Dana-Farber Oncologists Differ Widely on the Use of Multiplex Tumor Genomic Testing

A new study by researchers at the Dana-Farber Cancer Institute suggests that not all doctors are ready to embrace tests that may identify hundreds of genomic changes in a patient’s tumor sample for the purpose of determining appropriate treatment.

Many cancer researchers believe that cutting-edge advances in genomics will pave the way for personalized or “precision” cancer medicine for all patients in the near future. A new study by researchers at the Dana-Farber Cancer Institute, however, suggest that not all doctors are ready to embrace tests that look for hundreds of genomic changes in a patient’s tumor sample, while others plan to offer this type of cancer genomic tumor testing to most of their patients. The study findings were published recently in the Journal of Clinical Oncology [1], along with an accompanying editorial. [2]

The wide variation in attitudes was in part determined by physicians’ “genomic confidence.” Physicians who had a lot of confidence in their ability to use and explain genomic findings were more likely to want to prescribe the test and consider using test results when making treatment recommendations. Other physicians had lower levels of genomic confidence and were more reluctant to offer such testing. These findings are particularly interesting because the survey was carried out at the Dana-Farber/Brigham and Women’s Cancer Center (DF/BWCC), which has a comprehensive research program. The DF/BWCC research program allows all consenting patients to have genomic tumor testing, which is capable of finding gene mutations and other DNA alternations that drive a patient’s cancer. In some cases, the genomic tumor profiles identify “druggable” targets that may allow doctors to use specific drugs known to be effective against particular gene mutations or alterations.

The researchers were perplexed by another key study survey finding: 42 percent of responding oncologists approved of telling patients about genomic tumor test results even when their significance for the patient’s outlook and treatment is uncertain. This issue comes with the growing use of predictive multiplex genomic testing, which can identify tens or hundreds of gene mutations simultaneously and often detects rare DNA variants that may or may not be relevant to the treatment of an individual’s cancer.

“Some oncologists said we shouldn’t return these results to the patient, and others say ‘of course we should give them to the patient’,” said Stacy W. Gray, M.D., AM, of Dana-Farber, first author of the report. “I think the fact that we found so much variation in physicians’ confidence about their ability to use genetic data at a tertiary care, National Cancer Institute-designated Comprehensive Cancer Center makes us pause and wonder about how confident physicians in the community are about dealing with this,” she said. “It begs the question at a national level, how are we going to make sure that this technology for cancer care is adequately delivered?”

The study survey was conducted in 2011 and early 2012 as a baseline assessment of physicians’ attitudes prior to the rollout of the genomic tumor testing project referred to as “Profile” (which formerly utilized a technology platform called “OncoMap“) at DF/BWCC.

For purposes of the study, a total of 160 Dana-Farber adult cancer physicians – including medical oncologists (43%), surgeons (29%), and radiation oncologists (19%) – participated in the survey. They were asked about their current use of multiplex tumor genomic testing, their attitudes about multiplex testing, and their confidence in the ability to understand and use genomic data. The survey did not include a direct test of the physicians’ knowledge.

Among the many intriguing findings of this study, a wide variability in interest in multiplex tumor genomic testing was identified—25% of respondents anticipated testing more than 90% of their patients, whereas 17% of respondents anticipated testing 10% or less. Beliefs related to the potential value of multiplex tumor genomic testing were largely positive; most expressed belief that this form of testing would increase treatment (73%) and research options (90%) for patients, as well as both physician (80%) and patient satisfaction (80%).

Despite the foregoing, less than 50% of the physicians planned to view the multiplex tumor genomic testing results routinely. Moreover, the majority of respondents planned only to “rarely” or “sometimes” use the clinically relevant results (58%), called “Tier 1” by the study authors, and potentially actionable results (88%), called “Tier 2,” to assist them in the treatment of patients. However, the respondents more often indicated that results of multiplex tumor genomic tests should be shared with patients, particularly findings revealing the presence of a Tier 1 (clinically relevant) genomic variant—87% believed that these findings should be discussed—versus a Tier 2 (potentially actionable) genomic variant (50%), or a Tier 3 (uncertain significance) genomic variant (40%). A substantial minority (39%) also disagreed with a Dana-Farber Cancer Institute policy prohibiting the disclosure of Tier 3 genomic variants to patients.

Interestingly, despite limited exposure to routine genomic tests for a large portion of the respondents, the stated “genomic confidence” of participating physicians was quite high. The majority of participants reported that they were “somewhat” or “very” confident in their (i) knowledge of genomics (78%), (ii) ability to explain genomics (86%), and (iii) ability to use genomic results to guide treatment (74%); however, a substantial minority of the Dana-Farber physicians (28%) reported genomic confidence of “not very” or “not at all confident.”

Based upon the study survey findings, Dr. Gray and her colleagues conclude that there is “little consensus” on how physicians plan to use multiplex tumor genomic testing for personalized cancer care, and they suggest the need for evidence-based guidelines to help doctors determine when testing is indicated.

“I think one of the strengths of this study is that its information comes from an institution where ‘precision cancer medicine’ is available to everyone,” commented Barrett Rollins, M.D., Ph.D., Dana-Farber’s Chief Scientific Officer and a co-author of the paper. “It highlights the fact there’s a lot of work to be done before this can be considered a standard approach in oncology.”

The senior author of the study is Jane Weeks, M.D., MSc, of Dana-Farber; additional authors include Angel Cronin, MS, of Dana-Farber and Katherine Hicks-Courant, BA, of the University of Massachusetts Medical School.

The research was supported by the Dana-Farber Cancer Institute. Dr. Gray also receives support from the American Cancer Society (120529-MRSG-11-006-01-CPPB) and the National Human Genome Research Institute (U01HG006492)

Pursuant to a new phase of Profile, initiated by Dana-Farber in 2013, a more advanced technology platform (called “OncoPanel“) utilizes “massively parallel” or “next-generation” sequencing to read the genetic code of approximately 300 genes in each patient’s tumor sample. “Massively parallel” refers to the technology’s capacity for sequencing large numbers of genes simultaneously. The 300 genes evaluated in connection with the OncoPanel were chosen because they have been implicated in a variety of cancers.

In addition to the complete DNA sequencing of more than 300 genomic regions to detect known and unknown cancer-related mutations, the OncoPanel technology can also examine those regions for gains and losses of DNA sequences and rearrangements of DNA on chromosomes. The results are entered into a database for research purposes, but, if a patient agrees, the clinically important findings can also be returned to their doctor for use in the clinic.

The OncoPanel advanced sequencing platform is an important update to Dana-Farber’s original OncoMap platform. OncoPanel can detect not only commonly known gene mutations, but also other critical types of cancer-related DNA alterations not previously identified. In contrast, OncoMap was limited to screening for known cancer-related gene mutations. The OncoPanel testing is done at the Center for Advanced Molecular Diagnostics, a CLIA-certified laboratory operated by the Department of Pathology at Brigham and Women’s Hospital.

References:

1./ Gray SW, et al. Original Reports – Health Services and Outcomes: Physicians’ Attitudes About Multiplex Tumor Genomic Testing. J. Clin. Oncol., published online before print on March 24, 2014, doi:10.1200/JCO.2013.52.4298.

2./ Hall MJ. Conflicted Confidence: Academic Oncologists’ Views on Multiplex Tumor Genomic Testing. J. Clin. Oncol. Editorial, published online before print March 24, 2014, doi:10.1200/JCO.2013.54.8016

 

TGen-led Study Discovers Genetic Cause of a Rare Type of Ovarian Cancer

TGen-led study discovers genetic cause of a rare type of ovarian cancer. Scientific breakthrough could lead to new cancer treatments; study inspired by the memory of Taryn Ritchey, a 22-year-old patient who lost her battle to the disease.

The cause of a rare type of ovarian cancer that most often strikes girls and young women has been uncovered by an international research team led by the Translational Genomics Research Institute (TGen), according to a study published online recently by the renowned scientific journal, Nature Genetics. [1] In a scientific rarity, two additional studies with similar results were also published online on the same day in Nature Genetics, producing immediate validation and reflecting a scientific consensus that usually takes months or even years to accomplish. [2-3]

By applying its groundbreaking work in genomics, TGen led a study that included: Scottsdale Healthcare, Mayo Clinic, Johns Hopkins University, St. Joseph’s Hospital and Medical Center; Evergreen Hematology and Oncology, Children’s Hospital of Alabama, the Autonomous University of Barcelona, British Columbia Cancer Agency, University of British Columbia, and the University Health Network-Toronto.

The findings revealed a “genetic superhighway” mutation in a gene found in the overwhelming majority of patients with small cell carcinoma of the ovary, hypercalcemic type, also known as “SCCOHT.” This rare type of ovarian cancer is usually not diagnosed until it is in its advanced stages. It does not respond to standard chemotherapy, and 65 percent of patients with the disease die within 2 years. SCCOHT can affect girls as young as 14 months, and women as old as 58 years – with a mean age of only 24 years old. In this study, the youngest patient was 9 years old.

The three separate groups of international researchers reported strikingly similar scientific findings related to SCCOHT, as provided below.

• Identification of germline (i.e., inherited) and somatic (lifetime acquired) inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT cases, in addition to SMARCA4 protein loss in 82% (14/17) of the SCCOHT tumors. Notably, only 0.4% (2/485) of the other primary ovarian tumors tested possessed similar genomic characteristics. [Ref. 1]

• Identification of recurrent inactivating mutations in the SMARCA4 gene in 12 of 12 SCCOHT tumor samples. [Ref. 2]

• Indentification of germline inactivating mutations in familial cases of SCCOHT. Through additional analysis of non-familial tumors, the researchers determined that nearly 100% of tumors carry SMARCA4 mutations, and 38 of 40 lack protein expression.[Ref. 3]

Collectively, these findings implicate inactivating mutations in the SMARCA4 gene as a major cause of SCCOHT, and may lead researchers to improvements in genetic counseling, as well as the development of new targeted therapy treatment approaches.

Dr. Jeffrey Trent, President and Research Director of TGen, is the study’s senior author.

“This is a thoroughly remarkable study. Many genetic anomalies can be like a one-lane road to cancer; difficult to negotiate. But these findings indicate a genetic superhighway that leads right to this highly aggressive disease,” said Dr. Jeffrey Trent, President and Research Director of TGen, and the study’s senior author. “The correlation between mutations in SMARCA4 and the development of SCCOHT is simply unmistakable.”

Dr. Trent added that while the breakthrough is for a relatively rare cancer, discovering the origins of this type of ovarian cancer could have implications for more common diseases.

Much of the work in this study was inspired by the memory of Taryn Ritchey, a 22-year-old TGen patient who in 2007 lost her battle with ovarian cancer, the 5th leading cause of cancer death among American women.

“Taryn would be incredibly excited about this amazing new study, and she would be glad and thankful that other young women like her might now be helped because of TGen’s ongoing research,” said Taryn’s mother Judy Jost of Cave Creek, Arizona. “My daughter never gave up, and neither has TGen.”

The SMARCA4 gene – previously associated with lung, brain and pancreatic cancer – was the only recurrently mutated gene in the study’s samples. The implications of this discovery, therefore, may be widespread.

“The findings in this study represent a landmark in the field. The work identifies SMARCA4 mutations as the culprit, and most future research on this disease will be based on this remarkable discovery,” said Dr. Bert Vogelstein, Director of the Ludwig Center at Johns Hopkins University, Investigator at the Howard Hughes Medical Institute, and pioneer in the field of cancer genomics. He did not participate in the study but is familiar with its findings.

“The past decade of research has taught us that cancer is a vastly complex disease. Profound patient-to-patient variability has made treatment and diagnosis for many tumor types at times very difficult. In this case, however, we have found a single genetic event driving SCCOHT in nearly every patient,” said Dr. William Hendricks, a TGen Staff Scientist and another author of the study.

“We have shown that loss of SMARCA4 protein expression is extremely specific to SCCOHT and can facilitate the diagnosis of SCCOHT,” said Dr. Anthony N. Karnezis, a fellow at the British Columbia Cancer Agency located in Vancouver, Canada, and one of the study’s authors.

Pilar Ramos, a TGen Research Associate, is the study’s lead author. “By definitively identifying the relationship between SMARCA4 and SCCOHT, we have high confidence that we have set the stage for clinical trials that could provide patients with immediate benefit.”

“By definitively identifying the relationship between SMARCA4 and SCCOHT, we have high confidence that we have set the stage for clinical trials that could provide patients with immediate benefit.”

“We set out to uncover any small sliver of hope for women afflicted with this rare cancer. What we found instead are the nearly universal underpinnings of SCCOHT,” said Pilar Ramos, a TGen Research Associate, and the study’s lead author. “By definitively identifying the relationship between SMARCA4 and SCCOHT, we have high confidence that we have set the stage for clinical trials that could provide patients with immediate benefit.”

The TGen-led study was supported by grants from: the Marsha Rivkin Center for Ovarian Cancer Research, the Anne Rita Monahan Foundation, the Ovarian Cancer Alliance of Arizona, the Small Cell Ovarian Cancer Foundation, and philanthropic support to the TGen Foundation. Further support was provided by the Terry Fox Research Initiative’s New Frontiers Program in Cancer, and the Canadian Institutes of Health Research.

For more information about TGen’s research into small cell carcinoma of the ovary (SCCO), or to participate in a future study, visit: www.tgen.org/scco.

About TGen

Translational Genomics Research Institute (TGen) is a Phoenix, Arizona-based non-profit organization dedicated to conducting cutting-edge genomic research to accelerate breakthroughs in healthcare. TGen is focused on helping patients with cancer, neurological disorders and diabetes, through cutting edge translational research (the process of rapidly moving research towards patient benefit). TGen physicians and scientists work to unravel the genetic components of both common and rare complex diseases in adults and children. Working with collaborators in the scientific and medical communities literally worldwide, TGen makes a substantial contribution to help our patients through efficiency and effectiveness of the translational process. For more information, visit: www.tgen.org.

References:

1./ Ramos P, et al.  Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nature Genetics (published online 23 March 2014) doi:10.1038/ng.2928.

2./ Jelinic P, et al. Recurrent SMARCA4 mutations in small cell carcinoma of the ovary. Nature Genetics (published online 23 March 2014) doi:10.1038/ng.2922.

3./ Witkowski L, et al.  Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type.  Nature Genetics (published online 23 March 2014) doi:10.1038/ng.2931

Additional Information:

• Ovarian cancer breakthrough discovered by Phoenix scientists, by Adam Longo, http://www.kptv.com, March 23, 2014. [Includes CBS5 video news story].

• Select SCCHOT PubMed Medical Study Citations

• Small Cell Ovarian Cancer Foundation

 

Tel Aviv University Researchers Target Drug-Resistant Ovarian Tumors with Nanotechnology

Tel Aviv University researchers devise a fast and effective nanotechnology — called “gagomers” — to combat drug-resistant ovarian cancer.

Professor Dan Peer of Tel Aviv University’s Department of Cell Research and Immunology has proposed a new strategy to tackle drug-resistant ovarian cancer using a new nanoscale drug-delivery system designed to target specific cancer cells. The study was published in February in the journal ACS Nano.

Nanotechnology usually refers to an object that is 1-to–100 nanometers in size. A nanometer is a billionth of a meter. By comparison, the width of a strand of hair is approximately 100,000 times larger than a nanometer.

Prof. Peer and his team — Keren Cohen and Rafi Emmanuel from Peer’s Laboratory of Nanomedicine and Einat Kisin-Finfer and Doron Shabbat, from TAU’s Department of Chemistry — devised a cluster of nanoparticles called “gagomers,” which are made from fats and coated with a kind of polysugar. When filled with chemotherapy drugs (in this case doxorubicin), these clusters accumulate in tumors, producing dramatic therapeutic benefits.

The objective of Peer’s research is two-fold: to provide a specific target for anti-cancer drugs to increase their therapeutic benefits, and to reduce the toxic side effects of anti-cancer therapies.

Why Chemotherapy Fails

According to Prof. Peer, traditional courses of chemotherapy are not an effective line of attack. Chemotherapy’s failing lies in the inability of the medicine to be absorbed and maintained within the tumor cell long enough to destroy it. In most cases, the chemotherapy drug is almost immediately ejected by the cancer cell, severely damaging the healthy organs that surround it, leaving the tumor cell intact.

Gagomers (labeled in color) accumulating on ovarian cancer cells.
(Credit: Image courtesy of American Friends of Tel Aviv University)

But with this new nanotechnology therapy, Peer and his colleagues saw a 25-fold increase in tumor-accumulated medication and a dramatic dip in toxic accumulation in healthy organs. Tested on laboratory mice, the gagomer affects a change in drug-resistant ovarian cancer tumor cells. Receptors on tumor cells recognize the sugar that encases the gagomer, allowing the binding gagomer to slowly release tiny particles of chemotherapy into the cancerous cell. As more and more of the drug accumulates within the tumor cell, the cancer cells begin to die off within 24-48 hours. In this preclinical setting, the doxorubicin encased gagomers even outperformed pegylated liposomal doxorubicin (Doxil) — a standard of care drug used to treat recurrent ovarian cancer.

“Tumors become resistant very quickly. Following the first, second, and third courses of chemotherapy, the tumors start pumping drugs out of the cells as a survival mechanism,” said Prof. Peer. “Most patients with tumor cells beyond the ovaries relapse and ultimately die due to the development of drug resistance. We wanted to create a safe drug-delivery system, which wouldn’t harm the body’s immune system or organs.”

A Personal Perspective

Prof. Peer chose to tackle ovarian cancer in his research because his mother-in-law passed away at the age of 54 from the disease. “She received all the courses of chemotherapy and survived only a year and a half,” Peer said. “She died from the drug-resistant aggressive tumors.”

“At the end of the day, you want to do something natural, simple, and smart. We are committed to try to combine both laboratory and therapeutic arms to create a less toxic, focused drug that combats aggressive drug-resistant cancerous cells,” said Prof. Peer. “We hope the concept will be harnessed in the next few years in clinical trials on aggressive tumors,” said Prof. Peer.

Sources:

• Researchers Devise a Fast and Effective Mechanism to Combat One of the Most Aggressive Cancers, American Friends of Tel Aviv University, Press Release, February 24, 2014. [PDF Full Text Version]

• Keren Cohen, et al. Modulation of Drug Resistance in Ovarian Adenocarcinoma Using Chemotherapy Entrapped in Hyaluronan-Grafted Nanoparticle Clusters. ACS Nano, 2014; 140206084950005 DOI: 10.1021/nn500205b

Novel “Jantibody Fusion Protein” Cancer Vaccine Holds Promise Against Ovarian Cancer

A novel approach to cancer immunotherapy – strategies designed to induce the immune system to attack cancer cells – may provide a new and cost-effective weapon against some of the most deadly tumors, including ovarian cancer and mesothelioma.

A novel approach to cancer immunotherapy – strategies designed to induce the immune system to attack cancer cells – may provide a new and cost-effective weapon against some of the most deadly tumors, including ovarian cancer and mesothelioma. Investigators from the Massachusetts General Hospital (MGH) Vaccine and Immunotherapy Center (VIC) report in the Journal of Hematology & Oncology that a protein engineered to combine a molecule targeting a tumor-cell-surface antigen with another protein that stimulates several immune functions prolonged survival in animal models of both tumors.

“Some approaches to creating cancer vaccines begin by extracting a patient’s own immune cells, priming them with tumor antigens and returning them to the patient, a process that is complex and expensive,” says Mark Poznansky, M.D., Ph.D., director of the MGH Vaccine and Immunotherapy Center and senior author of the report. “Our study describes a very practical, potentially broadly applicable and low-cost approach that could be used by oncologists everywhere, not just in facilities able to harvest and handle patient’s cells.”

The MGH team’s vaccine stimulates the patient’s own dendritic cells, a type of immune cell that monitors an organism’s internal environment for the presence of viruses or bacteria, ingests and digests pathogens encountered, and displays antigens from those pathogens on their surface to direct the activity of other immune cells. As noted above, existing cancer vaccines that use dendritic cells require extracting cells from a patient’s blood, treating them with an engineered protein or nucleic acid that combines tumor antigens with immune-stimulating molecules, and returning the activated dendritic cells to the patient.

Fusion protein activates immune cells against tumors. The Jantibody fusion protein, combining an antibody fragment targeting an antigen found on tumor cells with an immune-response-inducing protein (MTBhsp70), activates dendritic cells against several tumor antigens and induces a number of T-cell-based immune responses. (Jianping Yuan, PhD, MGH Vaccine and Immunotherapy Center)

The approach developed by the MGH team starts with the engineered protein, which in this case fuses an antibody fragment targeting a protein called mesothelin – expressed on the surface of such tumors as mesothelioma, ovarian cancer and pancreatic cancer – to a protein from the tuberculosis bacteria that stimulates the activity of dendritic and other immune cells. In this system, the dendritic cells are activated and targeted against tumor cells while remaining inside the patient’s body.

In the experiments described in the paper, the MGH team confirmed that their mesothelin-targeting fusion protein binds to mesothelin on either ovarian cancer or mesothelioma cells, activates dendritic cells, and enhances the cells’ processing and presentation of several different tumor antigens, inducing a number of T-cell-based immune responses. In mouse models of both tumors, treatment with the fusion protein significantly slowed tumor growth and extended survival, probably through the activity of cytotoxic CD8 T cells.

“Many patients with advanced cancers don’t have enough functioning immune cells to be harvested to make a vaccine, but our protein can be made in unlimited amounts to work with the immune cells patients have remaining,” explains study co-author Jeffrey Gelfand, MD, senior scientist at the Vaccine and Immunotherapy Center. “We have created a potentially much less expensive approach to making a therapeutic cancer vaccine that, while targeting a single tumor antigen, generates an immune response against multiple antigens. Now if we can combine this with newly-described ways to remove the immune system’s “brakes” – regulatory functions that normally suppress persistent T-cell activity – the combination could dramatically enhance cancer immunotherapy.”

Poznansky adds that the tumors that might be treated with the mesothelin-targeting vaccine – ovarian cancer, pancreatic cancer and mesothelioma – all have poor survival rates. “Immunotherapy is generally nontoxic, so this vaccine has the potential of safely extending survival and reducing the effects of these tumors, possibly even cutting the risk of recurrence. We believe that this approach could ultimately be used to target any type of cancer and are currently investigating an improved targeting approach using personalized antigens.” The MGH team just received a two-year grant from the Department of Defense Congressionally Directed Medical Research Program to continue their research.

Poznansky is an associate professor of Medicine, and Gelfand is a clinical professor of Medicine at Harvard Medical School. Jianping Yuan, Ph.D., of the MGH Vaccine and Immunotherapy Center (VIC) is the lead author of the Journal of Hematology and Oncology report. Additional co-authors include Pierre LeBlanc, Ph.D., Satoshi Kashiwagi M.D., Ph.D., Timothy Brauns, and Svetlana Korochkina, Ph.D., MGH VIC; and Nathalie Scholler, M.D., Ph.D., University of Pennsylvania School of Medicine.

The authors dedicate their report to Janet Gelfand, the wife of Jeffrey Gelfand, who died of ovarian cancer in 2006 and inspired their investigation. In her honor they named their tumor-targeting fusion protein “Jantibody.” Support for the study includes grants from the Edmund Lynch Jr. Cancer Fund, Arthur Luxenberg Esq., Perry Weitz Esq., the VIC Mesothelioma Research and Resource Program, and the Friends of VIC Fund.

Massachusetts General Hospital, founded in 1811, is the original and largest teaching hospital of Harvard Medical School. The MGH conducts the largest hospital-based research program in the United States, with an annual research budget of more than $775 million and major research centers in AIDS, cardiovascular research, cancer, computational and integrative biology, cutaneous biology, human genetics, medical imaging, neurodegenerative disorders, regenerative medicine, reproductive biology, systems biology, transplantation biology and photomedicine.

Sources:

• Novel cancer vaccine holds promise against ovarian cancer, mesothelioma — Antigen-targeting fusion protein should be less expensive, more accessible than current approaches, Massachusetts General Hospital, Press Release, March 5, 2014.

• Yuan J et al., A novel mycobacterial Hsp70-containing fusion protein targeting mesothelin augments antitumor immunity and prolongs survival in murine models of ovarian cancer and mesothelioma. J Hematol Oncol. 2014 Feb 24;7(1):15. doi: 10.1186/1756-8722-7-15. (Abstract – PMID: 24565018; Full Text – PMCID: PMC3943805)