deficient human colon cancer cells by activating p73- and E2F1-mediated expression of PUMA and Siva-1. Apoptosis. 2011 Jan;16(1):35-44. PubMed PMID:20812030.
81/Lau LM, et. al. HDM2 antagonist Nutlin-3 disrupts p73-HDM2 binding and enhances p73 function. Oncogene. 2008 Feb 7;27(7):997-1003. Epub 2007 Aug 13. PubMed PMID: 17700533.
82/Ambrosini G, et. al. Mouse double minute antagonist Nutlin-3a enhances chemotherapy-induced apoptosis in cancer cells with mutant p53 by activating E2F1. Oncogene. 2007 May 24;26(24):3473-81. Epub 2006 Dec 4. PubMed PMID: 17146434.
83/Apontes P, et. al. Exploring long-term protection of normal human fibroblasts and epithelial cells from chemotherapy in cell culture. Oncotarget. 2011 Mar;2(3):222-33. PubMed PMID: 21447859.
84/Carvajal D, et. al. Activation of p53 by MDM2 antagonists can protect proliferating cells from mitotic inhibitors. Cancer Res. 2005 Mar 1;65(5):1918-24. PubMed PMID: 15753391.
85/Cheok CF, et. al. Combination of nutlin-3 and VX-680 selectively targets p53 mutant cells with reversible effects on cells expressing wild-type p53. Cell Death Differ 2010; 17:1486-500. PubMed PMID: 20203688.
86/Sur S, et. al. A panel of isogenic human cancer cells suggests a therapeutic approach for cancers with inactivated p53. Proc Natl Acad Sci U S A 2009; 106:3964-9. PubMed PMID: 19225112. PubMed PMCID: PMC2656188.
87/Choong ML, et. al. Specific activation of the p53 pathway by low dose actinomycin D: a new route to p53 based cyclotherapy. Cell Cycle. 2009 Sep 1;8(17):2810-8. Epub 2009 Sep 13. PubMed PMID: 19657224.
88/Ohnstad HO, et. al. MDM2 antagonist Nutlin-3a potentiates antitumour activity of cytotoxic drugs in sarcoma cell lines. BMC Cancer. 2011 May 30;11:211. PubMed PMID: 21624110.
89/Zheng T, et. al. Nutlin-3 cooperates with doxorubicin to induce apoptosis of human hepatocellular carcinoma cells through p53 or p73 signaling pathways. J Cancer Res Clin Oncol. 2010. PubMed PMID: 20174822.
90/Rajeshkumar NV, et al. MK-1775, a potent Wee1 inhibitor, synergizes with gemcitabine to achieve tumor regressions, selectively in p53-deficient pancreatic cancer xenografts. Clin Cancer Res. 2011 May 1;17(9):2799-806. Epub 2011 Mar 9. PubMed PMID: 21389100.
91/Stathis A, et. al. Targeting Wee1-like protein kinase to treat cancer. Drug News Perspect. 2010 Sep;23(7):425-9. Review. PubMed PMID: 20862394.
92/Leijen S, et. al. Abrogation of the G2 checkpoint by inhibition of Wee-1 kinase results in sensitization of p53-deficient tumor cells to DNA-damaging agents. Curr Clin Pharmacol. 2010 Aug;5(3):186-91. Review. PubMed PMID: 20406171.
93/Schellens JH, et. al. A phase I and pharmacological study of MK-1775, a Wee1 tyrosine kinase inhibitor, in both monotherapy and in combination with gemcitabine, cisplatin, or carboplatin in patients with advanced solid tumors. J Clin Oncol 27:15s, 2009 (suppl; abstr 3510). [2009 ASCO Annual Meeting]
94/Phase II Pharmacological Study With Wee-1 Inhibitor MK-1775 Combined With Carboplatin in Patients With p53 Mutated Epithelial Ovarian Cancer and Early Relapse (< 3 Months) or Progression During Standard First Line Treatment, ClinicalTrials.gov Identifier: NCT01164995.
95/A Randomized, Phase II Study Evaluating MK-1775 in Combination With Paclitaxel and Carboplatin Versus Paclitaxel and Carboplatin Alone in Adult Patients With Platinum Sensitive p53 Mutant Ovarian Cancer, ClinicalTrials.gov Identifier: NCT 01357161.
96/Knudsen ES, et. al. Targeting the RB-pathway in cancer therapy. Clin Cancer Res. 2010 Feb 15;16(4):1094-9. Epub 2010 Feb 9. PubMed PMID: 20145169; PubMed PMCID: PMC2822892.
97/Egger G, et. al. Inhibition of histone deacetylation does not block resilencing of p16 after 5-aza-2′-deoxycytidine treatment. Cancer Res 2007;67:346–53. PubMed PMID: 17210717.
98/A list of open ovarian cancer and solid tumor clinical trials utilizing HDAC inhibitors.
99/Lapenna S, et. al. Cell cycle kinases as therapeutic targets for cancer. Nat Rev Drug Discov 2009;8:547–66. PubMed PMID: 19568282.
100/Toogood PL, et. al. Discovery of a potent and selective inhibitor of cyclin-dependent kinase 4/6. J Med Chem 2005;48:2388–406. PubMed PMID: 15801831.
101/Fry DW, et. al. Specific inhibition of cyclin–dependent kinase 4/6 by PD 0332991 and associated antitumor activity in human tumor xenografts. Mol Cancer Ther 2004;3:1427–38. PubMed PMID: 15542782.
102/Konecny GE, et. al. Expression of p16 and retinoblastoma determines response to CDK4/6 inhibition in ovarian cancer. Clin Cancer Res. 2011 Mar 15;17(6):1591-602. Epub 2011 Jan 28. PubMed PMID: 21278246.
103/Tetsu O, et. al. Proliferation of cancer cells despite CDK2 inhibition. Cancer Cell 2003;3:233–45. PubMed PMID: 12676582.
104/Ortega SO, et. al. Cyclin-dependent kinase 2 is essential for meiosis but not for mitotic cell division in mice. Nat Genet 2003;35:25–31. PubMed PMID: 12923533.
105/Geng Y, et. al. Cyclin E ablation in the mouse. Cell 2003;114:431–43. PubMed PMID: 12941272.
106/Schwartz GK, et. al. Phase I study of PD 0332991, a cyclin-dependent kinase inhibitor, administered in 3-week cycles (Schedule 2/1). Br J Cancer. 2011 Jun 7;104(12):1862-8. doi: 10.1038/bjc.2011.177. Epub 2011 May 24. PubMed PMID: 21610706.
107/A Phase I Clinical, Pharmacokinetic, And Pharmacodynamic Evaluation Of 2 Schedules Of Oral PD 0332991, A Cyclin-Dependent Kinase Inhibitor, In Patients With Advanced Cancer. ClinicalTrials.gov Identifier: NCT00141297.
108/A list of open clinical trials utilizing PD 0332991.
109/Morris EJ, et. al. Functional identification of Api5 as a suppressor of E2F-dependent apoptosis in vivo. PLoS Genet 2006;2:e196. PubMed PMID: 17112319; PubMed PMCID: PMC1636698.
110/Moon NS, et. al. A gradient of epidermal growth factor receptor signaling determines the sensitivity of rbf1 mutant cells to E2F-dependent apoptosis. Mol Cell Biol 2006;26:7601–15. PubMed PMID: 16954388; PubMed PMCID: PMC1636876.
111/A list of open ovarian cancer and solid tumor clinical trials utilizing PI3K inhibitors.
112/A list of open ovarian cancer and solid tumor clinical trials utilizing AKT inhibitors.
113/A list of open ovarian cancer and solid tumor clinical trials utilizing mTOR inhibitors.
114/A list of open ovarian cancer and solid tumor clinical trials utilizing BRAF inhibitors.
115/A list of open ovarian cancer and solid tumor clinical trials utilizing MEK inhibitors.
117/Janku F, et. al. PIK3CA mutations in patients with advanced cancers treated with PI3K/AKT/mTOR axis inhibitors. Mol Cancer Ther. 2011 Mar;10(3):558-65. Epub 2011 Jan 7. PubMed PMID: 21216929.
118/Experimental Drug NVP-BEZ235 Slows Ovarian Cancer Growth in Mice; Solid Tumor Clinical Trials Ongoing, by Paul Cacciatore, Libby’s H*O*P*E*™, May 2, 2011.
119/Kinross KM, et. al. In Vivo Activity of Combined PI3K/mTOR and MEK Inhibition in a KrasG12D;Pten Deletion Mouse Model of Ovarian Cancer. Mol Cancer Ther. 2011 Jul 19. [Epub ahead of print] PubMed PMID: 21632463.
120/Wee S, et. al. PI3K pathway activation mediates resistance to MEK inhibitors in KRAS mutant cancers. Cancer Res. 2009 May 15;69(10):4286-93. Epub 2009 Apr 28. PubMed PMID: 19401449.
121/Steelman LS, et. al. Roles of the Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR pathways in controlling growth and sensitivity to therapy-implications for cancer and aging. Aging (Albany NY). 2011 Mar;3(3):192-222. PubMed PMID: 21422497; PubMed PMCID: PMC3091517.
122/Pilarsky C et. al. Identification and validation of commonly overexpressed genes in solid tumors by comparison of microarray data. Neoplasia. 2004 Nov-Dec;6(6):744-50. PubMed PMID: 15720800; PubMed PMCID: PMC1531678.
123/Gartel AL. et. al. A new target for proteasome inhibitors: FoxM1. Expert Opin Investig Drugs. 2010 Feb;19(2):235-42. Review. PubMed PMID: 20074015.
124/Pandit B, et. al. New potential anti-cancer agents synergize with bortezomib and ABT-737 against prostate cancer. Prostate. 2010 Jun 1;70(8):825-33. PubMed PMID: 20058240.
125/Bhat UG, et. al. FoxM1 is a general target for proteasome inhibitors. PLoS One. 2009 Aug 12;4(8):e6593. PubMed PMID: 19672316; PubMed Central PMCID: 2721658.
126/Wang Z, et. al. Forkhead box M1 transcription factor: a novel target for cancer therapy. Cancer Treat Rev. 2010 Apr; 36(2):151-6. PubMed PMID: 20022709; PubMed PMCID: PMC2838950.
127/Wang Z, et. al. FoxM1 is a novel target of a natural agent in pancreatic cancer. Pharm Res. 2010 Jun;27(6):1159-68. Epub 2010 Mar 31. PubMed PMID: 20354770; PubMed Central PMCID: PMC2975383.
128/Feldmann G, et. al. Cyclin-dependent kinase inhibitor Dinaciclib (SCH727965) inhibits pancreatic cancer growth and progression in murine xenograft models. Cancer Biol Ther. 2011 Oct 1;12(7). [Epub ahead of print] PubMed PMID: 21768779.
129/Santo L, et. al. A novel small molecule multi-cyclin-dependent kinase inhibitor, induces apoptosis in multiple myeloma via GSK-3beta activation and RNA polymerase II inhibition. Oncogene. 2010 Apr 22;29(16):2325-36. PubMed PMID: 20101221.
130/DePinto W, et. al. In vitro and in vivo activity of R547: a potent and selective cyclin-dependent kinase inhibitor currently in phase I clinical trials. Mol Cancer Ther. 2006 Nov;5(11):2644-58. PubMed PMID: 17121911.
131/Lavecchia A, et. al. CDC25A and B dual-specificity phosphatase inhibitors: potential agents for cancer therapy. Curr Med Chem. 2009;16(15):1831-49. Review. PubMed PMID: 19442149.
132/Rose SL, et. al. Notch 1 signaling is active in ovarian cancer. Gynecol Oncol. 2010 Apr;117(1):130-3. Epub 2010 Jan 8. PubMed PMID: 20060575.
134/Chen X, et. al. Jagged1 expression regulated by Notch3 and Wnt/β-catenin signaling pathways in ovarian cancer. Oncotarget. 2010 Jul;1(3):210-8. PubMed PMID: 20953350; PubMed Central PMCID: PMC2953807.
135/Choi JH, et. al. Jagged-1 and Notch3 juxtacrine loop regulates ovarian tumor growth and adhesion. Cancer Res. 2008 Jul 15;68(14):5716-23. PubMed PMID: 18632624; PubMed Central PMCID: PMC2562671.
136/A list of open ovarian cancer and solid tumor clinical trials utilizing NOTCH inhibitors.
137/2011 ASCO: Matching Targeted Therapies To Specific Tumor Gene Mutations Key to Personalized Cancer Treatment, by Paul Cacciatore, Libby’s H*O*P*E*™, June 3, 2011.
138/Massachusetts General Hospital Cancer Center To Genetically Profile All Patient Tumors, by Paul Cacciatore, Libby’s H*O*P*E*™, March 14, 2009.
139/Dana-Farber Researchers “OncoMap” The Way To Personalized Treatment For Ovarian Cancer, by Paul Cacciatore, Libby’s H*O*P*E*™, November 16, 2010.
140/British Columbian Researchers Make Groundbreaking Genetic Discovery In Endometriosis-Associated Ovarian Cancers, by Paul Cacciatore, Libby’s H*O*P*E*™, September 8, 2010.
141/Caris Life Sciences Launches Molecular Profiling Service For Ovarian Cancer Patients, by Paul Cacciatore, Libby’s H*O*P*E*™, January 14, 2011.
142/Largest Study Matching Genomes To Potential Anticancer Treatments Releases Initial Results, by Paul Cacciatore, Libby’s H*O*P*E*™, August 3, 2010.
143/Vidwans SJ, et. al. A melanoma molecular disease model. PLoS One. 2011 Mar 30;6(3):e18257. PubMed PMID: 21479172; PubMed PMCID: PMC3068163.
144/The American Society of Clinical Oncology and CollabRx Partner to Develop Online Apps for Planning Cancer Treatment, News Release, The American Society of Clinical Oncology, April 5, 2011.
145/Utility of Chemotherapy Sensitivity and Resistance Assays for Optimizing Treatment for Patients with Solid Tumors, by Harold J. Burstein, MD, PhD, and Jaffer A. Ajani, MD, American Society of Clinical Oncology Annual Meeting, Expert Editorial, ASCO Daily News (Issue #3; Section C), June 6, 2011.
146/We should note that Libby’s H*O*P*E*™ does not receive any direct or indirect renumeration from the aforementioned private companies.
147/Schrag D, et. al. (ASCO Working Group on Chemotherapy Sensitivity and Resistance Assays). American Society of Clinical Oncology Technology Assessment: chemotherapy sensitivity and resistance assays. J Clin Oncol. 2004 Sep 1;22(17):3631-8. Epub 2004 Aug 2.PubMed PMID: 15289488.
148/Samson DJ, et. al. Chemotherapy sensitivity and resistance assays: a systematic review. J Clin Oncol. 2004 Sep 1;22(17):3618-30. Epub 2004 Aug 2. Review. PubMed PMID: 15289487.
149/Herzog TJ, et. al. Chemosensitivity testing with ChemoFx and overall survival in primary ovarian cancer. Am J Obstet Gynecol. 2010 Jul;203(1):68.e1-6. Epub 2010 Mar 12. PubMed PMID: 20227055.
150/Zhao D, et. al. Application of ATP-tumor chemosensitivity assay in primary epithelial ovarian cancer. Zhonghua Zhong Liu Za Zhi. 2010 May;32(5):368-72. Chinese. PubMed PMID: 20723436.
151/Zhao D, et. al. Application of ATP-tumor chemosensitivity assay in recurrent epithelial ovarian cancer. Zhonghua Zhong Liu Za Zhi. 2010 Nov;32(11):855-8. Chinese. PubMed PMID: 21223693.
152/Gallion H, et. al. Progression-free interval in ovarian cancer and predictive value of an ex vivo chemoresponse assay. Int J Gynecol Cancer. 2006 Jan-Feb;16(1):194-201. PubMed PMID: 16445633.
154/Konecny G, et. al. Correlation of drug response with the ATP tumorchemosensitivity assay in primary FIGO stage III ovarian cancer. Gynecol Oncol. 2000 May;77(2):258-63. PubMed PMID: 10785475.
155/Cree IA, et. al. A prospective randomized controlled trial of tumour chemosensitivity assay directed chemotherapy versus physician’s choice in patients with recurrent platinum-resistant ovarian cancer. Anticancer Drugs. 2007 Oct;18(9):1093-101. PubMed PMID: 17704660.
156/Salom EM, et. al. Can we increase response rate (RR) and overall survival (OS) by individualizing chemotherapy in ovarian cancer (OC): The role of a new chemotherapy (CT) induced apoptosis assay. J Clin Oncol 28:15s, 2010 (suppl; abstr 5112)(2010 American Society of Clinical Oncology Annual Meeting).
157/Loizzi V, et. al. Survival outcomes in patients with recurrent ovarian cancer who were treated with chemoresistance assay-guided chemotherapy. Am J Obstet Gynecol. 2003 Nov;189(5):1301-7. PubMed PMID: 14634558.
158/Kurbacher CM, et. al. Use of an ex vivo ATP luminescence assay to direct chemotherapy for recurrent ovarian cancer. Anticancer Drugs. 1998 Jan;9(1):51-7. PubMed PMID: 9491792.
159/Havrilesky LJ, et. al. Impact of a chemoresponse assay on treatment costs for recurrent ovarian cancer. Am J Obstet Gynecol. 2010 Aug;203(2):160.e1-7. Epub 2010 Apr 24. PubMed PMID: 20417480.
160/Nagourney RA, et. al. Phase II trial of gemcitabine plus cisplatin repeating doublet therapy in previously treated, relapsed ovarian cancer patients. Gynecol Oncol. 2003 Jan;88(1):35-9. PubMed PMID: 12504624.
161/Di Nicolantonio F, et. al. Use of an ATP-based chemosensitivity assay to design new combinations of high-concentration doxorubicin with other drugs for recurrent ovarian cancer. Anticancer Drugs. 2002 Jul;13(6):625-30. PubMed PMID: 12172508.
162/National Comprehensive Cancer Network Clinical Practice Guidelines in Oncology™ – Ovarian cancer including fallopian tube cancer and primary peritoneal cancer. V2.2011. National Comprehensive Cancer Network, Inc. [free NCCN website registration required to view Adobe Reader PDF document]
163/A list of clinical studies evaluating ChemoFx®.
165/Arienti C, et. al. Peritoneal carcinomatosis from ovarian cancer: chemosensitivity test and tissue markers as predictors of response to chemotherapy. J Transl Med. 2011 Jun 20;9:94. PubMed PMID: 21689426; PubMed PMCID: PMC3141502.
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167/Michalski CW, et. al. Ex vivo chemosensitivity testing and gene expression profiling predict response towards adjuvant gemcitabine treatment in pancreatic cancer. Br J Cancer. 2008 Sep 2;99(5):760-7. PubMed PMID: 18728667; PubMed Central PMCID: PMC2528151.
168/Schink JC, et. al. Point: chemosensitivity assays have a role in the management of recurrent ovarian cancer. J Natl Compr Canc Netw. 2011 Jan;9(1):115-20. PubMed PMID: 21233247.
169/Markman M. Counterpoint: chemosensitivity assays for recurrent ovarian cancer. J Natl Compr Canc Netw. 2011 Jan;9(1):121-4. PubMed PMID: 21233248.
Appendix 1 – DNA & RNA
Double-stranded DNA molecule inside the cell nucleus. (Photo: The Cancer Genome Atlas)
Often compared to a recipe or a code, DNA (deoxyribonucleic acid) is a set of blueprints that contains the instructions our cells require to construct other cell components, such as proteins and RNA (ribonucleic acid) molecules. The DNA segments that carry this genetic information are called “genes.” DNA is the genetic material that contains the instructions used in the development and functioning of our cells. DNA consists of two strands that wind around each other like a twisted ladder. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases–adenine (A), cytosine (C), guanine (G), or thymine (T). DNA is generally stored in the nucleus of our cells. The primary purpose of DNA molecules is the long-term storage of genomic information.
RNA is the genetic material that “transcribes” (i.e., copies) DNA instructions and “translates” (i.e., synthesizes) them into proteins. It is RNA’s job to transport the genetic information out of the cell’s nucleus and use it as instructions for building proteins. The so-called “transcriptome” consists of all RNA molecules within our cells, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). The sequence of RNA mirrors the sequence of the DNA from which it was transcribed or copied. Consequently, by analyzing the entire collection of RNAs (i.e., the transcriptome) in a cell, researchers can determine when and where each gene is turned on or off in our cells and tissues. Unlike DNA, the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time.
Messenger RNA (mRNA) is a single-stranded RNA molecule that is complementary to one of the DNA strands of a gene. The mRNA is an RNA version of the gene that leaves the cell nucleus (where DNA is stored) and moves to the cell cytoplasm where proteins are made. During protein synthesis, a “ribosome” moves along the mRNA, reads its base sequence, and uses the genetic code to translate each three-base triplet, or “codon,” into its corresponding amino acid.
Once the protein is manufactured, the gene (i.e., the DNA code segment) which originally encoded the protein, via mRNA, is considered “expressed.” Gene expression should not be confused with gene “amplification.” Gene amplification is an increase in the number of copies of a gene sequence. Cancer cells sometimes produce multiple copies of genes in response to signals from other cells or their environment. When gene amplification results in the excessive production of an encoded protein, it is often referred to as gene “overexpression.”
Once ignored completely, and overlooked until 1993, microRNAs (miRNAs), a newly-recognized class of small, non-coding RNAs, have emerged as a central player in controlling cell survival, growth, differentiation and death. MiRNAs regulate gene expression after transcription (i.e., copying) by interacting with protein-encoding mRNAs. MiRNAs are encoded in the human genome and function as natural regulators of global gene expression. To date, more than 700 human miRNAs have been identified, which are estimated to regulate 30% of all human genes. MiRNAs are expressed and processed by proteins within the cell’s nucleus and cytoplasm, and negatively regulate the expression of genes with sequences that are complementary to specific miRNAs. Each miRNA appears to regulate the expression of tens to hundreds of genes, thereby functioning as a “master-switch” which regulates and coordinates multiple cellular/biological pathways (See Appendix 5) in important processes such as embryonic development, immune response, and cellular growth and proliferation.
Appendix 2 – Genes , Chromosomes & Proteins
How cells package genetic information: DNA, Genes & Chromosomes. A chromosome translocation is a genetic abnormality that can result in cancer. (Photo: The Cancer Genome Atlas)
As noted in Appendix 1, the DNA segments that carry genetic information are called “genes.” The “genome” is the entire set of genetic instructions found in a human cell. The genome consists of 23 pairs of chromosomes. These chromosomes are composed of six billion individual DNA letters. In the English alphabet there are 26 letters: A through Z. In the alphabet of our genes there are four letters: A, C, G and T. “Genomics” is the study of the sequence of these letters in our DNA and how each string of letters passes information to help each cell in your body work properly.
A gene is essentially a sentence made up of the bases — A , C , G , and T — which describes how to make a protein. Any change in the sequence of bases — and therefore in the protein instructions — is called a “mutation.” Just like the changing of a letter in a word or a word in a sentence can change the meaning of that word or sentence, a mutation can change the instruction contained in the gene. Any changes to those instructions can alter the gene’s meaning and change the protein that is made, or how or when a cell makes that protein.
“Gene expression” is the process by which the information encoded in a gene is used to direct the assembly of a protein. The cell reads the sequence of the gene in groups of three bases. Each group of three bases (or codon) corresponds to one of 20 different amino acids used to build the protein. Gene mutations can (i) result in a protein that cannot carry out its normal function in the cell, (ii) prevent the protein from being made at all, or (iii) cause too much or too little of a normal protein to be made. Gene mutations occur in two general ways as noted below.
Inherited or Germline Mutations — This form of general mutation is inherited from a parent. Mutations that are passed from parent to child are called “hereditary” mutations or “germline” mutations (because they are present in the egg and sperm cells, which are also called “germ cells”). This type of mutation is present throughout a person’s life in virtually every cell in the body.
Acquired or Somatic Mutations — This form of general mutation occurs in the DNA of individual cells during a person’s lifetime. These changes can be caused by environmental factors such as ultraviolet radiation from the sun, or can occur if a mistake is made as DNA copies itself during cell division. Acquired mutations in somatic cells (i.e., other than sperm and egg cells) generally can not be passed on to the next generation.
A “chromosome” is an organized package of DNA found in the nucleus of the cell. Humans have 23 pairs of chromosomes–22 pairs of numbered chromosomes, called “autosomes,” and one pair of sex chromosomes, referred to as “X” and “Y.” Each parent contributes one chromosome to each pair so that offspring get half of their chromosomes from their mother and half from their father.
An “exon” is the portion of a gene that codes for amino acids. The parts of the gene sequence that are expressed in the protein are called “exons,” because they are expressed, while the parts of the gene sequence that are not expressed in the protein are called “introns,” because they come in between–or interfere with–the exons. The “exome” is the part of the genome formed by exons.
“Proteins” participate in virtually every process within cells. A protein is composed of one or more long chains of amino acids, the sequence of which corresponds to the DNA sequence of the gene that encodes it. The synthesis or production of a protein requires the transcription or copying of DNA code by mRNA, which travels from the cell’s nucleus to its cytoplasm. The mRNA code that is transcribed or copied from DNA is subsequently translated or synthesized into a protein built from amino acids. When this manufacturing process works uninterrupted, and a protein is produced, the gene (i.e., the original DNA code segment) is considered expressed.
Proteins play a variety of roles in the cell, including structural (cytoskeleton), mechanical (muscle), biochemical (enzymes), and cell signaling (hormones). Proteins are also an essential part of a healthy diet.
Appendix 3 – Specific Types of Gene Mutations
The DNA sequence of a gene can be altered by a mutation in several ways. Gene mutations have varying effects on health, depending on where they occur and whether they alter the function of essential proteins. The various types of gene mutations include:
A “missense” mutation is a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.
A “nonsense” mutation is also a change in one DNA base pair. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all.
An “insertion” mutation changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly.
A “deletion” mutation changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s).
A “duplication” mutation consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein.
A “frameshift” mutation occurs when the addition or loss of DNA bases changes a gene’s “reading frame.” A reading frame consists of 3 base groups that each code for one amino acid. A frameshift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations.
“Nucleotide repeats” are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide repeat is made up of 4-base-pair sequences. A “repeat expansion” mutation increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.
Apendix 4 – Epigenetics & Gene Silencing
A genome is the complete set of DNA in a cell. DNA carries the instructions for building all of the proteins that make each living creature unique. Derived from the Greek word “epi,” the term “epigenome” means “above” the genome. The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it and when to do it. The marks, which are not part of the DNA itself, can be passed on from cell to cell as cells proliferate, and from one generation to the next.
What does the epigenome do?
Each person’s body contains trillions of cells, all of which have essentially the same genome. Yet some cells are optimized for use in muscles, others for bones, the brain, the stomach and the remainder of the human body. What makes these cells different? The protein-coding parts of our genome (i.e., genes) do not make proteins all of the time in all of your cells. Instead, different sets of genes are turned on or off in various kinds of cells at different points in time. Differences in the types and amounts of proteins produced determine how cells look, grow and act. The epigenome influences which genes are active — and which proteins are produced — in a particular cell. So, the epigenome is what tells your skin cells to behave like skin cells, heart cells like heart cells, and so on.
What makes up the epigenome?
The epigenome is made up of chemical compounds, some of which come from natural sources like food and others from man-made sources like medicines or pesticides. As it marks the genome with these chemical tags, the epigenome serves as the intersection between the genome and the environment. The epigenome marks your genome in two primary, both of which play a role in turning genes off or on.
The first type of mark, called “DNA methylation,” directly affects the DNA in your genome. In this process, chemical tags called “methyl groups” attach to the backbone of the DNA molecule in specific places. The methyl groups turn genes off or on by affecting interactions between DNA and the cell’s protein-making machinery.
The second kind of mark, called “histone modification,” indirectly affects the DNA in your genome. Histones are spool-like proteins that enable DNA’s very long molecules to be wound up neatly into chromosomes inside the cell nucleus. A variety of chemical tags can grab hold of the tails of histones, changing how tightly or loosely they package DNA. If the wrapping is tight, a gene may be hidden from the cell’s protein-making machinery, and consequently be switched off. In contrast, if the wrapping is loosened, a gene that was formerly hidden may be turned on.
Is the epigenome inherited?
Just as the genome is passed along from parents to their offspring, the epigenome can also be inherited. The chemical tags found on the DNA and histones of eggs and sperm can be conveyed to the next generation.
What is imprinting?
As noted above, our genome contains two copies of every gene — one inherited from our mother and one from our father. For some genes, only the copy from the mother ever gets switched on, and for others, only the copy from the father. This pattern is called “imprinting.” The epigenome serves to distinguish between the two copies of an imprinted gene. For example, only the father’s copy of a gene called IGF2 (insulin-like growth factor 2) is able to make its protein. That is because marks in the epigenome keep the mother’s IGF2 gene copy switched off in every cell of the body. Some diseases are caused by abnormal imprinting.
Can the epigenome change?
While all cells in your body contain essentially the same genome, the chemical tags on the DNA and histones get rearranged in different cell types. The epigenome can also change throughout a person’s lifetime. A good example relates to identical twins. Although they share nearly the same genome, their bodies may not be exactly identical. One twin may weigh more, for example, or develop arthritis. Researchers think that at least some of these differences are due to changes in the epigenome.
What makes the epigenome change?
Lifestyle and environmental factors can expose a person to chemical tags that change the epigenome. In other words, our epigenome may change based on what we eat and drink, whether we smoke, what medicines we take, what pollutants we encounter and even how quickly our body ages. There is also some evidence from animal and human studies that indicates that what a female eats and drinks during pregnancy may change the epigenome of her offspring. Most epigenomic changes are probably harmless, but some changes may trigger or increase the severity of disease. Already, researchers have linked changes in the epigenome to various cancers, diabetes, autoimmune diseases, and mental illnesses.
How do changes in the epigenome contribute to cancer?
Cancers are caused by a combination of changes to the genome and the epigenome. Adding or removing methyl groups can switch genes involved in cell growth off or on. If such changes occur at the wrong time or in the wrong cell, they can wreak havoc, thereby converting normal cells into cancer cells.
For example, in a type of brain tumor called “glioblastoma,” doctors have had some success in treating patients with a drug called “temozolomide,” which kills cancer cells by adding methyl groups to DNA. But that’s only part of a very complex picture. Cells also contain a gene called “MGMT” (O-6-methylguanine-DNA methyltransferase), which produces a protein that subtracts methyl groups — an action that counteracts the effects of temozolomide. In some glioblastomas, however, the switch for the MGMT gene has been turned off by methylation, which blocks production of the protein that counteracts temozolomide. Consequently, glioblastoma patients whose tumors have methylated MGMT genes are far more likely to respond to temozolomide than those with unmethylated MGMT genes.
Changes in the epigenome also activate growth-promoting genes in stomach cancer, colon cancer and the most common type of kidney cancer. In other cancers, changes in the epigenome silence genes that normally serve to keep cell growth in check. Moreover, it is now recognized that in addition to genetic alterations, epigenetic mechanisms, such as DNA methylation and histone modifications play an important role in the development and progression of ovarian cancer by affecting chromatin structure, as well as gene and miRNA expression.
How are researchers exploring the epigenome?
Researchers are exploring the epigenome through the research field known as “epigenomics,” which is the study of all chemical tags on the genome that control the activities of genes. This is different from genomics, which is the study of all the changes that occur in the order, or sequence, of the DNA building blocks that make up the genome. Experts once thought that diseases were caused mainly by changes, or mutations, in DNA sequence – changes that either disrupt protein production or lead to abnormal proteins. Recently, researchers have learned that changes in the epigenome may cause or contribute to many diseases, making epigenomics a vital part of efforts to better understand the human body and improve human health.
To come up with a complete list of all possible changes that can lead to cancer, the National Institutes of Health (NIH) started “The Cancer Genome Atlas” (TCGA”). As noted above, these researchers are comparing the genomes and epigenomes of normal cells to those of cancer cells. They are looking for any changes (i.e., mutations) in the DNA sequence; changes in the number and structure of chromosomes; changes in the amounts of proteins produced by genes; and changes in the number of methyl groups on the DNA. Understanding all of the changes that turn a normal cell into a cancer cell could speed efforts to develop new and better ways of diagnosing, treating and preventing cancer. To learn more about this effort, visit www.cancergenome.nih.gov.
As part of its Roadmap for Medical ResearchEpigenomics Program, NIH also plans to develop a map of the epigenomic marks that occur on the human genome. The effort will require the development of better technologies to quickly and efficiently detect epigenomic marks, as well as improved understanding of the factors that drive these changes.
A cellular/biological pathway is a series of actions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Cellular pathways can also turn genes on and off, or spur a cell to move.
How do biological pathways work?
For our bodies to develop properly and stay healthy, many things must work together at many different levels – from organs to cells to genes.
Cells are constantly receiving cues from both inside and outside the body, which are prompted by such things as injury, infection, stress or even food. To react and adjust to these cues, cells send and receive signals through biological pathways. The molecules that make up biological pathways interact with signals, as well as with each other, to carry out their designated tasks.
Cellular pathways can act over short or long distances. For example, some cells send out signals to nearby cells to repair localized damage from a scratch on the knee. Other cells produce substances such as hormones, which that travel through your blood to distant target cells.
Cellular pathways can also produce small or large outcomes. For example, some pathways subtly affect how the body processes drugs, while others play a major role in how a fertilized egg develops into a baby.
There are many other examples of how biological pathways help our bodies work. The pupil in our eye opens or closes in response to light. If our skin senses that the temperature is rising, the body sweats to cool down.
It is important to keep in mind that cellular pathways do not always work properly. When something goes wrong in a pathway, the result can be a disease such as cancer or diabetes.
What are some types of cellular/biological pathways?
There are many types of cellular pathways. Some of the most common are involved in metabolism, the regulation of genes, and the transmission of signals.
“Metabolic pathways” make possible the chemical reactions that occur in our bodies. An example of a metabolic pathway is the process by which our cells break down food into energy molecules, which can be stored for later use. Other metabolic pathways help to build molecules.
“Gene regulation pathways” turn genes on and off. Such action is vital because genes produce proteins, which are the key components needed to carry out nearly every task in our bodies.
“Signal transduction pathways” or signaling pathways move a signal from the cell exterior to the cell interior. Different cells are able to receive specific signals through structures on their surface, called “receptors.” After interacting with a receptor, the signal travels through the cell where its message is transmitted by specialized proteins, which, in turn, trigger a specific action in the cell. For example, a chemical signal from outside the cell could be turned into a protein signal inside the cell. In turn, that protein signal could be converted into a signal that prompts the cell to move.
What is a cellular/biological network?
Researchers are learning that cellular pathways are far more complicated than once thought. Most pathways do not start at point “A” and end at point “B.” In fact, many pathways have no real boundaries, and they often work together (i.e., “cross-talk”) to accomplish tasks or provide redundancy. When multiple cellular pathways interact with each other, it is called a “biological network.”
How do researchers find cellular pathways?
Researchers discovered many important cellular pathways through laboratory studies of cultured cells, bacteria, fruit flies, mice and other organisms. Many of the pathways identified in these model systems are the same or have similar counterparts in humans.
Still, many biological pathways remain unknown. It will take many years of research to identify and understand the complex connections among all of the molecules in all cellular pathways, as well as to understand how these pathways work together.
What can biological pathways tell us about disease?
Researchers are able to learn a lot about human disease from studying cellular pathways. Identifying what genes, proteins and other molecules are involved in a cellular pathway can provide clues about what goes wrong when a disease occurs.
For example, researchers may compare certain cellular pathways in a healthy person to the same pathways in a person with a disease to discover the root(s) of the disorder. Keep in mind that problems in any number of steps along a cellular pathway can often lead to the same disease.
How can biological pathway information improve health?
Finding out what cellular pathway is involved in a disease — and identifying which step of the pathway is affected in each patient — could lead to more personalized strategies for diagnosing, treating and preventing disease.
Currently, researchers are using information about cellular pathways to develop new and better drugs. It likely will take some time before we routinely see drugs that are specifically designed to target cellular pathways. Nevertheless, doctors are already beginning to use pathway information to more effectively choose and combine existing drugs.
Why are cancer researchers excited about cellular/biological pathways?
Until recently, many scientific researchers hoped that most types of cancers were driven by a single genetic error and could be treated by designing drugs to target those specific errors. Much of that hope was based on the success of imatinib (Gleevec®), a drug that was specifically designed to treat a blood cancer called “chronic myeloid leukemia” (CML). CML occurs because of a single genetic glitch that leads to the production of a defective protein, which in turn, spurs uncontrolled cell growth. Gleevec binds to that protein, thereby stopping its activity and producing dramatic results in many CML patients. A similar approach was used in the development of the blockbuster drug trastuzumab (Herceptin®), which is used to treat an aggressive subtype of breast cancer. In both cases, the cancer cell possessed the gene defect, however, most or all of the normal cells did not.
Unfortunately, the “one-target, one-drug” approach has not held up for most other types of cancer. Recent projects that deciphered the genomes of cancer cells have found an array of different genetic mutations that can lead to the same cancer in different patients. Based upon the genetic profile of a patient’s particular tumor, we hope that patients could receive the drug or drug combination that is most likely to work for them.
The complexity of this findings is clearly daunting. Instead of attempting to discover ways to attack one well-defined genetic enemy, researchers are now faced with the prospect of fighting lots of little enemies. Fortunately, this complex view can be simplified by looking at which cellular pathways are disrupted by the genetic mutations. Rather than designing dozens of drugs to target dozens of mutations, drug developers could focus their attentions on just two or three cellular pathways. Patients could then receive the drug combination that is most likely to work for them based on the pathways affected in their particular tumors.
Example: Imagine a thousand people from all across the U.S. traveling towards the front door of a single building in Los Angeles. How would you keep all of these people from entering the building?
If you had limitless resources, you could hire workers to go out and stop each person as he or she drove down the highway, arrived at the train station or waited at the airport. Such actions would represent the one-target, one-drug approach.
But if you wanted to save a lot of time and money, you could just block the door to the building. This action represents the pathway-based strategy which many researchers are now pursuing to design drugs for cancer and other common diseases.
The cellular pathway approach is further complicated by the fact that many pathways are essential for the proliferation and survival of both cancer and normal cells. In this case, the hope is to design a drug that is capable of targeting only the defective pathways in cancer cells.
Appendix 6 – Targeting DNA Repair Through PARP Inhibition
Normally functioning BRCA1 (BReast CAncer-1) and BRCA2 (BReast CAncer-2) genes are necessary for major DNA repair through a process known as “homologous recombination” (HR). HR is a form of genetic recombination in which two similar DNA strands exchange genetic material. This process is critical to a cell’s ability to repair its DNA in the event that it becomes severely damaged, so the cell can continue to function. For discussion purposes, it is helpful to think of HR as the cell’s primary or major DNA “repair kit.”
A cell’s DNA structure can be damaged by a wide variety of intentional factors (e.g., select cancer treatments) or unintentional factors (e.g., ultraviolet light, ionizing radiation, man-made chemicals, etc.). For example, chemotherapy regimens used in the treatment of cancer, including alkylating agents, topoisomerase inhibitors, and platinum drugs, are designed to damage DNA and prevent cancer cells from reproducing.
In approximately 10% to 15% percent of germline (i.e., inherited) ovarian cancers, the BRCA 1 or BRCA2 gene is damaged or mutated, and therefore, the HR DNA repair kit is defective. The TCGA researchers determined that up to 50% of HGS-OvCa tumors possess BRCA gene-related or other defects in the HR DNA pair pathway. When the BRCA1 or BRCA2 gene is mutated, a secondary or minor DNA repair mechanism called “base-excision repair” usually compensates for the lack of HR DNA repair. As such, base-excision repair represents a secondary or minor DNA “repair kit.”
DNA repair enzymes such as PARP (poly (ADP-ribose) polymerase), whose activity and expression are upregulated in tumor cells, are believed to dampen the intended effect of chemotherapy and generate drug resistance. When the PARP1 protein – which is necessary for base-excision repair of “single-strand” DNA breaks – is inhibited in ovarian cancer cells possessing a BRCA gene mutation, DNA repair is drastically reduced. Ovarian cancer tumors that are caused by a mutation in the BRCA1 or BRCA2 gene are susceptible to cell death through PARP inhibition because BRCA-mutated genes are functionally incapable of repairing “double-strand” DNA breaks via HR. Without the ability to repair single strand breaks (due to therapeutic PARP inhibition) or subsequently resulting double strand DNA breaks (due to the lack of HR DNA repair by BRCA-mutated genes), the cancer cell dies through so-called “synthetic lethality.” Healthy cells are unaffected if PARP is blocked because they either contain one or two working BRCA1/BRCA2 genes which can perform DNA repair via HR. Accordingly, PARP inhibitors enhance the potential of chemotherapy (and radiation therapy) to induce ovarian cancer cell death.
Appendix 7 – PARP Inhibitors: A New Class of Targeted Therapy
PARP inhibitors represent a new, targeted approach to treating certain types of cancers. PARP inhibition has the potential to overwhelm cancer cells with lethal DNA damage by exploiting impaired DNA repair function inherent in some cancers, including breast and ovarian cancers with defects in the BRCA1 gene or BRCA 2 gene, and other DNA repair molecules. Inhibition of PARP leads to the cell’s failure to repair single strand DNA breaks, which, in turn, causes double strand DNA breaks. These effects are particularly detrimental to BRCA-mutated cancer cells that are deficient in repairing double strand DNA breaks due to lack of HR, and ultimately lead to cancer cell death. PARP inhibitors are the first targeted treatment to be developed for women with inherited forms of breast and ovarian cancer carrying faults or mutations in the BRCA-1 or BRCA-2 gene. Early results from clinical trials are showing promise for patients with these rare inherited forms of cancers.
Early preclinical research, including the findings above published by the The Cancer Genome Atlas, suggest that PARP inhibitors could provide benefit to women with germline (i.e., inherited) or somatic (i.e., lifetime acquired) BRCA gene mutations, as well as other defects in the HR DNA repair pathway. If ultimately proven true, the PARP class of drugs could provide benefit for up to 50% of high-grade, serous ovarian cancer patients.
Exelixis, Inc. reported expanded Phase 2 study data with respect to cabozantinib (XL184) use in advanced ovarian cancer patients at the recent 2011 American Society of Clinical Oncology Annual Meeting. The overall solid tumor Phase 2 safety and tolerability data reference six deaths, including two ovarian cancer patients.
Ronald J. Buckanovich, M.D., Ph.D., Assistant Professor, Departments of Internal Medicine & Obstetrics and Gynecology, University of Michigan
On May 19, 2011, we reported promising cabozantinib phase 2 solid tumor (including ovarian) data, which was presented at an ASCO press briefing held in advance of the 2011 ASCO Annual Meeting. As noted in our May 19 article, cabozantinib demonstrated excellent activity against several solid tumors, including ovarian cancer. In addition, we reported that cabozantinib showed promising activity in ovarian cancer patients independent of prior response to platinum drug-based therapies.
Ronald J. Buckanovich, M.D., Ph.D., Assistant Professor, Departments of Internal Medicine & Obstetrics and Gynecology, University of Michigan, presented the expanded cabozantinib Phase 2 data relating to use of the drug in advanced ovarian cancer patients, on June 4 at the 2011 ASCO Annual Meeting.
Ovarian Cancer Patient Population & Overall Response Rate
(Image Source: Exelixis, Inc.)
The cabozantinib trial is an ongoing phase 2 adaptive randomized discontinuation trial. As of the February 11, 2011 cut-off date, accrual in the cabozantinib study cohort was complete at 70 patients.
The 70 patients enrolled in the ovarian cancer cohort received oral cabozantinib (100 mg) daily over a 12 week “Lead-in Stage.” These patients had a minimum follow-up of at least 12 weeks and were thus evaluable for safety and the primary efficacyendpoint of response per RECIST (Response Evaluation Criteria in Solid Tumors).
Patient tumor response was assessed every 6 weeks. Receipt of cabozantinib treatment beyond the 12 week open label Lead-in Stage was based upon patient response: (1) patients with a partial response (PR) or complete response (CR) continued taking cabozantinib, (2) patients with stable disease (SD) were randomized to the cabozantinib treatment arm or the placebo treatment arm (collectively referred to as the “Blinded Randomized Stage”), and (iii) patients with progressive disease (PD) discontinued study treatment. The study primary endpoint was overall response rate (ORR) per RECIST in the Lead-in Stage, and progression free survival (PFS) in the Blinded Randomized Stage. Accrual in any cohort could be halted for high ORR or PD.
Approximately half of the 70 patients enrolled in the cohort were considered platinum drug-refractory/-resistant (49%), defined as a platinum drug-free interval of 6 months or less, and the remainder of patients (51%) had platinum-sensitive disease based on a platinum-free interval greater than 6 months.
The baseline patient tumor histologiccharacteristics are as follows: serous ovarian cancer (79%), clear cell ovarian cancer (4%), endometrioid ovarian cancer (6%), and other forms of ovarian cancer (11%)
More than half the patients (57%) received 2 or more prior lines of platinum therapy prior to trial enrollment. Some patients also had additional prior lines of therapy with agents such as pegylated liposomal doxorubicin (brand name: Doxil®) or topotecan (brand name: Hycamtin®) (32%), gemcitabine (brand name: Gemzar®) (29%), and VEGF (vascular endothelial growth factor) pathway inhibitors (10%).
Evidence of objective tumor regression was observed in 73% of patients with at least 1 post-baseline medical imaging scan. The best overall response rate per RECIST criteria was 24% (16 PRs and 1 CR). The overall Week-12 disease control rate (DRC = CR + PR + SD) was 53%. The Week-12 DCRs in the platinum drug-refractory, -resistant, and -sensitive groups were 36%, 39%, and 67%, respectively.
Based on an observed high rate of clinical activity, randomization was halted, and randomized patients were unblinded. At this point, the unblinded randomized patients that were treated with placebo were allowed to “cross-over” to treatment with cabozantinib. Disease stabilization was experienced by some ovarian cancer patients who had progressive disease prior to treatment cross-over.
“These latest results in metastatic ovarian cancer demonstrate the potential broad utility of cabozantinib beyond bone-predominant types of cancers such as castration-resistant prostate cancer. The high rates of durable response with our dual inhibitor of MET and VEGFR2 compare favorably to those of other single-agent targeted therapies and cytotoxic agents in development,” said Michael M. Morrissey, Ph.D., president and chief executive officer of Exelixis. “These results underscore the potential of cabozantinib in metastatic ovarian cancer, and we are in discussions with leading cooperative groups to plan further evaluation of cabozantinib in randomized trials for this indication.”
Activity in Platinum Drug-Sensitive, -Refractory, and -Resistant Disease
Ignace Vergote, M.D., Ph.D., senior author of the cabozantinib (XL184) ASCO presentation & Chairman, Leuven Cancer Institute, University of Leuven, European Union
(Image Source: Exelixis, Inc.)
Two of 11 patients (18%) with platinum refractory disease, defined as a platinum-free interval of <1 month, achieved a confirmed response (1 CR and 1 PR).
In the subset of patients with platinum-resistant disease, defined as a platinum-free interval of 1-6 months, 5 of 23 (22%) achieved a PR.
Ten of 36 patients (28%) with platinum sensitive disease achieved a PR.
A total of 37 patients experienced reductions in the ovarian cancer tumor marker CA-125 (cancer antigen-125), including 8 with decreases greater than 50%. There is no consistent concordance between CA-125 changes and tumor regression. The median duration of response has not yet been reached with 36 weeks of median follow-up.
“The continued activity of cabozantinib in a larger population of ovarian cancer patients is very encouraging, especially with respect to the clinical benefit observed in both platinum-sensitive and platinum-resistant/refractory disease. This activity profile has not been observed with other single-agent TKIs [tyrosine kinase inhibitors], and cabozantinib has the potential to be an important new treatment for ovarian cancer,” said Ignace Vergote, M.D., Ph.D., senior author of the presentation and Chairman of the Leuven Cancer Institute at the University of Leuven, European Union. “The high rate of disease control in platinum-resistant and platinum-refractory disease suggests that cabozantinib may help to address the substantial unmet medical need faced by patients who have sub-optimal responses to platinum-based therapies. I believe that further evaluation will help to define the potential role of cabozantinib in the treatment of ovarian cancer.”
Six Deaths Reported (Including Two Ovarian Cancer Patients)
If you examine the Exelixis press release dated June 4 (entitled, Exelixis’ Cabozantinib Demonstrates Encouraging Clinical Activity in Patients with Metastatic Ovarian Cancer — Disease control rate of 53% at week 12, response rate of 24%), which addresses data for cabozantinib use in advanced ovarian cancer patients, pay particular attention to the wording under the heading entitled, “Safety and Tolerability.” Within the wording set forth under that heading, you will find the following statement: “Two cabozantinib-related grade 5 AEs [adverse events], one enterocutaneous fistula and one intestinal perforation, were reported after the Lead-In phase.” Pursuant to the CTCAE guidelines, a “grade 5 adverse event” is defined as “death related to AE [adverse event].”
We should also note that the two ovarian cancer deaths were summarized briefly in the ASCO presentation regarding cabozantinib use in advanced ovarian cancer.
The reporting of all six deaths is set forth in the Exelixis press release, dated June 5, 2011 (entitled, Exelixis’ Cabozantinib Demonstrates Broad Clinical Activity in Multiple Tumor Types), in similar fashion. Within this release, the sentence provided under the heading “Safety and Tolerability” states: “There were 6 (1%) cabozantinib-related grade 5 [adverse] events, all of which were reported after the Lead-In phase of the trial: respiratory compromise (breast cancer), hemorrhage (NSCLC [non-small cell lung cancer]), enterocutaneous perforation (ovarian cancer), intestinal perforation (ovarian cancer), gastrointestinal hemorrhage (pancreatic cancer), and death (CRPC [castrate resistant prostate cancer]).”
Exelixis Chief Executive Michael Morrissey said the safety statistics are consistent with targeted cancer therapies like cabozantinib that block a pathway used by tumor cells to secure blood vessels.
Cowen & Co analyst Eric Schmidt said the rate of cabozantinib treatment-related deaths — 1 percent — was “no different from what we have seen for every other Phase 1 and 2 trials here at ASCO.”
“While drug safety is of less concern in cancer indications than in others, the apparent morbidities associated with cabo[zantinib] use will confound interpretation of clinical benefit in a trial designed to show anything less than overall survival,” Canaccord analyst George Farmer said in a research note.
In a note to investors, Piper Jaffray analyst Edward Tenthoff said: “The company is exploring lower doses, but the concern is that cabo[zantinib] will not retain the impressive efficacy seen to date.”
Mr. Morrissey said Exelixis plans to move forward with the current daily 100 mg dose of the drug.
Dr. Nicholas J. Vogelzang (Director, Comprehensive Cancer Centers of Nevada) Discusses Mortalities in the Cabozantinib (XL184) Trial
Take Away Message
Cabozantinib demonstrates promising activity in both platinum drug-sensitive and platinum drug-resistant/-refractory ovarian cancer.
Week 12 overall disease control rate of 53%.
Response rates of 18% in platinum-refractory, 22% in platinum-resistant and 28% in platinum-sensitive patients.
Cabozantinib shows encouraging duration of response.
After 36 weeks of follow-up, median duration of response not reached.
Tolerability profile is consistent with that of other tyrosine kinase inhibitors (6 solid tumor patient deaths (1% of all solid tumor pts), including 2 ovarian cancer patients (3% of ovarian cancer pts)).
Discordant effects observed between CA-125 changes and clinical activity.
Simultaneous targeting of MET and VEGFR2 with cabozantinib results in robust effects in patients with advanced ovarian cancer.
Non-randomized expansion cohort is currently accruing in platinum-resistant/-refractory ovarian cancer.
About the MET & VEGFR2 Pathways
To learn more about (i) the role of MET in cancer, (ii) the relationship between the MET and VEGFR pathways, and (iii) the dual inhibition of MET and VEGFR2, visit http://www.metinhibition.com/.
About Cabozantinib (XL184)
Cabozantinib (XL184) is a potent, dual inhibitor of MET and VEGFR2. Cabozantinib is an investigational agent that provides coordinated inhibition of metastasis and angiogenesis to kill tumor cells while blocking their escape pathways. The therapeutic role of cabozantinib is currently being investigated across several tumor types. MET is upregulated in many tumor types, thus facilitating tumor cell escape by promoting the formation of more aggressive phenotypes, resulting in metastasis. MET-driven metastasis may be further stimulated by hypoxic conditions (i.e., deprivation of adequate oxygen supply) in the tumor environment, which are often exacerbated by selective VEGF-pathway inhibitors. In preclinical studies, cabozantinib has shown powerful tumoricidal, anti-metastatic and anti-angiogenic effects, including: (i) extensive apoptosis of malignant cells; (ii) decreased tumor invasiveness and metastasis; (iii) decreased tumor and endothelial cell proliferation; (iv) blockade of metastatic bone lesion progression; and (v) disruption of tumor vasculature.
Exelixis, Inc. is a biotechnology company committed to developing small molecule therapeutics for the treatment of cancer. Exelixis is focusing its resources and development efforts exclusively on cabozantinib, its most advanced solely-owned product candidate, in order to maximize the therapeutic and commercial potential of this compound. Exelixis believes cabozantinib has the potential to be a high-quality, differentiated pharmaceutical product that can make a meaningful difference in the lives of patients. Exelixis has also established a portfolio of other novel compounds that it believes have the potential to address serious unmet medical needs. For more information, please visit the company’s web site at www.exelixis.com
EC145, in combination with pegylated liposomal doxorubicin (Doxil®/Caelyx®) in patients with platinum-resistant ovarian cancer, met its primary endpoint by showing an 85 percent (2.3 month) improvement in median progression-free survival in the intent-to-treat population, and a 260 percent (4.0 month) improvement in a subset of folate receptor positive patients. The final EC145 phase 2 clinical study data were presented today at the 2011 American Society of Clinical Oncology Annual Meeting.
EC145 delivers a very potent vinca chemotherapy directly to cancer cells by targeting the folate receptor expressed on cancer cells, but not on most normal cells. Approximately 80-90 percent of ovarian and lung cancers express the receptor, as do many other types of cancer. Click on the picture above to view a video regarding EC145's mechanism of action. (Photo: Endocyte, Inc.)
Endocyte, Inc., a biopharmaceutical company developing targeted small molecule drug conjugates (SMDCs) and companion imaging diagnostics for personalized therapy, today announced that the phase 2 PRECEDENT trial, which is investigating the company’s lead drug candidate, EC145, in combination with pegylated liposomal doxorubicin (PLD)(brand name: Doxil®/Caelyx®) in patients with platinum-resistant ovarian cancer, met its primary endpoint by showing: (i) an 85 percent (2.3 month) improvement in medianprogression-free survival (PFS) in the intent-to-treat population, and (ii) a 260 percent (4.0 month) improvement in a subset of folatereceptor positive patients. EC145 in combination with PLD showed limited additional toxicity compared to standard therapy with PLD alone. The most commonly occurring adverse events were neutropenia, small intestine obstruction, and palmar-plantar erythrodysesthesia (or hand-foot syndrome). EC145 is a therapeutic that targets the folate receptor and EC20 is a companion imaging diagnostic used to assess folate receptor presence.
These final PFS data from the PRECEDENT trial were presented today at the 2011 Annual Meeting of the American Society of Clinical Oncology (ASCO), in Chicago, Illinois and are available at http://investor.endocyte.com/events.cfm.
“I am encouraged by these data as EC145 is the first drug candidate to demonstrate a significant improvement in PFS in a randomized trial of patients with platinum-resistant ovarian cancer, a very challenging disease with a high unmet need. Historical data show that for these patients on standard therapy, PFS is approximately three months and overall survival is approximately twelve months. No new drug has been approved in the U.S. for this indication in over a decade,” said Wendel Naumann, M.D., Associate Director of Gynecologic Oncology at Blumenthal Cancer Center, Carolinas Medical Center. “In addition the companion imaging diagnostic, EC20, is designed to identify patients who over-express the targeted receptor and are most likely to respond to EC145. This represents a personalized therapeutic approach that I believe will help oncologists direct patients to the most promising treatment.”
EC145 Phase 2 PRECEDENT Clinical Study Data
The Phase 2 PRECEDENT trial was an international, multi-center, randomized study of 149 women with platinum-resistant ovarian cancer. Patients were randomized to receive EC145 plus PLD or PLD alone at a standard dose until disease progression or death. The primary endpoint of the study was progression-free survival. Secondary endpoints included response rate and overall survival.
The EC145 phase 2 PRECEDENT trial results are summarized below.
85 Percent (2.3 Month) Improvement in Median Progression-Free Survival for All Patients
Patients receiving EC145 in combination with PLD, regardless of folate receptor expression, had a median progression free survival of 5.0 months compared to 2.7 months for patients receiving single agent PLD. The hazard ratio for PFS was 0.626 (p=0.031). The overall response rate was 28 percent in the EC145 combination group versus 16 percent in the PLD-alone group. CA-125 (cancer antigen-125) responses were also more common in patients receiving EC145 in combination with PLD compared to those receiving PLD alone, with response rates (based on CA-125 blood serum measurement) of 38 percent and 19 percent, respectively.
260 Percent (4.0 Month) Improvement in Median Progression-Free Survival for Patients Most Positive for Folate Receptor
The study also utilized EC20, an investigational companion imaging diagnostic that is designed to identify patients with folate receptor positive tumors. As expected, in the folate receptor positive patients the improvement in PFS was even greater. In the subpopulation most positive for the folate receptor, PFS increased 4.0 months from 1.5 months to 5.5 months. The hazard ratio for PFS was 0.381 (p=0.018). This represents more than a 60 percent reduction in the risk of progression and provides evidence supporting the mechanism of action through targeting of the folate receptor. The overall response rate was 22 percent in the EC145 combination group versus 7 percent in the PLD alone group. CA-125 responses were also more common in patients receiving EC145 in combination with PLD compared to those receiving PLD alone, 43 percent and 13 percent, respectively.
“We see tremendous potential for continued development of EC145 based on these data that demonstrate, for the first time, a significant improvement in PFS in patients with platinum resistant ovarian cancer,” said Ron Ellis, President and Chief Executive Officer of Endocyte. “We have already advanced EC145 into Phase 3 evaluation with the PROCEED trial, which has a similar design to the PRECEDENT trial, and plan to file for regulatory approval in the European Union based on the PFS data from the PRECEDENT study.”
Plan to File PRECEDENT Data for Conditional Approval in Europe
As a result of Endocyte’s interaction with the European Medicines Agency (EMA), including a meeting with the Scientific Advice Working Party and written advice from the Committee for Medicinal Products for Human Use (CHMP), the Company will prepare marketing applications for both EC145 and EC20. Based on feedback from the CHMP, Endocyte plans to seek conditional marketing authorization for patients with platinum-resistant ovarian cancer who test positive for the folate receptor using the EC20 companion imaging diagnostic.
Phase 3 PROCEED Trial Initiated
Endocyte recently announced the initiation of patient enrollment in the Phase 3 PROCEED trial of EC145, which is structured to replicate the PRECEDENT trial design. The Phase 3 trial is a randomized, double-blinded trial of EC145 in combination with PLD compared to PLD plus placebo. The patient population — those with platinum-resistant ovarian cancer — will be the same as in the PRECEDENT trial, and the primary endpoint will be progression-free survival in patients selected by EC20 as folate-receptor positive. The trial will also be statistically powered for overall survival as a secondary endpoint with projected enrollment in excess of 500 patients. The trial will be conducted in approximately 150 sites in the U.S., Canada, and Europe. More information regarding the trial is available at www.clinicaltrials.gov.
EC145 is a conjugate of the vitamin folate and a super-potent vinca alkaloid. Folate is required for cell division and rapidly dividing cancer cells often over-express folate receptors in order to capture enough folate to support cell division. By attaching a chemotherapy drug to folate through proprietary chemistry, EC145 targets cancer cells while avoiding most normal cells. This targeted approach is designed to provide treatment with super-potent drugs while lowering toxicity compared to standard chemotherapy.
EC20 is a folate-targeted molecular imaging agent that is being developed as a non-invasive method to identify tumors that over-express folate receptors. These tumors are the molecular target of Endocyte’s folate-targeted therapeutic compounds such as EC145. To date, EC20 has been administered to over 500 patients and has been found to be well tolerated.
Endocyte is a biopharmaceutical company developing targeted therapies for the treatment of cancer and inflammatory diseases. Endocyte uses its proprietary technology to create novel small molecule drug conjugates (SMDCs) and companion imaging diagnostics for personalized targeted therapies. The company’s SMDCs actively target receptors that are over-expressed on diseased cells, relative to healthy cells. This targeted approach is designed to enable the treatment of patients with highly active drugs at greater doses, delivered more frequently, and over longer periods of time than would be possible with the untargeted drug alone. The companion imaging diagnostics are designed to identify patients whose disease over-expresses the target of the therapy and who are therefore more likely to benefit from treatment.
EntreMed, Inc. announced that ENMD-2076 demonstrated clinical activity — a six-month progression free survival rate of 19% — when administered as a single agent to platinum drug-resistant recurrent ovarian cancer patients. The announcement is based upon interim phase 2 data presented today at the 2011 American Society of Clinical Oncology Annual Meeting.
Ursula A. Matulonis, M.D., Medical Director, Gynecologic Oncology, Dana-Farber Cancer Institute; Associate Professor of Medicine, Harvard Medical School
ENMD-2076 demonstrated clinical activity when administered daily orally as a single agent. Interim data from 57 evaluable patients showed a six-month progression free survival rate of 19 percent. Of the evaluable patients, four patients achieved a partial response and 30 patients achieved stable disease as measured by RECISTv1.1. Median overall survival has not yet been reached. The side effect profile was consistent with activity against ENMD-2076’s molecular targets, in particular, VEGFR2 (vascular endothelial growth factor receptor-2) and Aurora A. Studies to evaluate potential markers of ENMD-2076 in this patient group are ongoing.
Dr. Matulonis commented on the results of the study, “ENMD-2076 has demonstrated impressive anti-cancer activity in platinum-resistant ovarian cancer which is notoriously difficult to treat, and these patients have few options.”
EntreMed’s chief medical officer, Carolyn F. Sidor, M.D., M.B.A., added, “These results are very encouraging as they support further development of ENMD-2076 and also help us clarify its developmental path in ovarian cancer. We are currently designing the next clinical trial in this indication and look forward to opportunities to make ENMD-2076 available to ovarian cancer patients in the future.”
ENMD-2076 is an orally-active, Aurora A/angiogenickinase inhibitor with a unique kinase selectivity profile and multiple mechanisms of action. ENMD-2076 has been shown to inhibit a distinct profile of angiogenic tyrosine kinase targets in addition to the Aurora A kinase. Aurora kinases are key regulators of mitosis (cell division), and are often over-expressed in human cancers. ENMD-2076 also targets the VEGFR, Flt-3 and FGFR3 kinases which have been shown to play important roles in the pathology of several cancers. ENMD-2076 has shown promising activity in phase I clinical trials in solid tumor cancers, leukemia, and multiple myeloma. While ENMD-2076 is currently in a phase 2 trial in ovarian cancer, preclinical and clinical activities are ongoing in assessing the compound’s applicability in other forms of cancer.
EntreMed, Inc. is a clinical-stage pharmaceutical company committed to developing ENMD-2076, a selective angiogenic kinase inhibitor, for the treatment of cancer. ENMD-2076 is currently in a multi-center phase 2 study in ovarian cancer and in several phase 1 studies in solid tumors, multiple myeloma, and leukemia.
Customizing targeted therapies to each tumor’s molecular characteristics, instead of a “one-size-fits-all” approach by tumor type, may be more effective for some types of cancer, according to research presented today at the American Society of Clinical Oncology annual meeting by the M.D. Anderson Cancer Center. In patients with end-stage disease, matched patients achieved a 27% response rate, versus 5% in those unmatched.
Apostolia M. Tsimberidou, M.D., Ph.D., Associate Professor, Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
Marking the largest scale on which this approach has been examined to date, the study analyzed the results of matching targeted therapies with specific genemutations in patients. The data indicated that this strategy was associated with higher rates of response, survival and failure-free survival than observed in non-matched patients.
Pairing Patient and Treatment
“This preliminary study strongly suggests that molecular analysis is needed to use the right drug for the right patient. Up to this point, we have treated tumor types, but this study shows we cannot treat all patients with a tumor type the same way. We need to take into consideration a number of factors, and this study suggests that a personalized approach is needed to improve clinical outcomes for patients with cancer,” said Tsimberidou.
The identification of pathways involved in carcinogenesis, metastasis and drug resistance; new technologies enabling tumor molecular analysis; and the discovery of targeted therapies have stimulated research focusing on the use of targeted agents as part of a personalized medicine approach, she said.
“Over the past decades, a personalized medicine approach using Gleevec has changed the way we treat chronic myeloid leukemia, as well as survival rates,” said Razelle Kurzrock, M.D., professor and chair of the M.D. Anderson Department of Investigational Cancer Therapeutics. “We wanted to apply a similar approach to solid tumors.”
“Ultimately, to best match treatments to patients and offer the most therapeutic benefit, assessing a patient’s molecular markers has to become the standard at diagnosis. …
This study affirms what we in the cancer community have been talking about for a decade – matching drugs to patients. The time is now. The drugs are here. The technology is here, and with our program at M.D. Anderson we can bring the two together in hopes to offer the most personalized care for our patients. …”
–Razelle Kurzrock, M.D., Professor & Chair, Department of Investigational Cancer Therapeutics, University of Texas M.D. Anderson Cancer Center
Research Methods and Results
In the initial analysis, Tsimberidou analyzed 1,144 patients with metastatic or inoperable cancer who underwent testing for molecular aberrations at M.D. Anderson. Their median age was 58, and the median number of prior treatments was four. Of these patients, 460 had one or more gene aberrations, including:
Patients with gene aberrations were treated on clinical trials with matched targeted agents, when available. Regimens included one or more therapies targeting PIK3CA, mTOR, BRAF, MEK, multikinases, KIT or EGFR. Outcomes of patients with gene aberrations treated with matched therapy were compared with those patients with gene aberrations who were not treated with matched therapy because of issues such as eligibility, study availability; insurance coverage and/or logistical problems with the study calendar.
For the 175 patients with one aberration, the response rate was 27 percent with matched targeted therapy. The response rate was 5 percent in 116 patients when treated with non-matched therapy.
Patients who received matched targeted therapy had median survival of 13.4 months, while median survival for patients treated with unmatched targeted therapy was nine months. Median failure-free survival in patients who received matched targeted therapy was 5.2 months, compared to 2.2 months for patients who received unmatched targeted therapy.
Further Research Needed
These preliminary results merit further investigation and confirmatory, prospective studies are needed, especially because the study was not a randomized study and therefore biases could influence the results.
“M.D. Anderson’s goal is to better understand the biology involved in each patient’s carcinogenesis by testing each tumor for genetic abnormalities driving tumor growth to guide treatment selection. This strategy will lead to the optimization of personalized therapy,” Tsimberidou said.
Another goal is to match targeted therapies to patients earlier in treatment.
“When Gleevec was first introduced, it was tested in patients in blast crisis and the response rate was about 15 percent. In contrast, when tested in the front line setting, and with the introduction of similar but increasingly potent second- and third-generation drugs, patients’ response rate was close to 100 percent, and now their expected survival is 25 years and counting,” said Kurzrock. “Ultimately, to best match treatments to patients and offer the most therapeutic benefit, assessing a patient’s molecular markers has to become the standard at diagnosis.”
About the Phase I Program – The Time is Now
The M.D. Anderson’s Phase I program is the largest of its kind and accounts for the majority – but not all – of the institution’s earliest clinical studies. In 2010, of the 11,000 patients who participated in M.D. Anderson clinical trials, more than 1,150 were enrolled in one of the 120 Phase I trials in the program.
Currently, tumors are tested for up to 12 molecular aberrations, but at the rate technology is rapidly advancing, Kurzrock expects that number to climb to more than 100 in the near future.
Patients treated in the Phase I Program are typically very ill and all other approved therapies have failed them. Yet they are “fighters” who are willing to try anything, including studies not specific to their diagnosis to test the effectiveness of a new drug, drug combination or delivery method, said Kurzrock.
“This study affirms what we in the cancer community have been talking about for a decade – matching drugs to patients,” said Kurzrock. “The time is now. The drugs are here. The technology is here, and with our program at M.D. Anderson we can bring the two together in hopes to offer the most personalized care for our patients.”
In addition to Tsimberidou and Kurzrock, other authors on the all-M.D. Anderson study included N. G. Iskander, David S. Hong, M.D., Jennifer J. Wheler, M.D., Siqing Fu, M.D., Ph.D., Sarina A. Piha-Paul, M.D., Aung Naing, M.D., Gerald Falchook, Filip Janku, M.D., Ph.D., all assistant professors of the Department of Investigational Cancer Therapeutics; Raja Luthra, Ph.D., professor, Department of Hematopathology, Research and Sijin Wen, Ph.D., Division of Quantitative Sciences.
Libby’s H*O*P*E*™ Commentary — Use of Molecular Profiling and Chemosensitivity Testing To Determine Individualized Ovarian Cancer Treatment
It is wonderful that various medical research institutions, including M.D. Anderson, are beginning to match targeted therapies to a patient’s specific molecular tumor characteristics. This approach is generally referred to as “molecular profiling,” and it represents one promising method of matching an individual cancer patient to an effective therapy. As noted in the related Libby’s H*O*P*E*™ postings set forth below, there are several medical and scientific institutions which are pursuing development of molecular profiling for clinical study use. In the most recent related posting listed below, we discuss the molecular profile testing that is commercially available through The Clearity Foundation and Caris Life Sciences.
In the future, it may be helpful to use a form of chemosensitivity testing (e.g., the type of testing provided by Precision Therapeutics, Rational Therapeutics, and the Weisenthal Cancer Group), which is based upon the measurement of actual cancer cell death, as a second method to match a cancer patient to a potential drug or drug combination within the context of a clinical study. In fact, we would like to see a future prospective, randomized ovarian cancer clinical trial in which enrolled women are provided with treatment after assignment to one of three clinical trial arms: (i) treatment based upon the standard of care (e.g., paclitaxel and carboplatin), (ii) treatment based upon molecular profiling, or (iii) treatment based upon chemosensitivity testing. This type of study may uncover additional ovarian cancer treatment insights (both molecular and functional) with respect to the most lethal gynecologic cancer, while ultimately helping women with forms of the disease that may not possess a known molecular characteristic that is potentially “targetable” by an existing clinical trial drug or compound.
This combination of “bottom-up” scientific research (i.e., molecular profiling) performed side-by-side with “top-down” research (i.e., chemosensitivity testing) may represent an effective and efficient approach — albeit provocative — for evaluation of optimal personalized ovarian cancer treatment.
It is important to note that Libby’s H*O*P*E*™ and its founder Paul Cacciatore do not receive financial renumeration or benefit of any kind from the companies referred to in the paragraphs above.
About the University of Texas M.D. Anderson Cancer Center
The University of Texas M.D. Anderson Cancer Center in Houston ranks as one of the world’s most respected centers focused on cancer patient care, research, education and prevention. MD Anderson is one of only 40 comprehensive cancer centers designated by the National Cancer Institute. For seven of the past nine years, including 2010, M.D. Anderson has ranked No. 1 in cancer care in “America’s Best Hospitals,” a survey published annually in U.S. News & World Report.
Cabozantinib (XL184) demonstrated high rates of disease control in patients with prostate, ovarian and liver cancers. The investigators concluded that cabozantinib exhibits clinical activity in ovarian cancer patients with advanced disease, regardless of prior platinum drug status, as reflected by the high rates of response.
ASCO Releases Studies From Upcoming Annual Meeting – Important Advances in Targeted Therapies, Screening, and Personalized Medicine
The meeting, which is expected to draw approximately 30,000 cancer specialists, will be held June 3-7, 2011, at McCormick Place in Chicago, Illinois. The theme of this year’s meeting is “Patients. Pathways. Progress.”
“This year marks the 40th anniversary of the signing of the National Cancer Act, a law that led to major new investments in cancer research. Every day in our offices, and every year at the ASCO meeting, we see the results of those investments. People with cancer are living longer, with a better quality of life, than ever before,” said George W. Sledge Jr., M.D., President of ASCO, Ballve-Lantero Professor of Oncology and professor of pathology and laboratory medicine at the Indiana University School of Medicine.
“With our growing understanding of the nature of cancer development and behavior, cancer is becoming a chronic disease that a growing number of patients can live with for many years,” said Dr. Sledge. “The studies released today are the latest examples of progress against the disease, from new personalized treatments, to new approaches to screening and prevention.”
Novel Multi-targeted Agent Cabozantinib (XL184) Has Significant Effect on Several Advanced Solid Tumors, and Can Shrink or Eliminate Bone Metastases
Cabozantinib (XL184) – an oral inhibitor of MET and VEGFR2kinases involved in the development and progression of many cancers – showed strong responses in patients with various advanced cancers in a phase II trial. The drug demonstrated particularly high rates of disease control for advanced prostate, ovarian and liver cancers, which are historically resistant to available therapies. The drug also fully or partially eliminated bone metastases in patients with breast and prostate cancers and melanoma.
Michael S. Gordon, M.D., President & Chief Executive Officer, Pinnacle Oncology Hematology.
“Cabozantinib appears to have significant effects on several treatment-resistant tumors, as well as impressive effects on bone metastases. In addition, these effects are associated with rapid improvement in pain, a reduction in opiate narcotic requirements and improvement in anemia,” said lead author Michael S. Gordon, M.D., a medical oncologist at Pinnacle Oncology Hematology located in Scottsdale, Arizona. “The implications of these results are very exciting—it is unusual to find a targeted therapy, absent of a molecular mutation in tumors, that works in bony disease and has this activity.”
To be eligible for the study, patients had to have advanced, progressive solid tumors, with or without bone metastases. Of 398 evaluable patients (of 483 enrolled in the trial), 39 percent had bone metastases at baseline. Patients received cabozantinib over 12 weeks. The trial was designed as a “discontinuation” trial, in which those who had partial responses stayed on the drug; those with stable disease were randomized to cabozantinib or placebo; and patients with progressive disease were removed from the trial. This novel type of clinical trial design more quickly evaluates the disease-stabilizing activity of growth-inhibitory agents like cabozantinib, compared to the traditional model of randomizing all patients to either the experimental arm or placebo.
Among 398 patients evaluable with all types of cancer included in the trial, the collective overall response rate was 9 percent (34 of 398). The highest disease control rates (partial response and stable disease) at week 12 were 76 percent for liver cancer (22 of 29 patients), 71 percent for prostate cancer (71 of 100 patients), and 58 percent for ovarian cancer (32 of 51 patients). [emphasis added].
Of the 51 evaluable ovarian cancer patients noted above, 28 are platinum drug resistant, 17 are platinum drug sensitive, and 6 have unknown status. The median number of systemic treatments prior to trial enrollment was 2. The overall response rate (complete response and partial response based on modified RECIST criteria) for ovarian cancer was 12/51 (24%). Upon breakdown, the response rate was 5/28 (18%) for platinum drug resistant patients, and 5/17 (29%) for platinum drug sensitive patients. Five additional partial responses await confirmation. After a median follow-up of 4 months (range: 1 to 11 months), the median duration of response and median progression free survival have not been reached. The most common related adverse events ( ≥grade 3) among ovarian cancer patients were hand-foot syndrome (10%), diarrhea (8%) and fatigue (4%). Drug dose reductions and permanent discontinuations for adverse events occurred in 43% and 10% of the ovarian cancer patients, respectively. Based on these findings, the investigators concluded that cabozantinib exhibits clinical activity in ovarian cancer patients with advanced disease, regardless of prior platinum drug status, as reflected by the high rates of response. [emphasis added] Accordingly, randomization in the ovarian cancer cohort was halted & patients unblinded due to the observed high efficacy.
Fifty-nine of 68 patients with bone metastases (including patients with breast and prostate cancers and melanoma) experienced either partial or complete disappearance of the cancer on bone scans, often with significant pain relief and other improved cancer-related symptoms.
The reduction of bone metastases and pain relief was an unexpected finding in this study, Dr. Gordon said. Independent review by radiologists confirmed that bone metastases disappeared in the majority of patients who had bone metastases when they entered the study. The majority of these patients had castration-resistant prostate cancer (CRPC), but patients with breast cancer and melanoma also had disappearance of bone metastases. Bone metastases greatly contribute to morbidity and mortality in patients with these types of cancer, which typically spread to the bone.
Due to these results, the study has been expanded to include more CRPC patients. Similarly, the high rate of lasting responses in ovarian cancer patients led researchers to also expand the study to evaluate the drug’s effect on patients with a particularly resistant form of the disease known as platinum drug resistant/refractory ovarian cancer. [emphasis added]
This study expansion results will help determine the design of future phase III trials, which will assess whether the drug extends patients lives or has other longer-term benefits among patients with specific cancer types. At present, cabozantinib is being investigated for use as a single agent. Additional studies will evaluate the efficacy and tolerability of appropriate combinations with other agents for future indications.
For the solid tumor patients collectively, the most common grade three or above adverse events were fatigue (9 percent) and hand-foot syndrome (8 percent). Dose reductions were required in 41 percent of patients due to side effects; 12 percent were removed from the trial for adverse events.
A group of international researchers reported sustained responses in two ovarian clear cell cancer (OCCC) patients with chemotherapy-resistant disease, who were treated with the anti-angiogenesis inhibitor sunitinib (Sutent®). The researchers emphasize the growing realization that OCCC is molecularly and clinically distinct as compared to other forms of ovarian cancer, and note significant common scientific characteristics possessed by both OCCC and renal clear cell cancer.
Clear Cell Carcinoma of the Ovary
Ovarian clear cell cancer (OCCC) is a rare form or subtype of epithelial ovarian cancer that is generally refractory to platinum-based chemotherapy. A group of international researchers from the United Kingdom, Australia, Japan, Canada and the United States recently reported results from comprehensive OCCC tumor gene expression and copy number testing, which was designed to identify potential therapeutic targets of OCCC.
Based upon the findings above, the researchers highlighted the importance of specific therapeutic targets in the treatment of OCCC, and suggested that more extensive clinical trials with sunitinib in OCCC patients are warranted. The overarching findings of this study provide significant impetus to the growing realization that OCCC is molecularly and clinically distinct as compared to other forms of ovarian cancer.
Open Ovarian Cancer and Solid Tumor Clinical Trials Testing MET Inhibitors (as of 3/25/11)
We provide below a list of MET inhibitors that are currently available through open ovarian cancer and solid tumor clinical trials. A few caveats are noteworthy.
First, the association between MET inhibiton and ovarian clear cell cancer inhibition has NOT been established as a form of treatment in large randomized, prospective clinical trials.
Second, most of the clinical trials listed below are phase I studies designed to test the biological activity and safety of the drug — not the effectiveness. Patients enrolled in a phase I trial are generally the first humans to receive the study drug.
Third, all patients should seek advice from their doctor in advance of deciding to enroll in a clinical trial. Many of the clinical drugs listed below inhibit one or more cellular functions in addition to MET.
List of open solid tumor clinical trials testing AMG 208.
List of open solid tumor clinical trials testing MGCD-265.
Recommendations stemming from recent clinical trials highlight notable updates to the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines™) for Ovarian Cancer at the National Comprehensive Cancer Network® (NCCN®) 16th Annual Conference.
Robert J. Morgan, Jr., M.D., Professor of Medical Oncology, City of Hope Comprehensive Cancer Center; Chair, NCCN Guidelines Panel for Ovarian Cancer
“Regardless of the type of cancer, the NCCN Guidelines for Ovarian Cancer reflect the importance of stage and grade of disease on prognosis and treatment recommendations,” said Dr. Morgan.
The NCCN Guidelines continue to recommend that women with borderline epithelial ovarian cancer of low malignant potential be primarily surgically managed. In contrast to patients with frankly invasive ovarian carcinoma, women with borderline disease tend to be younger and are often diagnosed with stage I disease.
“The benefits of postoperative chemotherapy has not been demonstrated for patients who have no microscopically demonstrable invasive implants, said Dr. Morgan. “Even patients with advanced stage disease at presentation have an excellent prognosis and chemotherapy should be avoided.”
“However, the dose-dense regimen is more toxic, and patients discontinued dose-dense paclitaxel therapy more often than those receiving standard therapy,” stated Dr. Morgan. “As with all treatment decisions, the patient needs to weigh the potential benefits and risks and discuss them thoroughly with their physician.”
Dr. Morgan discussed two additional phase 3 trials assessing bevacizumab (Avastin®:, Genentech/Roche) combined with carboplatin/paclitaxel in the upfront setting compared to carboplatin/paclitaxel alone.[3-4] Although data regarding overall survival and quality of life have not been reported yet, the studies did indicate that the median progression-free survival increased in patients receiving bevacizumab as a first line and maintenance therapy.
“Only modest improvements in progression-free survival were observed in both of these trials. The NCCN Guidelines Panel prefers to await mature results of these trials prior to recommending the routine addition of bevacizumab to carboplatin/paclitaxel,” said Dr. Morgan.
As such, the updated NCCN Guidelines includes new language detailing the Panel’s view on bevacizumab encouraging participation in ongoing clinical trials that are further investigating the role of anti-angiogenesis agents in the treatment of ovarian cancer, both in the upfront and recurrence settings.
Biomarkers continue to emerge as an area of interest in predicting future patterns of the disease. In patients with ovarian cancer, Dr. Morgan discussed the value of monitoring CA-125 levels in regards to a recent study comparing early versus delayed treatment of relapsed ovarian cancer.
“Often, levels of CA-125 have been shown to rise prior to a clinical or symptomatic relapse in women with ovarian cancer. This trial looked at whether there was a benefit of early treatment on the basis of increased CA-125 concentrations compared with delayed treatment on the basis of clinical recurrence,” said Dr. Morgan.
The study, which was published in The Lancet, found that there was no survival benefit to early institution of treatment based on increased CA-125 levels and that the quality of life was superior in patients in the late treatment arm.
“The results of the trial suggest that the utility of the routine monitoring of CA-125 levels in limited,” said Dr. Morgan. “The NCCN Guidelines Panel encourages patients and their physicians to actively discuss the pros and cons of CA-125 monitoring based upon these findings and have updated the NCCN Guidelines to include language supporting this recommendation.”
Virtually all drugs used in oncology have the potential to cause adverse drug reactions while being infused, which can be classified as either infusion or allergic reactions. Recently, hypersensitivity to platinum compounds has been recognized as a potential issue for patients being administered these compounds.
“Platinum compounds remain very important in the treatment of ovarian cancer in both the upfront and recurrence settings, so it was important to design strategies to allow for the safe desensitization of these agents in patients who develop allergies,” said Dr. Morgan.
Standard desensitization regimens include slowly increasing infusion concentrations over several hours. However, Dr. Morgan noted that these procedures must be done in a specific manner in order to be safely administered and pointed to the recommendations within the updated NCCN Guidelines discussing the management of drug reactions.
In conclusion, Dr. Morgan emphasized that although steady progress is being made in the treatment of ovarian cancer, further trials are necessary to investigate the role of targeted agents alone and in combination in newly diagnosed and recurrent ovarian cancer. In addition, enrollment of patients with ovarian cancer must be encouraged.
The National Comprehensive Cancer Network® (NCCN®), a not-for-profit alliance of 21 of the world’s leading cancer centers, is dedicated to improving the quality and effectiveness of care provided to patients with cancer. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of high-quality cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers. The primary goal of all NCCN initiatives is to improve the quality, effectiveness, and efficiency of oncology practice so patients can live better lives. For more information, visit NCCN.org.
The NCCN Member Institutions are:
City of Hope Comprehensive Cancer Center
Dana-Farber/Brigham and Women’s Cancer Center
Massachusetts General Hospital Cancer Center
Duke Cancer Institute
Fox Chase Cancer Center
Huntsman Cancer Institute at the University of Utah
Fred Hutchinson Cancer Research Center / Seattle Cancer Care Alliance
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
Robert H. Lurie Comprehensive Cancer Center of Northwestern University
Memorial Sloan-Kettering Cancer Center
H. Lee Moffitt Cancer Center & Research Institute
The Ohio State University Comprehensive Cancer Center – James Cancer Hospital and Solove Research Institute
Roswell Park Cancer Institute
Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine
St. Jude Children’s Research Hospital / University of Tennessee Cancer Institute
Stanford Comprehensive Cancer Center
University of Alabama at Birmingham Comprehensive Cancer Center
UCSF Helen Diller Family Comprehensive Cancer Center
University of Michigan Comprehensive Cancer Center
UNMC Eppley Cancer Center at The Nebraska Medical Center
An analysis conducted by Ohio State University cancer researchers found that adding the targeted therapy bevacizumab to the first-line treatment of patients with advanced ovarian cancer is not cost effective.
Dr. David E. Cohn is a gynecologic oncologist & researcher at The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital & Richard J. Solove Research Institute. He is also the lead author of the bevacizumab cost-effectiveness study.
Bevacizumab is a novel targeted therapy designed to inhibit angiogenesis, the process by which new blood vessels develop and carry vital nutrients to a tumor.
Although a discussion regarding cost-effectiveness of a potentially life-extending intervention invariably suggests the rationing of limited health care resources, the intent of this study was to provide a framework with which to evaluate the pending results of a clinical trial of three different interventions for ovarian cancer, said Cohn.
“We do not suggest that bevacizumab, also known by the brand name Avastin, should be withheld from a patient with ovarian cancer, but rather argue that studies evaluating the effectiveness of new treatments should also be interpreted with consideration of the expense,” says Cohn, who collaborated with Dr. J. Michael Straughn Jr., an associate professor of obstetrics and gynecology at the University of Alabama at Birmingham.
“We put together a model looking at the variety of treatment arms on this clinical trial, each of which included 600 patients,” said Cohn. “Given the fact that the addition of the drug was associated with 3.8 months of additional survival without cancer, we set out to determine whether or not that benefit of survival was justified by the expense of the drug.”
The model showed that standard chemotherapy for patients in the clinical trial would cost $2.5 million, compared to $78.3 million for patients who were treated with standard chemotherapy and bevacizumab, plus additional maintenance treatments of bevacizumab for almost one year.
Bevacizumab has been used in the treatment of recurrent ovarian cancer, and the U.S. Food and Drug Administration has approved it for the treatment of colorectal, lung, breast, brain (glioblastoma) and renal cell [kidney] cancers.
Typically each treatment with bevacizumab costs $5,000, with most of those costs directly attributable to the cost of the drug, Cohn said.
Effectiveness was defined as months of progression-free survival, and costs were calculated as total costs per strategy. Cost-effectiveness strategies were defined as the cost per year of progression-free survival. Incremental cost-effectiveness ratio was defined as the costs per progression-free year of life saved.
“Ultimately, we found that if you reduced the drug cost to 25 percent of the baseline, it does become cost effective to treat patients with bevacizumab,” said Cohn. “Or, if the survival could be substantially increased above the 3.8 months of progression-free survival, that could lead to cost-effective treatment for patients with advanced ovarian cancer.”
Ovarian cancer is the most lethal gynecologic cancer, with almost 14,000 women expected to die from the disease this year, according to the American Cancer Society.
“It is anticipated that in the future, there will be increased scrutiny regarding the individual and societal costs of an effective medication,” said Cohn. “We hope that future clinical trials will incorporate the prospective collection of cost, toxicity and quality-of-life data to allow for a fully informed interpretation of the results.”
Big Cost For Little Gain in Ovarian Cancer – JCO Editorial
Results of the cost-effectiveness model reported above by Cohen et. al. reveal that paclitaxel plus carboplatin plus bevacizumab, followed by bevacizumab maintenance (PCB-B), as tested in the GOG 218 phase III clinical trial, costs $78.3 million ($1,305,000 per patient) with an incremental cost-effectiveness ratio of $401,088 per progression-free year of life saved. It is important to note that traditional cost-effectiveness study models utilize the costs of improvements in overall survival, as compared to the traditional cost-effective standard of $50,000 per year of life saved, or more recently, $100,000 per year of life saved. Cohen et. al. found that the traditional standard of $100,000 per progression free year of life saved can be achieved in calculating the incremental cost-effectiveness ratio, but only at a bevacizumab drug price point that is 25% below the actual drug cost.
Martee L. Hensley, M.D., Gynecologic Medical Oncology Service, Memorial Sloan-Kettering Cancer Center
First, Dr. Hensley notes that the “costs” accounted for by the Ohio State University researchers only refer to the additional monies incurred by adding bevacizumab to the standard of care paclitaxel-carboplatin treatment. Specifically, the researchers used a standard cost metholodolgy based upon estimates of drug costs using Medicare reimbursement rates. The model used does not include indirect costs (e.g., patient out-of-pocket expenses, time lost from work associated with 51 weeks of bevacizumab maintenance, etc.). The only costs related to toxicity of treatment included by researchers were those associated with management of intestinal perforations. Dr. Hensley highlights the fact that the cost model does not include management of grade 2 or worse hypertension or other potential problems that may be caused by bevacizumab or the other chemotherapy drugs. To the extent that additional costs are added to the model, the cost-effectiveness ratio generated by the researchers would worsen.
Second, Dr. Hensley explains that out of necessity, the researchers’ cost-effectiveness model used PFS data due to the unavailability of overall survival or quality adjusted overall survival data in connection with the three most recent bevacizumab phase III clinical trials. This model construct assumes that the 3.8 month improvement in PFS (as reported by the GOG 218 trial investigators) provides an improvement in the patient’s experience. Dr. Hensley emphasizes that most ovarian cancer recurrences are identified while the patient is still asymptomatic, with the help of CA-125 blood testing and computed tomography imaging (i.e., CT scan). Stated differently, it may not be correct to assume that remaining radiographically progression-free for an addtional 3.8 months would improve a patient’s quality of life. If GOG 218 ultimately finds that PCB-B does not improve overall survival, then the drug’s cost-effectiveness will drift farther away from an acceptable level, says Hensley.
Third, Dr. Hensley points out that only when PFS associated with PCB-B use was hypothetically extended to 32.1 months (observed PFS in GOG 218 was 14.1 months) by the researchers did the incremental cost-effectiveness ratio approach $100,000 per progression-free year of life saved. Hensley believes that the bevacizumab data accrued to date suggests that a 32.1 month PFS is unlikely. Notably, median PFS is only 24 months among lower-risk patients with optimally debulked stage III ovarian cancer treated with intraperitoneal-based platinum drug/taxane drug therapy.
Fourth, Dr. Hensley explains that it may be possible to achieve a better incremental cost-effectiveness ratio based upon preliminary data derived from the Gynaecologic Cancer Intergroup (GCIG) phase III randomized clinical trail of paclitaxel plus carboplatin, with or without bevacizumab and bevacizumab maintenace therapy (ICON7 trial). The bevacizumab dose tested in ICON7 was only half of that used in GOG 218 (7.5 mg/kg versus 15 mg/kg), and the duration of maintenance therapy in ICON7 was only 36 weeks of continued treatment as compared to 51 weeks in GOG 218. Preliminary results reported by the GCIG in ICON7 indicate that bevacizumab creates a PFS advantage in line with that produced in GOG 218, but at half the dose. Based on these facts, Hensley states that potential use of lower-dose and shorter-duration bevacizumab would improve the incremental cost-effectiveness ratio. Moreover, if lower dose/shorter duration bevacizumab use is also found to reduce the frequency of grade 2 or worse hypertension, the overall costs associated with the drug would also be lower, says Hensley.
Dr. Hensley believes that there are additional steps to be taken (and questions to be answered) which could improve an evaluation of the role and costs of bevacizumab:
Is there a clinically meaningful overall survival advantage to PCB-B over paclitaxel plus carboplatin? If PCB-B is not effective, then by definition, it is not cost-effective.
Is the data from ICON7 sufficient to permit treatment at half the dose for 9 months instead of 12 months? If so, total bevacizumab costs would be lower.
Is there a subset of patients who benefit dramatically from PCB-B?
If there is a subset of patients who benefit dramatically from PCB-B, it is necessary to study this group of women to determine if potential biomarkers can identify which patients will or will not benefit from the addition of bevacizumab. Identifying biomarkers that can predict response means commitment to correlative studies as part of large clinical trials.
In sum, Dr. Hensley believes that buying bevacizumab at $78.3 million for 3.8 months of progression-free survival on behalf of approximately 600 women is not sustainable in today’s health care delivery system. Moreover, the incurrence of such costs may hinder basic clinical research to find better compounds that improve PFS by a more meaningful magnitude, says Dr. Hensley. From Hensley’s perspective, it appears that the stage is set for a potential collision between medicine and policy with respect to where and how a finite number of health care dollars will be spent.
About the Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute
The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (cancer.osu.edu) is one of only 40 Comprehensive Cancer Centers in the United States designated by the National Cancer Institute. Ranked by U.S. News & World Report among the top cancer hospitals in the nation, The Arthur G. James Hospital is the 205-bed adult patient-care component of the cancer program at The Ohio State University. The OSUCCC – James is one of only seven funded programs in the country approved by the NCI to conduct both phase I and II clinical trials.
“Cornell Dots” — brightly glowing nanoparticles — may soon be used to light up cancer cells to aid in diagnosing and treating cancer. The U.S. Food and Drug Administration (FDA) has approved the first clinical trial in humans of the new technology. It is the first time the FDA has approved using an inorganic material in the same fashion as a drug in humans.
“Cornell Dots” (or “C dots”) — brightly glowing nanoparticles — may soon be used to light up cancer cells to aid in diagnosing and treating cancer. The U.S. Food and Drug Administration (FDA) has approved the first clinical trial in humans of the new technology. It is the first time the FDA has approved using an inorganic material in the same fashion as a drug in humans.
Michelle Bradbury, M.D., Ph.D., Clinician-Scientist, Neuroradiology Service, Memorial Sloan-Kettering Cancer Center; Assistant Professor, Radiology, Weill Cornell Medical College; Lead Study Investigator
“This is a very exciting and important first step for this new particle technology that we hope will ultimately lead to significant improvements in patient outcomes and prognoses for a number of different cancers.”
— Michelle Bradbury, M.D., Ph.D., lead investigator of the study and clinician-scientist on Memorial Sloan-Kettering’s Neuroradiology Service and an assistant professor of radiology at Weill Cornell Medical College
C dots were initially developed as optical probes at Cornell University, Ithaca, by Ulrich Wiesner, Ph.D., a professor of materials science and engineering who, along with Hybrid Silica Technologies, the supplier of C dots, has spent the past eight years precisely engineering these particles. C dots are silica spheres less than 8 nanometers in diameter that enclose several dye molecules. (A nanometer is one-billionth of a meter, about the length of three atoms in a row.) The silica shell, essentially glass, is chemically inert and small enough to pass through the body and out in the urine. For clinical applications, the dots are coated with polyethylene glycol so the body will not recognize them as foreign substances.
C dots were subsequently modified at Memorial Sloan-Kettering for use in PET (positron emission tomography) imaging. C dots are tiny silica spheres that contain dye that glows three times more brightly than simple free dyes when excited by light of a specific wavelength. C dots can “light up” cancer cells, and act as tumor tracers for tracking the movement of cells and assisting in the optical diagnosis of tumors near the skin surface. The attachment of a radioactive label produces a new generation of multimodal (PET-optical) particle probes that additionally enable deeper detection, imaging, and monitoring of drug delivery using three-dimensional PET techniques.
Ulrich Wiesner, Ph.D. (left), a Cornell University Professor of Materials Science & Engineering, works with graduate students Jennifer Drewes & Kai Ma to characterize the size & brightness of C dots in their Bard Hall lab. (Photo: Jason Koski/University Photography)
Using PET scans, C dots can be imaged to evaluate various biological properties of the tumors, including tumor accumulation, spread of metastatic disease to lymph nodes and distant organs, and treatment response to therapy. The information gained from imaging tumors targeted with this multimodal platform may also assist physicians in defining tumor borders for surgery, and improving real-time visualization of small vascular beds, anatomic channels, and neural structures during surgery.
The purpose of this trial is to evaluate the distribution, tissue, uptake, and safety of the particles in humans by PET imaging. This study will provide data that will serve as a baseline to guide the design of future surgical and oncologic applications in the clinic. “The use of PET imaging is an ideal imaging technology for sensitively monitoring very small doses of this new particle probe in first-in-human trials,” added Steven Larson, M.D., Chief of Memorial Sloan-Kettering’s Nuclear Medicine Service.
Memorial Sloan-Kettering nanochemist Oula Penate Medina, Ph.D., notes that “this is an important trial in that it will help to answer a number of key questions regarding future potential applications of this multimodal system. Once the door has been opened, new and emerging fields, such as targeted drug delivery, can be investigated. We expect that these particles can be adapted for multiple clinical uses, including the early diagnosis and treatment of various cancers, as well as for sensing changes in the microenvironment.”
“This clinical trial is the culmination of a longstanding collaborative effort with our colleagues at Cornell and Hybrid Silica Technologies, as well as a testament to our own institutional colleagues here at the Center,” Dr. Bradbury said. “With the support of many, in particular the Office of Clinical Research, we’ve pushed to translate the C dots from a laboratory idea to our first FDA IND-approved inorganic nanomedicine drug product to be tested in the clinic,” Dr. Bradbury said.
DNA (deoxyribonucleic acid) is the genetic material that contains the instructions used in the development and functioning of our cells. DNA is generally stored in the nucleus of our cells. The primary purpose of DNA molecules is the long-term storage of information. Often compared to a recipe or a code, DNA is a set of blueprints that contains the instructions our cells require to construct other cell components, such as proteins and RNA (ribonucleic acid) molecules. The DNA segments that carry this genetic information are called “genes.”
A gene is essentially a sentence made up of the bases A (adenine), T (thymine), G (guanine), and C (cytosine) that describes how to make a protein. Any change in the sequence of bases — and therefore in the protein instructions — is a mutation. Just like changing a letter in a sentence can change the sentence’s meaning, a mutation can change the instruction contained in the gene. Any changes to those instructions can alter the gene’s meaning and change the protein that is made, or how or when a cell makes that protein.
Gene mutations can (i) result in a protein that cannot carry out its normal function in the cell, (ii) prevent the protein from being made at all, or (iii) cause too much or too little of a normal protein to be made.
Targeting DNA Repair Through PARP Inhibition
Targeting DNA repair through PARP inhibition in BRCA gene-mutated cancer cells. "DSB" stands for DNA "Double Stand Break." (Photo Credit: AstraZeneca Oncology)
Normally functioning BRCA1 and BRCA2 genes are necessary for DNA repair through a process known as “homologous recombination” (HR). HR is a form of genetic recombination in which two similar DNA strands exchange genetic material. This process is critical to a cell’s ability to repair its DNA in the event that it becomes damaged, so the cell can continue to function.
A cell’s DNA structure can be damaged by a wide variety of intentional (i.e., select cancer treatments) or unintentional (ultraviolet light, ionizing radiation, man-made chemicals, etc.) factors. For example, chemotherapy regimens used in the treatment of cancer, including alkylating agents, topoisomerase inhibitors, and platinum drugs, are designed to damage DNA and prevent cancer cells from reproducing.
In approximately 10 percent of inherited ovarian cancers, the BRCA 1 or BRCA2 gene is damaged or mutated. When the BRCA1 or BRCA2 gene is mutated, a backup type of DNA repair mechanism called “base-excision repair” usually compensates for the lack of DNA repair by HR. Base-excision repair represents a DNA “emergency repair kit.” DNA repair enzymes such as PARP, whose activity and expression are upregulated in tumor cells, are believed to dampen the intended effect of chemotherapy and generate drug resistance.
When the PARP1 protein – which is necessary for base-excision repair – is inhibited in ovarian cancer cells possessing a BRCA gene mutation, DNA repair is drastically reduced, and the cancer cell dies through so-called “synthetic lethality.” In sum, PARP inhibitors enhance the potential of chemotherapy (and radiation therapy) to induce cell death. Healthy cells are unaffected if PARP is blocked because they either contain one or two working BRCA1 or BRCA2 genes which do an effective DNA repair job through use of HR.
PARP Inhibitors: A New Class of Targeted Therapy
PARP inhibitors represent a new, targeted approach to treating certain types of cancers. PARP inhibition has the potential to overwhelm cancer cells with lethal DNA damage by exploiting impaired DNA repair function inherent in some cancers, including breast and ovarian cancers with defects in the BRCA1 gene or BRCA 2 gene, and other DNA repair molecules. Inhibition of PARP leads to the cell’s failure to repair single strand DNA breaks, which, in turn, causes double strand DNA breaks. These effects are particularly detrimental to cancer cells that are deficient in repairing double strand DNA breaks and ultimately lead to cancer cell death.
PARP inhibitors are the first targeted treatment to be developed for women with inherited forms of breast and ovarian cancer carrying faults or mutations in a BRCA gene. Early results from clinical trials are showing promise for patients with the rare inherited forms of these cancers.
Study Hypothesis: PARP Inhibitors May Be Effective Against a Large Proportion of Non-Inherited Ovarian Cancers
As noted above, PARP inhibitors selectively target HR–defective cells and have shown good clinical activity in hereditary breast and ovarian cancers associated with BRCA1 or BRCA2 mutations. The U.K. researchers hypothesized that a high proportion (up to 50%) of sporadic (non-inherited) epithelial ovarian cancers could be deficient in HR due to genetic or epigenetic inactivation of the BRCA1, BRCA2, or other HR-related genes, which occur during a woman’s lifetime. Therefore, PARP inhibitors could prove beneficial to a larger group of ovarian cancer patients, assuming a patient’s HR status can be properly identified.
To test this hypothesis, the U.K. researchers developed a functional assay to test the HR status of primary ovarian cancer cultures derived from patients’ ascitic fluid. The test, referred to as the “RAD51 assay,” scans the cancer cells and identifies which tumor samples contain defective DNA repair ability (i.e., HR-deficient) which can be targeted by the PARP inhibitor. The researchers tested the HR status of each culture, and then subjected each one to in vitrocytotoxicity testing using the potent PARP inhibitor PF-01367338 (formerly known as AG-14699).
Study Results: 90% of HR-Deficient Ovarian Cancer Cultures Respond to PARP Inhibition
Upon testing completion, the U.K. researchers discovered that out of 50 primary cultures evaluated for HR status and cytotoxicity to the PARP inhibitor, approximately 40% of the cultures evidenced normal HR activity, while 60 percent of the cultures evidenced deficient HR activity. Cytotoxicity to PARP inhibitors was observed in approximately 90 percent of the HR deficient cultures, while no cytotoxicity was seen in the cultures that evidenced normal HR activity. Specifically, the PARP inhibitor PF-01367338 was found to selectively block the spread of ovarian tumor cells with low RAD51 expression.
Based upon the findings above, the U.K. researchers concluded that HR-deficient status can be determined in primary ovarian cancer, and that such status correlates with in vitro response to PARP inhibition. Accordingly, the researchers concluded that potentially 50 to 60 percent of ovarian cancers could benefit from PARP inhibitors, but they note that use of the RAD51 assay as a biomarker requires additional clinical trial testing. Although the RAD51 assay test that was used by the U.K. researchers to examine tumor samples in the laboratory is not yet suitable for routine clinical practice, the U.K. research team hopes to refine it for use in patients.
Upon presentation of the testing results, Dr. Asima Mukhopadhyay said:
“Our results show that this new test is almost 100 percent effective in identifying which ovarian cancer patients could benefit from these promising new drugs. We have only been able to carry out this work because of the great team we have here which includes both doctors and scientists.”
“Now we hope to hone the test to be used directly with patients and then carry out clinical trials. If the trials are successful we hope it will help doctors treat patients in a personalised and targeted way based on their individual tumour. It is also now hoped that PARP inhibitors will be useful for a broad range of cancers and we hope this test can be extended to other cancer types.”
“It’s exciting to see the development of promising new ‘smart’ drugs such as PARP inhibitors. But equally important is the need to identify exactly which sub-groups of patients will benefit from these new treatments. Tests like this will become invaluable in helping doctors get the most effective treatments quickly to patients, sparing them from unnecessary treatments and side effects.”
Dr. Asima Mukhopadhyay is a doctor and clinical research fellow working at the Queen Elizabeth Hospital, Gateshead and the Northern Institute for Cancer Research at Newcastle University. Queen Elizabeth Hospital is run by Gateshead Health NHS Foundation Trust and is the home for gynecological oncology for the North East of England and Cumbria. She received a bursary to attend the conference, which was awarded on the merit of her work.
Key researchers on the study included Dr. Richard Edmondson, who was funded by the NHS, and Professor Nicola Curtin, who was funded by the Higher Education Funding Council. Dr Asima Mukhopadhyay is funded by the NHS.
Dr Richard Edmondson is a consultant gynecological oncologist at the Northern Gynaecological Oncology Centre, Gateshead and a Senior Lecturer at the Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, and is a member of the research team.
Nicola Curtin is Professor of Experimental Cancer Therapeutics at Newcastle University and is the principal investigator of this project.
Current and future work involves working closely with Pfizer. Pfizer developed one of the PARP inhibitors and supported this project.
About The Newcastle Cancer Centre
The Newcastle Cancer Centre at the Northern Institute for Cancer Research is jointly funded by three charities: Cancer Research UK, Leukaemia and Lymphoma Research, and the North of England Children’s Cancer Research Fund. Launched in July 2009, the Centre is based at the Northern Institute for Cancer Research at Newcastle University. The Centre brings together some of the world’s leading figures in cancer research and drug development. They play a crucial role in delivering the new generation of cancer treatments for children and adults by identifying new drug targets, developing new drugs and verifying the effectiveness and safety of new treatments. This collaborative approach makes it easier for researchers to work alongside doctors treating patients, allowing promising new treatments to reach patients quickly.
About the NCRI Cancer Conference
The National Cancer Research Institute (NCRI) Cancer Conference is the UK’s major forum for showcasing the best British and international cancer research. The Conference offers unique opportunities for networking and sharing knowledge by bringing together world leading experts from all cancer research disciplines. The sixth annual NCRI Cancer Conference was held from November 7-10, 2010 at the BT Convention Centre in Liverpool. For more information visit www.ncri.org.uk/ncriconference.
About the NCRI
The National Cancer Research Institute (NCRI) was established in April 2001. It is a UK-wide partnership between the government, charity and industry which promotes cooperation in cancer research among the 21 member organizations for the benefit of patients, the public and the scientific community. For more information visit www.ncri.org.uk.
NCRI members include: the Association of the British Pharmaceutical Industry (ABPI); Association for International Cancer Research; Biotechnology and Biological Sciences Research Council; Breakthrough Breast Cancer; Breast Cancer Campaign; CancerResearch UK; CHILDREN with LEUKAEMIA, Department of Health; Economic and Social Research Council; Leukaemia & Lymphoma Research; Ludwig Institute for Cancer Research; Macmillan Cancer Support; Marie Curie Cancer Care; Medical Research Council; Northern Ireland Health and Social Care (Research & Development Office); Roy Castle Lung Cancer Foundation; Scottish Government Health Directorates (Chief Scientist Office);Tenovus; Welsh Assembly Government (Wales Office of Research and Development for Health & Social Care); The Wellcome Trust; and Yorkshire Cancer Research.