Research » MRA Research Awards » Team Science

Epigenetics in Melanoma: Mechanistic Evaluation and Novel Therapies

Sokoloff Family-MRA Team Science Award

Principal Investigators: 

Marcus Bosenberg, M.D., Ph.D., Yale University
Frank Slack, Ph.D., Yale University
Young Investigator: Narendra Wajapeyee, Ph.D., Yale University
Mentor: Marcus Bosenberg

Although recent treatment advances including BRAF inhibitor therapy and immunotherapy approaches are promising, most advanced melanoma patients still have a bad prognosis. Much progress has been made in the identification of key genetic changes in melanoma, however despite the observation that non-genetic alterations, including DNA methylation, appear to be nearly universal in human melanoma, the specific functional contribution of these changes to melanoma formation is largely unknown. DNA methyltransferases (DNMTs) modify DNA and alter the expression of individual genes, but do not alter the DNA coding sequence. We evaluated the effects of inactivation of specific DNMTs in melanoma. Interestingly, while inactivation of the Dnmt1 DNA methyltransferase did not prevent melanoma formation, inactivation of Dnmt3b markedly reduced melanoma formation. Dnmt3b in part appears to control the levels of specific micro RNAs (miRNAs) to regulate melanoma growth. These findings demonstrate that DNMT3B and specific miRNAs play a critical role in melanoma formation and are promising targets for new melanoma treatments. We propose to: 1). Determine the mechanism of requirement for DNA methylation in melanoma, 2). Determine the functional role of miRNAs in melanoma formation and progression, and 3). Discover new specific DNA methyltransferase inhibitors that can eventually be used to treat melanoma patients. We anticipate that the proposed experiments will identify the cascade of signaling changes brought about by altered DNA methylation and miRNA expression that are needed for melanoma formation and progression. Within the period of the grant, we also expect to produce new DNMT inhibitors that are suitable for clinical trials. These drugs could have a major and rapid impact in treating melanoma and other forms of cancer.

Targeting BRAF-mutant melanoma brain metastases 

Generously supported by the Hess Foundation

Principal Investigators: 

Michael Davies, M.D., Ph.D., University of Texas M.D. Anderson Cancer Center
Erik Sulman, M.D., Ph.D., University of Texas M.D. Anderson Cancer Center
Hussein Tawbi, M.D., Ph.D., University of Pittsburgh
Young Investigator: Georgina Long, Melanoma Institute Australia
Mentor: Richard Scolyer, Co-Director of Research, Melanoma Institute Australia

Brain metastases are diagnosed in ~60% of patients with stage IV melanoma, and the average survival for these patients is only 4 months. Recently, the investigators in this grant proposal helped to design and lead the BREAK-MB trial, which tested the safety and efficacy of the selective BRAF inhibitor dabrafenib in melanoma patients with brain metastases. This trial demonstrated that dabrafenib treatment was safe in these patients and the majority achieved clinical responses. However, similar to patients with extracranial (non-brain) metastases, most of the clinical responses were relatively short. Studies of tissue samples from other types of metastases have identified a number of molecular changes that occur with BRAF inhibitor treatment, including several that cause resistance and disease progression, which have been used to design more effective therapeutic approaches. However, no such studies have been performed in patients with brain metastases. Research in multiple cancer types, including melanoma, has demonstrated that brain metastases harbor many molecular differences compared to metastases in other sites. Thus, understanding the effects of BRAF inhibitor treatment in brain metastases may identify specific strategies to improve clinical outcomes in these patients. In order to test the hypothesis that the molecular effects of approved doses of BRAF inhibitors differ in brain and extracranial metastases, we are conducting a clinical trial in patients with at least 1 brain metastasis that can be cured with surgery. The patients will be treated with the BRAF inhibitor (dabrafenib) for ~1 week prior to surgical removal of the brain metastasis and at least one extracranial metastasis. In this grant we will use our combined resources and expertise to compare the molecular and immunological effects of dabrafenib treatment on the brain and extracranial metastases in order to identify rational new treatment strategies for brain metastasis patients.

Human anti-MICA Monoclonal Antibodies for Melanoma Immunotherapy

Principal Investigators: 

Glenn Dranoff, M.D., Dana-Farber Cancer Institute
Kai Wucherpfennig, M.D., Ph.D., Dana-Farber Cancer Institute
Helman Family-MRA Young Investigator: Michael Goldberg, Ph.D., Dana-Farber Cancer Institute
Mentors: Glenn Dranoff and Kai Wucherpfennig

We demonstrated that some metastatic melanoma patients who are treated with vaccines composed of their own tumor cells and/or an antibody that improves immune function (anti-CTLA-4) achieve long-lasting benefits. Our analysis of these long-term responding patients uncovered an important aspect of the immune response to melanoma. This characteristic involves an immune reaction that is directed to a target called MICA, which is a protein expressed at high levels on the surface of many melanomas (and also other cancers), but not on healthy tissues. Unfortunately, melanoma cells devise ways to release some of the MICA from the surface, and the shed form of MICA inhibits the immune response. We found, however, that melanoma vaccines and CTLA-4 treatment can stimulate some patients to make a strong antibody response to MICA. These antibodies can overcome the suppressive effects of soluble MICA, and in turn promote the destruction of melanoma cells. We developed a new experimental strategy that allows us to isolate from patients who respond to these immunotherapies specific antibodies against the factors that are involved in melanoma destruction. We used this technique to isolate a panel of human antibodies to MICA. Our work to date has indicated that one of these antibodies is a compelling candidate for therapeutic testing in melanoma patients. This antibody reacts with all forms of MICA tested, suggesting that it might be applicable to a wide range of melanoma patients. Our preliminary studies also show that the antibody is able to overcome the immune suppressive effects of shed MICA that is present in the blood of different melanoma patients and to promote immune responses to melanomas growing in mice. In this application, we propose to learn more about the properties of this antibody and develop techniques to monitor the effects of administering the antibody in planned clinical trials in melanoma patients.

Molecular mechanisms of T cell inflamed melanoma to identify new targets

Principal Investigators: 

Thomas Gajewski, M.D., Ph.D, University of Chicago
Eugene Chang, M.D., University of Chicago
Kenan Onel, M.D., Ph.D., University of Chicago
GlaxoSmithKline-MRA Young Investigator: Ping Yu, M.D., University of Chicago
Mentor: Thomas Gajewski

Significant advances using immune-based therapies for melanoma have generated great enthusiasm both for researchers and for patients. A key feature of immunotherapies is the ability to induce a durable clinical benefit, with some patients likely being cured of their disease. However, despite this great promise, clinical responses are still seen in a minority of patients. We need to determine why some patients fail to respond to immunotherapies so that we can develop new strategies that expand the subset of patients who can benefit from these treatments. We recently have characterized the tumors in melanoma patients and have found a gene expression pattern and set of biologic features that appear to predict clinical response to immunotherapies. This biology is characterized by a pre-existing attempt of the host immune system to attack the tumor, with inflammatory features in the tumor site. The goal of this proposal is to determine why some patients generate this spontaneous smoldering immune response while some do not. Correlations are proposed using patient samples, and mechanisms will be evaluated in animal models. Our preliminary data are already encouraging. Knowledge of these mechanisms will provide a foundation to develop next-generation immunotherapies for melanoma.

Chromatin-based therapeutic combinations for the treatment of melanoma

Christie's-MRA Team Science Award

Principal Investigators: 

 Levi A Garraway, M.D., Ph.D., Dana-Farber Cancer Institute
Leonard Zon, M.D., Children’s Hospital Boston

Although there have been major treatment advances in the treatment of melanomas that carry mutations in the BRAF gene, responses are still short-lived (several months to a year). This is because the cancer cells eventually develop drug resistance: ways to avoid being killed by cancer drugs in current use (these drugs are called RAF and MEK inhibitors). The goal of this project is to identify new drugs that might be combined with RAF and MEK inhibitors to prevent or delay the emergence of such resistance mechanisms and ultimately achieve long-term control of this subtype of melanoma. Using powerful new technologies that can test each human gene for its ability to cause drug resistance, the laboratory of Dr. Levi Garraway identified over 100 genes able to drive resistance to RAF+MEK inhibitors in cultured melanoma cells. In parallel, Dr. Leonard Zon has used a fish model of melanoma (zebrafish) as a high-throughput means to identify biological processes that are operant in human melanoma. In this project, we will use both human melanoma cells and zebrafish to study an exciting new class of drugs called “chromatin-modifying factors” for their ability to kill BRAF-mutant melanoma cells in combination with RAF+MEK inhibitors in human melanoma cells and zebrafish melanoma tumors. So-called “chromatin-based” therapeutics show immense promise in cancer treatment. Once drugs targeting chromatin-modifying factors are identified and verified, we will design a clinical study that can test the feasibility of combining inhibitors of chromatin with RAF/MEK inhibitors in patients with BRAF-mutant melanoma. In summary, this research combines state of the art basic science with new drug discovery avenues to speed the development of novel cancer drug combinations aimed at further extending the survival of many melanoma patients.

Drivers in melanoma susceptibility, development and progression

L'Oreal Paris-MRA Team Science Award

Principal Investigators: 

Meenhard Herlyn, D.V.M., D.Sci., The Wistar Institute
Vivi Ann Florenes, Ph.D., Oslo University Hospital
Julia Newton-Bishop, M.D., Leeds University
Young Investigator: Todd Ridky, M.D., Ph.D., University of Pennsylvania
Mentor: Meenhard Herlyn

Individuals with genetically determined phenotypes such as light skin color which tans poorly, red hair, blue eyes or many moles are generally considered susceptible to melanoma compared to those with none of these attributes. However, only a few of these individuals contract the disease suggesting that both environmental and genetic traits play a major role in susceptibility. Recent research has identified 16 variant genes associated with risk for melanoma but we do not know how these gene variants contribute as co-drivers to melanoma development because normal cells from these carriers have not been studied experimentally. One major reason for the lack of data on the biological significance of melanoma risk genes is that the patients are only identified at later stages of their life when the melanocytes are very difficult to grow in tissue culture in high enough quantities for experimental studies. Our laboratories went an indirect route: we isolated normal fibroblasts from small punch biopsies of skin and reprogrammed them using four transcription factors in a technique that did not alter their genome structure. The 'induced pluripotent stem cells' acted similar to embryonic stem cells which can be turned into any of the >220 cells of the human body. Fortuitous for us, those cells readily become melanocytes when stimulated with growth factor signals. We now want to stress the cells when they are embedded in artificial skin using ultraviolet light in the B and A range to determine whether they show any abnormalities when compared to cells without the gene variants. In the second aim we will hit the melanocytes from melanoma risk individuals with driver oncogenes that cannot transform on their own but need the currently unknown co-driver(s). We expect from these studies the identification of co-drivers that cooperate with driver genes which will in the future be the targets for melanoma prevention and therapy.

Imaging and therapeutic targeting of lymphangiogenesis in melanoma

Principal Investigators: 

Maria S Soengas, Ph.D., Spanish National Cancer Research Center
Michael Detmar, M.D., Swiss Federal Institute of Technology, Zurich
Robert Ballotti, Ph.D., National Institute of Health and Medical Research, France
Corine Bertolotto, Ph.D., National Institute of Health and Medical Research, France
Stefan Endres, M.D., Ludwig Maximilian University, Munich
Collaborative Donor-MRA Young Investigator: Hector Peinado, Ph.D., Weill Cornell Medical College
Mentor: David Lyden, M.D., Ph.D., Weill Cornell Medical College

A main limitation for rational drug design in cancer, particularly in melanoma, is the lack of physiologically-relevant models and tracers to monitor metastatic cells in vivo. To overcome these complications we have assembled a team of experts in melanoma progression and drug response, tumor spectroscopy, biological chemistry, dermatology, pathology and oncology. Our main focus is neo-lymphangiogenesis. This is a process whereby cancer cells induce the formation of vessels (lymphatic capillaries) that favor tumor dissemination. We have customized new lymphatic probes, and have generated the first melanoma Lymphoreporter mouse model. A unique feature of this strategy is the possibility of imaging early events occurring before cells actually colonize distal organs. The metastatic behavior of melanoma cells can also be analyzed prior, during and after treatment. With this approach we have also found new potent blockers of lymphangiogenesis. The most effective of these compounds were nanoparticles based on dsRNA (referred to as BO-110 for simplicity). The ability of studying cells in their natural environment allowed for the identification of unexpected points of crosstalk with innate immunity programs, opening alternative avenues for therapeutic intervention. This proposal builds on this infrastructure to translate these results into the clinic. In particular, we will center on key melanoma oncogenes (including BRAF, NRAS, cMET or MITF), whose roles in lymphangiogenesis remain unknown. Further functional testing of BO-110 will be performed as single agent or in combination with therapeutic agents that are being actively pursued by the pharmaceutical industry. Results will be validated in biopsies obtained from patients at different stages of melanoma progression. The long-term goal of this proposal is to provide the melanoma community with new diagnostic and prognostic indicators, tools for pharmacological screening, and ultimately, more efficient anticancer treatments.

Studies on the mechanism(s) of resistance to RAF inhibitor-based therapies

Principal Investigators: 

David Solit, M.D., Memorial Sloan-Kettering Cancer Center
Jeffrey Gershenwald, M.D., University of Texas, M.D. Anderson Cancer Center
Jeffrey Sosman, M.D., Vanderbilt University
Jennifer Wargo, M.D., Massachusetts General Hospital
Katherine Nathanson, M.D., University of Pennsylvania
Keith Flaherty, M.D., Massachusetts General Hospital
Stewart Rahr-MRA Young Investigator: Ryan Sullivan, M.D., Massachusetts General Hospital
Mentor: Keith Flaherty, M.D., Massachusetts General Hospital

Cancers arise as a result of mutations in genes that control normal cellular growth. By identifying and studying the biology of these mutations, we hope to develop more effective and less toxic cancer therapies. One pathway that is frequently mutated in human tumors is the RAS/RAF/MEK/ERK (“classical MAP kinase”) pathway. Activating mutations in this pathway are commonly observed in several cancer types including melanoma in which they are found in over 70% of patients. The most common mechanism is mutation of the BRAF gene. Recent clinical results with selective inhibitor of BRAF have shown that these oral drugs have unprecedented clinical activity in patients with melanoma whose tumors harbor BRAF mutations. Although effective in approximately 80% of patients, resistance to RAF inhibitors invariably develops. The addition of a selective inhibitor of MEK, a downstream effector of the RAF protein, results in more profound and durable tumor responses than RAF inhibitor treatment alone, however, the development of drug resistance eventually occurs in essentially all patients. The focus of this MRA Team Science Award will be to determine the mechanisms of drug resistance in all patients treated with RAF inhibitor based combination strategies. To accomplish the proposed aims, we have assembled a multi-institutional team of investigators who have played central roles in the design and execution of the RAF inhibitor clinical trials. We believe that this Team Science proposal has the potential to be a model for future efforts in understanding the molecular mechanisms that mediate drug resistance in patients with melanoma. Further, we believe that the data generated will serve as the basis for rational combination strategies that induce durable and complete tumor regressions in most patients with BRAF mutant melanoma.

Personalized Medicine for Patients with BRAF wild-type (BRAFwt) Cancer

Stand Up to Cancer-Melanoma Research Alliance Melanoma Dream Team Translational Cancer Research Grant

Leader: Jeffrey M. Trent, Ph.D., Translational Research Institute (TGen)
Co‐Leader: Patricia M. LoRusso, D.O., Karmanos Cancer Institute (KCI)
Principal Investigators:
  - Svetomir Markovic, M.D., Ph.D., Mayo Clinic
  - Brian Nickoloff, M.D., Ph.D., Michigan State University College of Medicine
  - Nicholas J. Schork Ph.D., The Scripps Research Institute 
  - Aleksandar Sekulic, M.D., Ph.D., Mayo Clinic Arizona
  - Kristiina Vuori, M.D., Ph.D., Sanford‐Burnham Medical Center
  -Craig Webb, Ph.D., Van Andel Research Institute

About half of the patients with metastatic melanoma (MM) have a mutation in the BRAF gene. While recently developed inhibitors have demonstrated clinical efficacy in these patients, little progress has been made in identifying therapeutic targets to treat the other half –those patients with wild‐type BRAF (BRAFwt) tumors. This latter cohort is likely to reap the benefit of genome‐based treatments (i.e., personalized medicine). The goal of the Dream Team led by Drs. Trent and LoRusso is to select patients for sensitive mutations and match them to appropriate therapies based on their individual genomic signature. The hope is that such an approach may lead to more effective and durable therapeutic interventions over an unselective standard approach, potentially sparing patients from unnecessary toxicity, expense, and time wasted on ineffective therapies; time patients do not have. Drs. Trent and LoRusso have assembled a Dream Team of colleagues with expertise in the medical management of patients with MM, drug development, genomics research, biostatistics, and bioinformatics. They propose to iteratively refine and standardize statistical and informatics methodologies for matching treatments to the patient’s tumor, based on their individual molecular profile. Armed with this knowledge, and the results of an initial ‘feasibility’ study, they will conduct a randomized clinical trial to evaluate if molecularly‐informed personalized therapy selection, based on a patient’s tumor molecular profile, improves outcomes when compared to standard of care therapy in BRAFwt MM. If successful, this individualized medicine approach to the treatment of BRAFwt MM will not only lead to therapeutic benefit for this patient population, but may also serve as a new paradigm for many other tumor and disease types.