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Melanoma: HELP
Articles by Levi A. Garraway
Based on 43 articles published since 2009
(Why 43 articles?)
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Between 2009 and 2019, Levi Garraway wrote the following 43 articles about Melanoma.
 
+ Citations + Abstracts
Pages: 1 · 2
1 Review Melanoma: from mutations to medicine. 2012

Tsao, Hensin / Chin, Lynda / Garraway, Levi A / Fisher, David E. ·Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. ·Genes Dev · Pubmed #22661227.

ABSTRACT: Melanoma is often considered one of the most aggressive and treatment-resistant human cancers. It is a disease that, due to the presence of melanin pigment, was accurately diagnosed earlier than most other malignancies and that has been subjected to countless therapeutic strategies. Aside from early surgical resection, no therapeutic modality has been found to afford a high likelihood of curative outcome. However, discoveries reported in recent years have revealed a near avalanche of breakthroughs in the melanoma field-breakthroughs that span fundamental understanding of the molecular basis of the disease all the way to new therapeutic strategies that produce unquestionable clinical benefit. These discoveries have been born from the successful fruits of numerous researchers working in many-sometimes-related, although also distinct-biomedical disciplines. Discoveries of frequent mutations involving BRAF(V600E), developmental and oncogenic roles for the microphthalmia-associated transcription factor (MITF) pathway, clinical efficacy of BRAF-targeted small molecules, and emerging mechanisms underlying resistance to targeted therapeutics represent just a sample of the findings that have created a striking inflection in the quest for clinically meaningful progress in the melanoma field.

2 Review Applications of genomics in melanoma oncogene discovery. 2009

Berger, Michael F / Garraway, Levi A. ·The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. ·Hematol Oncol Clin North Am · Pubmed #19464593.

ABSTRACT: The identification of recurrent alterations in the melanoma genome has provided key insights into the biology of melanoma genesis and progression. These discoveries have come about as a result of the systematic deployment and integration of diverse genomic technologies, including DNA sequencing, chromosomal copy number analysis, and gene expression profiling. Here, the discoveries of several key melanoma oncogenes affecting critical cell pathways are described and the role played by evolving genomics technologies in melanoma oncogene discovery is examined. These advances are being exploited to improve prognosis and treatment of melanoma patients through the development of genome-based diagnostic and targeted therapeutic avenues.

3 Clinical Trial Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib Combination Treatment for BRAF Inhibitor-Refractory Metastatic Melanoma: A Phase 2 Clinical Trial. 2016

Chen, Guo / McQuade, Jennifer L / Panka, David J / Hudgens, Courtney W / Amin-Mansour, Ali / Mu, Xinmeng Jasmine / Bahl, Samira / Jané-Valbuena, Judit / Wani, Khalida M / Reuben, Alexandre / Creasy, Caitlyn A / Jiang, Hong / Cooper, Zachary A / Roszik, Jason / Bassett, Roland L / Joon, Aron Y / Simpson, Lauren M / Mouton, Rosalind D / Glitza, Isabella C / Patel, Sapna P / Hwu, Wen-Jen / Amaria, Rodabe N / Diab, Adi / Hwu, Patrick / Lazar, Alexander J / Wargo, Jennifer A / Garraway, Levi A / Tetzlaff, Michael T / Sullivan, Ryan J / Kim, Kevin B / Davies, Michael A. ·Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston. · Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston. · Beth Israel Deaconess Medical Center, Boston, Massachusetts. · Departments of Pathology and Translational and Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston. · Broad Institute, Cambridge, Massachusetts. · Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston7Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston. · Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston. · Massachusetts General Hospital, Boston. · California Pacific Medical Center Research Institute, San Francisco. · Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston11Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston. ·JAMA Oncol · Pubmed #27124486.

ABSTRACT: IMPORTANCE: Combined treatment with dabrafenib and trametinib (CombiDT) achieves clinical responses in only about 15% of patients with BRAF inhibitor (BRAFi)-refractory metastatic melanoma in contrast to the higher response rate observed in BRAFi-naïve patients. Identifying correlates of response and mechanisms of resistance in this population will facilitate clinical management and rational therapeutic development. OBJECTIVE: To determine correlates of benefit from CombiDT therapy in patients with BRAFi-refractory metastatic melanoma. DESIGN, SETTING, AND PARTICIPANTS: Single-center, single-arm, open-label phase 2 trial of CombiDT treatment in patients with BRAF V600 metastatic melanoma resistant to BRAFi monotherapy conducted between September 2012 and October 2014 at the University of Texas MD Anderson Cancer Center. Key eligibility criteria for participants included BRAF V600 metastatic melanoma, prior BRAFi monotherapy, measurable disease (RECIST 1.1), and tumor accessible for biopsy. INTERVENTIONS: Patients were treated with dabrafenib (150 mg, twice daily) and trametinib (2 mg/d) continuously until disease progression or intolerance. All participants underwent a mandatory baseline biopsy, and optional biopsy specimens were obtained on treatment and at disease progression. Whole-exome sequencing, reverse transcription polymerase chain reaction analysis for BRAF splicing, RNA sequencing, and immunohistochemical analysis were performed on tumor samples, and blood was analyzed for levels of circulating BRAF V600. MAIN OUTCOMES AND MEASURES: The primary end point was overall response rate (ORR). Progression-free survival (PFS) and overall survival (OS) were secondary clinical end points. RESULTS: A total of 28 patients were screened, and 23 enrolled. Among evaluable patients, the confirmed ORR was 10%; disease control rate (DCR) was 45%, and median PFS was 13 weeks. Clinical benefit was associated with duration of prior BRAFi therapy greater than 6 months (DCR, 73% vs 11% for ≤6 months; P = .02) and decrease in circulating BRAF V600 at day 8 of cycle 1 (DCR, 75% vs 18% for no decrease; P = .02) but not with pretreatment mitogen-activated protein kinase (MAPK) pathway mutations or activation. Biopsy specimens obtained during treatment demonstrated that CombiDT therapy failed to achieve significant MAPK pathway inhibition or immune infiltration in most patients. CONCLUSIONS AND RELEVANCE: The baseline presence of MAPK pathway alterations was not associated with benefit from CombiDT in patients with BRAFi-refractory metastatic melanoma. Failure to inhibit the MAPK pathway provides a likely explanation for the limited clinical benefit of CombiDT in this setting. Circulating BRAF V600 is a promising early biomarker of clinical response. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01619774.

4 Clinical Trial MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. 2014

Wagle, Nikhil / Van Allen, Eliezer M / Treacy, Daniel J / Frederick, Dennie T / Cooper, Zachary A / Taylor-Weiner, Amaro / Rosenberg, Mara / Goetz, Eva M / Sullivan, Ryan J / Farlow, Deborah N / Friedrich, Dennis C / Anderka, Kristin / Perrin, Danielle / Johannessen, Cory M / McKenna, Aaron / Cibulskis, Kristian / Kryukov, Gregory / Hodis, Eran / Lawrence, Donald P / Fisher, Sheila / Getz, Gad / Gabriel, Stacey B / Carter, Scott L / Flaherty, Keith T / Wargo, Jennifer A / Garraway, Levi A. ·1Department of Medical Oncology, Dana-Farber Cancer Institute; 2Department of Medicine, Brigham and Women's Hospital; 3Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston; 4Broad Institute of Harvard and MIT; and 5Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts. ·Cancer Discov · Pubmed #24265154.

ABSTRACT: Treatment of BRAF-mutant melanoma with combined dabrafenib and trametinib, which target RAF and the downstream MAP-ERK kinase (MEK)1 and MEK2 kinases, respectively, improves progression-free survival and response rates compared with dabrafenib monotherapy. Mechanisms of clinical resistance to combined RAF/MEK inhibition are unknown. We performed whole-exome sequencing (WES) and whole-transcriptome sequencing (RNA-seq) on pretreatment and drug-resistant tumors from five patients with acquired resistance to dabrafenib/trametinib. In three of these patients, we identified additional mitogen-activated protein kinase (MAPK) pathway alterations in the resistant tumor that were not detected in the pretreatment tumor, including a novel activating mutation in MEK2 (MEK2(Q60P)). MEK2(Q60P) conferred resistance to combined RAF/MEK inhibition in vitro, but remained sensitive to inhibition of the downstream kinase extracellular signal-regulated kinase (ERK). The continued MAPK signaling-based resistance identified in these patients suggests that alternative dosing of current agents, more potent RAF/MEK inhibitors, and/or inhibition of the downstream kinase ERK may be needed for durable control of BRAF-mutant melanoma.

5 Article A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. 2018

Jerby-Arnon, Livnat / Shah, Parin / Cuoco, Michael S / Rodman, Christopher / Su, Mei-Ju / Melms, Johannes C / Leeson, Rachel / Kanodia, Abhay / Mei, Shaolin / Lin, Jia-Ren / Wang, Shu / Rabasha, Bokang / Liu, David / Zhang, Gao / Margolais, Claire / Ashenberg, Orr / Ott, Patrick A / Buchbinder, Elizabeth I / Haq, Rizwan / Hodi, F Stephen / Boland, Genevieve M / Sullivan, Ryan J / Frederick, Dennie T / Miao, Benchun / Moll, Tabea / Flaherty, Keith T / Herlyn, Meenhard / Jenkins, Russell W / Thummalapalli, Rohit / Kowalczyk, Monika S / Cañadas, Israel / Schilling, Bastian / Cartwright, Adam N R / Luoma, Adrienne M / Malu, Shruti / Hwu, Patrick / Bernatchez, Chantale / Forget, Marie-Andrée / Barbie, David A / Shalek, Alex K / Tirosh, Itay / Sorger, Peter K / Wucherpfennig, Kai / Van Allen, Eliezer M / Schadendorf, Dirk / Johnson, Bruce E / Rotem, Asaf / Rozenblatt-Rosen, Orit / Garraway, Levi A / Yoon, Charles H / Izar, Benjamin / Regev, Aviv. ·Broad Institute of MIT and Harvard, Cambridge, MA, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA. · Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA. · Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA. · Massachusetts General Hospital Cancer Center, Boston, MA, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA. · Broad Institute of MIT and Harvard, Cambridge, MA, USA; Celsius Therapeutics, Cambridge, MA, USA. · Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium, Essen, Germany; Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany. · Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. · Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. · Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium, Essen, Germany. · Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA. · Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Brigham and Women's Hospital, Department of Surgical Oncology, Boston, MA, USA. · Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA, USA. Electronic address: benjamin_izar@dfci.harvard.edu. · Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Ludwig Center for Cancer Research at MIT, Boston, MA, USA; Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA. ·Cell · Pubmed #30388455.

ABSTRACT: Immune checkpoint inhibitors (ICIs) produce durable responses in some melanoma patients, but many patients derive no clinical benefit, and the molecular underpinnings of such resistance remain elusive. Here, we leveraged single-cell RNA sequencing (scRNA-seq) from 33 melanoma tumors and computational analyses to interrogate malignant cell states that promote immune evasion. We identified a resistance program expressed by malignant cells that is associated with T cell exclusion and immune evasion. The program is expressed prior to immunotherapy, characterizes cold niches in situ, and predicts clinical responses to anti-PD-1 therapy in an independent cohort of 112 melanoma patients. CDK4/6-inhibition represses this program in individual malignant cells, induces senescence, and reduces melanoma tumor outgrowth in mouse models in vivo when given in combination with immunotherapy. Our study provides a high-resolution landscape of ICI-resistant cell states, identifies clinically predictive signatures, and suggests new therapeutic strategies to overcome immunotherapy resistance.

6 Article Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. 2018

Shukla, Sachet A / Bachireddy, Pavan / Schilling, Bastian / Galonska, Christina / Zhan, Qian / Bango, Clyde / Langer, Rupert / Lee, Patrick C / Gusenleitner, Daniel / Keskin, Derin B / Babadi, Mehrtash / Mohammad, Arman / Gnirke, Andreas / Clement, Kendell / Cartun, Zachary J / Van Allen, Eliezer M / Miao, Diana / Huang, Ying / Snyder, Alexandra / Merghoub, Taha / Wolchok, Jedd D / Garraway, Levi A / Meissner, Alexander / Weber, Jeffrey S / Hacohen, Nir / Neuberg, Donna / Potts, Patrick R / Murphy, George F / Lian, Christine G / Schadendorf, Dirk / Hodi, F Stephen / Wu, Catherine J. ·Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA. · Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany; German Cancer Consortium (DKTK), 69121 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, 97080 Würzburg, Germany. · Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. · Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. · Department of Pathology, University of Bern, 3012 Bern, Switzerland. · Broad Institute, Cambridge, MA 02142, USA. · Broad Institute, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. · Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA. · Broad Institute, Cambridge, MA 02142, USA; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. · New York University Langone Medical Center, New York, NY 10016, USA. · Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. · Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA. · Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany; German Cancer Consortium (DKTK), 69121 Heidelberg, Germany. · Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA. Electronic address: cwu@partners.org. ·Cell · Pubmed #29656892.

ABSTRACT: CTLA-4 immune checkpoint blockade is clinically effective in a subset of patients with metastatic melanoma. We identify a subcluster of MAGE-A cancer-germline antigens, located within a narrow 75 kb region of chromosome Xq28, that predicts resistance uniquely to blockade of CTLA-4, but not PD-1. We validate this gene expression signature in an independent anti-CTLA-4-treated cohort and show its specificity to the CTLA-4 pathway with two independent anti-PD-1-treated cohorts. Autophagy, a process critical for optimal anti-cancer immunity, has previously been shown to be suppressed by the MAGE-TRIM28 ubiquitin ligase in vitro. We now show that the expression of the key autophagosome component LC3B and other activators of autophagy are negatively associated with MAGE-A protein levels in human melanomas, including samples from patients with resistance to CTLA-4 blockade. Our findings implicate autophagy suppression in resistance to CTLA-4 blockade in melanoma, suggesting exploitation of autophagy induction for potential therapeutic synergy with CTLA-4 inhibitors.

7 Article IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment. 2017

Nirschl, Christopher J / Suárez-Fariñas, Mayte / Izar, Benjamin / Prakadan, Sanjay / Dannenfelser, Ruth / Tirosh, Itay / Liu, Yong / Zhu, Qian / Devi, K Sanjana P / Carroll, Shaina L / Chau, David / Rezaee, Melika / Kim, Tae-Gyun / Huang, Ruiqi / Fuentes-Duculan, Judilyn / Song-Zhao, George X / Gulati, Nicholas / Lowes, Michelle A / King, Sandra L / Quintana, Francisco J / Lee, Young-Suk / Krueger, James G / Sarin, Kavita Y / Yoon, Charles H / Garraway, Levi / Regev, Aviv / Shalek, Alex K / Troyanskaya, Olga / Anandasabapathy, Niroshana. ·Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. · Department of Dermatology, Mount Sinai School of Medicine, NY, NY 10029, USA; Department of Genetics and Genomics Sciences Mount Sinai School of Medicine, NY, NY 10029 USA; Population Health Science and Policy, Mount Sinai School of Medicine, NY, NY 10029, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering and Science and Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of MIT, Harvard, and MGH, Cambridge, MA 02139, USA. · Department of Computer Science, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. · Department of Dermatology, Stanford University, Stanford, CA 94305, USA. · Department of Genetics and Genomics Sciences Mount Sinai School of Medicine, NY, NY 10029 USA. · Laboratory for Investigative Dermatology, Rockefeller University. New York, NY 10065, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA 02458, USA. · Department of Surgical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA 02115, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology and Koch Institute, MIT, Boston, MA 02142, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering and Science and Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of MIT, Harvard, and MGH, Cambridge, MA 02139, USA; Division of Health Science & Technology, Harvard Medical School, Cambridge, MA 02139, USA; Department of Immunology, Massachusetts General Hospital, Boston, MA 02115, USA. · Department of Computer Science, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Simons Center for Data Analysis, Simons Foundation, New York, NY 10010, USA. · Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Cancer Immunology and Melanoma, Harvard Cancer Center, Dana Farber Cancer Center, Boston, MA 02215, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address: nanandasabapathy@partners.org. ·Cell · Pubmed #28666115.

ABSTRACT: Homeostatic programs balance immune protection and self-tolerance. Such mechanisms likely impact autoimmunity and tumor formation, respectively. How homeostasis is maintained and impacts tumor surveillance is unknown. Here, we find that different immune mononuclear phagocytes share a conserved steady-state program during differentiation and entry into healthy tissue. IFNγ is necessary and sufficient to induce this program, revealing a key instructive role. Remarkably, homeostatic and IFNγ-dependent programs enrich across primary human tumors, including melanoma, and stratify survival. Single-cell RNA sequencing (RNA-seq) reveals enrichment of homeostatic modules in monocytes and DCs from human metastatic melanoma. Suppressor-of-cytokine-2 (SOCS2) protein, a conserved program transcript, is expressed by mononuclear phagocytes infiltrating primary melanoma and is induced by IFNγ. SOCS2 limits adaptive anti-tumoral immunity and DC-based priming of T cells in vivo, indicating a critical regulatory role. These findings link immune homeostasis to key determinants of anti-tumoral immunity and escape, revealing co-opting of tissue-specific immune development in the tumor microenvironment.

8 Article Systematic genomic and translational efficiency studies of uveal melanoma. 2017

Johnson, Chelsea Place / Kim, Ivana K / Esmaeli, Bita / Amin-Mansour, Ali / Treacy, Daniel J / Carter, Scott L / Hodis, Eran / Wagle, Nikhil / Seepo, Sara / Yu, Xiaoxing / Lane, Anne Marie / Gragoudas, Evangelos S / Vazquez, Francisca / Nickerson, Elizabeth / Cibulskis, Kristian / McKenna, Aaron / Gabriel, Stacey B / Getz, Gad / Van Allen, Eliezer M / 't Hoen, Peter A C / Garraway, Levi A / Woodman, Scott E. ·Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America. · The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America. · Ocular Melanoma Center and Retina Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States of America. · Orbital Oncology and Ophthalmic Plastic Surgery Program, Department of Plastic Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America. · Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America. · Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America. · Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America. · Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. ·PLoS One · Pubmed #28594900.

ABSTRACT: To further our understanding of the somatic genetic basis of uveal melanoma, we sequenced the protein-coding regions of 52 primary tumors and 3 liver metastases together with paired normal DNA. Known recurrent mutations were identified in GNAQ, GNA11, BAP1, EIF1AX, and SF3B1. The role of mutated EIF1AX was tested using loss of function approaches including viability and translational efficiency assays. Knockdown of both wild type and mutant EIF1AX was lethal to uveal melanoma cells. We probed the function of N-terminal tail EIF1AX mutations by performing RNA sequencing of polysome-associated transcripts in cells expressing endogenous wild type or mutant EIF1AX. Ribosome occupancy of the global translational apparatus was sensitive to suppression of wild type but not mutant EIF1AX. Together, these studies suggest that cells expressing mutant EIF1AX may exhibit aberrant translational regulation, which may provide clonal selective advantage in the subset of uveal melanoma that harbors this mutation.

9 Article Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. 2017

Fallahi-Sichani, Mohammad / Becker, Verena / Izar, Benjamin / Baker, Gregory J / Lin, Jia-Ren / Boswell, Sarah A / Shah, Parin / Rotem, Asaf / Garraway, Levi A / Sorger, Peter K. ·Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA mohammad_fallahisichani@hms.harvard.edu peter_sorger@hms.harvard.edu. · Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. · Broad Institute of Harvard and MIT, Cambridge, MA, USA. · HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA. · Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. ·Mol Syst Biol · Pubmed #28069687.

ABSTRACT: Treatment of BRAF-mutant melanomas with MAP kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use live-cell imaging, single-cell analysis, and molecular profiling to show that exposure of tumor cells to RAF/MEK inhibitors elicits a heterogeneous response in which some cells die, some arrest, and the remainder adapt to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g., NGFR), a melanocyte precursor, and grow slowly. This phenotype is transiently stable, reverting to the drug-naïve state within 9 days of drug withdrawal. Transcriptional profiling of cell lines and human tumors implicates a c-Jun/ECM/FAK/Src cascade in de-differentiation in about one-third of cell lines studied; drug-induced changes in c-Jun and NGFR levels are also observed in xenograft and human tumors. Drugs targeting the c-Jun/ECM/FAK/Src cascade as well as BET bromodomain inhibitors increase the maximum effect (E

10 Article Bidirectional cross talk between patient-derived melanoma and cancer-associated fibroblasts promotes invasion and proliferation. 2016

Izar, Benjamin / Joyce, Cailin E / Goff, Stephanie / Cho, Nancy L / Shah, Parin M / Sharma, Gaurav / Li, Jingjing / Ibrahim, Nageatte / Gold, Jason / Hodi, F Stephen / Garraway, Levi A / Novina, Carl D / Bertagnolli, Monica M / Yoon, Charles H. ·Division of Surgical Oncology, Department of Surgery, Brigham and Womens Hospital, Boston, MA, USA. · The Broad Institute of MIT and Harvard, Cambridge, MA, USA. · Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA. · Department of Cancer Immunology, Dana Farber Cancer Institute, Boston, MA, USA. · Department of Surgery, VA Boston Health Care Service, Surgical Service, West Roxbury, MA, USA. ·Pigment Cell Melanoma Res · Pubmed #27482935.

ABSTRACT: Tumor-stroma interactions are critical for epithelial-derived tumors, and among the stromal cell types, cancer-associated fibroblasts (CAFs) exhibit multiple functions that fuel growth, dissemination, and drug resistance. However, these interactions remain insufficiently characterized in non-epithelial tumors such as malignant melanoma. We generated monocultures of melanoma cells and matching CAFs from patients' metastatic lesions, distinguished by oncogenic drivers and immunoblotting of characteristic markers. RNA sequencing of CAFs revealed a homogenous epigenetic program that strongly resembled the signatures from epithelial cancers, including enrichment for an epithelial-to-mesenchymal transition (EMT). Melanoma CAFs in monoculture displayed robust invasive behavior while patient-derived melanoma monocultures showed very little invasiveness. Instead, melanoma cells showed increased invasion when co-cultured with CAFs. In turn, CAFs showed increased proliferation when exposed to melanoma conditioned media (CM), mediated in part by melanoma-secreted transforming growth factor-alpha that acted on CAFs via the epidermal growth factor receptor. This study provides evidence that bidirectional interactions between melanoma and CAFs regulate progression of metastatic melanoma.

11 Article Long-term drug administration in the adult zebrafish using oral gavage for cancer preclinical studies. 2016

Dang, Michelle / Henderson, Rachel E / Garraway, Levi A / Zon, Leonard I. ·Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA Howard Hughes Medical Institute, Boston, MA 02115, USA Harvard Medical School, Boston, MA 02138, USA mdang@fas.harvard.edu zon@enders.tch.harvard.edu. · Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA. · Harvard Medical School, Boston, MA 02138, USA Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. ·Dis Model Mech · Pubmed #27482819.

ABSTRACT: Zebrafish are a major model for chemical genetics, and most studies use embryos when investigating small molecules that cause interesting phenotypes or that can rescue disease models. Limited studies have dosed adults with small molecules by means of water-borne exposure or injection techniques. Challenges in the form of drug delivery-related trauma and anesthesia-related toxicity have excluded the adult zebrafish from long-term drug efficacy studies. Here, we introduce a novel anesthetic combination of MS-222 and isoflurane to an oral gavage technique for a non-toxic, non-invasive and long-term drug administration platform. As a proof of principle, we established drug efficacy of the FDA-approved BRAF(V600E) inhibitor, Vemurafenib, in adult zebrafish harboring BRAF(V600E) melanoma tumors. In the model, adult casper zebrafish intraperitoneally transplanted with a zebrafish melanoma cell line (ZMEL1) and exposed to daily sub-lethal dosing at 100 mg/kg of Vemurafenib for 2 weeks via oral gavage resulted in an average 65% decrease in tumor burden and a 15% mortality rate. In contrast, Vemurafenib-resistant ZMEL1 cell lines, generated in culture from low-dose drug exposure for 4 months, did not respond to the oral gavage treatment regimen. Similarly, this drug treatment regimen can be applied for treatment of primary melanoma tumors in the zebrafish. Taken together, we developed an effective long-term drug treatment system that will allow the adult zebrafish to be used to identify more effective anti-melanoma combination therapies and opens up possibilities for treating adult models of other diseases.

12 Article Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. 2016

Tirosh, Itay / Izar, Benjamin / Prakadan, Sanjay M / Wadsworth, Marc H / Treacy, Daniel / Trombetta, John J / Rotem, Asaf / Rodman, Christopher / Lian, Christine / Murphy, George / Fallahi-Sichani, Mohammad / Dutton-Regester, Ken / Lin, Jia-Ren / Cohen, Ofir / Shah, Parin / Lu, Diana / Genshaft, Alex S / Hughes, Travis K / Ziegler, Carly G K / Kazer, Samuel W / Gaillard, Aleth / Kolb, Kellie E / Villani, Alexandra-Chloé / Johannessen, Cory M / Andreev, Aleksandr Y / Van Allen, Eliezer M / Bertagnolli, Monica / Sorger, Peter K / Sullivan, Ryan J / Flaherty, Keith T / Frederick, Dennie T / Jané-Valbuena, Judit / Yoon, Charles H / Rozenblatt-Rosen, Orit / Shalek, Alex K / Regev, Aviv / Garraway, Levi A. ·Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA. bizar@partners.org aregev@broadinstitute.org levi_garraway@dfci.harvard.edu. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02142, USA. Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA. · Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. · Program in Therapeutic Sciences, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. · HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA. Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA. · Department of Surgical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. · Program in Therapeutic Sciences, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Ludwig Center at Harvard, Boston, MA 02215, USA. · Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02142, USA. Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA. Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA. Department of Immunology, Massachusetts General Hospital, Boston, MA 02114, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology and Koch Institute, MIT, Boston, MA 02142, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. bizar@partners.org aregev@broadinstitute.org levi_garraway@dfci.harvard.edu. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. bizar@partners.org aregev@broadinstitute.org levi_garraway@dfci.harvard.edu. ·Science · Pubmed #27124452.

ABSTRACT: To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, and endothelial cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, spatial context, and a drug-resistance program. In particular, all tumors harbored malignant cells from two distinct transcriptional cell states, such that tumors characterized by high levels of the MITF transcription factor also contained cells with low MITF and elevated levels of the AXL kinase. Single-cell analyses suggested distinct tumor microenvironmental patterns, including cell-to-cell interactions. Analysis of tumor-infiltrating T cells revealed exhaustion programs, their connection to T cell activation and clonal expansion, and their variability across patients. Overall, we begin to unravel the cellular ecosystem of tumors and how single-cell genomics offers insights with implications for both targeted and immune therapies.

13 Article Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. 2016

McGranahan, Nicholas / Furness, Andrew J S / Rosenthal, Rachel / Ramskov, Sofie / Lyngaa, Rikke / Saini, Sunil Kumar / Jamal-Hanjani, Mariam / Wilson, Gareth A / Birkbak, Nicolai J / Hiley, Crispin T / Watkins, Thomas B K / Shafi, Seema / Murugaesu, Nirupa / Mitter, Richard / Akarca, Ayse U / Linares, Joseph / Marafioti, Teresa / Henry, Jake Y / Van Allen, Eliezer M / Miao, Diana / Schilling, Bastian / Schadendorf, Dirk / Garraway, Levi A / Makarov, Vladimir / Rizvi, Naiyer A / Snyder, Alexandra / Hellmann, Matthew D / Merghoub, Taha / Wolchok, Jedd D / Shukla, Sachet A / Wu, Catherine J / Peggs, Karl S / Chan, Timothy A / Hadrup, Sine R / Quezada, Sergio A / Swanton, Charles. ·The Francis Crick Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London (UCL), London WC1E 6BT, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. · Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK. · Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. · Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1970 Frederiksberg C, Denmark. · The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. · The Francis Crick Institute, London WC2A 3LY, UK. · Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK. Department of Cellular Pathology, UCL, London WC1E 6BT, UK. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. · Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany. German Cancer Consortium (DKTK), 69121 Heidelberg, Germany. · Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. · Hematology/Oncology Division, 177 Fort Washington Avenue, Columbia University, New York, NY 10032, USA. · Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Weill Cornell Medical College, New York, NY 10065, USA. · Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Ludwig Collaborative Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. · Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Weill Cornell Medical College, New York, NY 10065, USA. Ludwig Collaborative Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Department of Internal Medicine, Brigham and Woman's Hospital, Boston, MA 02115, USA. · Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK. s.quezada@ucl.ac.uk charles.swanton@crick.ac.uk. · The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. s.quezada@ucl.ac.uk charles.swanton@crick.ac.uk. ·Science · Pubmed #26940869.

ABSTRACT: As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8(+)tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non-small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy-induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens.

14 Article Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma. 2016

Lissanu Deribe, Yonathan / Shi, Yanxia / Rai, Kunal / Nezi, Luigi / Amin, Samir B / Wu, Chia-Chin / Akdemir, Kadir C / Mahdavi, Mozhdeh / Peng, Qian / Chang, Qing Edward / Hornigold, Kirsti / Arold, Stefan T / Welch, Heidi C E / Garraway, Levi A / Chin, Lynda. ·Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030; ylissanu@mdanderson.org lchin@mdanderson.org. · Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030; Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborate Center for Cancer Medicine, Guangzhou 510060, China; · Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030; · Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77030; · The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom; · Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia; · Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215; Broad Institute of MIT and Harvard, Boston, MA 02141. · Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030; Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77030; ylissanu@mdanderson.org lchin@mdanderson.org. ·Proc Natl Acad Sci U S A · Pubmed #26884185.

ABSTRACT: PREX2 (phosphatidylinositol-3,4,5-triphosphate-dependent Rac-exchange factor 2) is a PTEN (phosphatase and tensin homolog deleted on chromosome 10) binding protein that is significantly mutated in cutaneous melanoma and pancreatic ductal adenocarcinoma. Here, genetic and biochemical analyses were conducted to elucidate the nature and mechanistic basis of PREX2 mutation in melanoma development. By generating an inducible transgenic mouse model we showed an oncogenic role for a truncating PREX2 mutation (PREX2(E824)*) in vivo in the context of mutant NRAS. Using integrative cross-species gene expression analysis, we identified deregulated cell cycle and cytoskeleton organization as significantly perturbed biological pathways in PREX2 mutant tumors. Mechanistically, truncation of PREX2 activated its Rac1 guanine nucleotide exchange factor activity, abolished binding to PTEN and activated the PI3K (phosphatidyl inositol 3 kinase)/Akt signaling pathway. We further showed that PREX2 truncating mutations or PTEN deletion induces down-regulation of the tumor suppressor and cell cycle regulator CDKN1C (also known as p57(KIP2)). This down-regulation occurs, at least partially, through DNA hypomethylation of a differentially methylated region in chromosome 11 that is a known regulatory region for expression of the CDKN1C gene. Together, these findings identify PREX2 as a mediator of NRAS-mutant melanoma development that acts through the PI3K/PTEN/Akt pathway to regulate gene expression of a cell cycle regulator.

15 Article Acquired BRAF inhibitor resistance: A multicenter meta-analysis of the spectrum and frequencies, clinical behaviour, and phenotypic associations of resistance mechanisms. 2015

Johnson, Douglas B / Menzies, Alexander M / Zimmer, Lisa / Eroglu, Zeynep / Ye, Fei / Zhao, Shilin / Rizos, Helen / Sucker, Antje / Scolyer, Richard A / Gutzmer, Ralf / Gogas, Helen / Kefford, Richard F / Thompson, John F / Becker, Jürgen C / Berking, Carola / Egberts, Friederike / Loquai, Carmen / Goldinger, Simone M / Pupo, Gulietta M / Hugo, Willy / Kong, Xiangju / Garraway, Levi A / Sosman, Jeffrey A / Ribas, Antoni / Lo, Roger S / Long, Georgina V / Schadendorf, Dirk. ·Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. Electronic address: douglas.b.johnson@vanderbilt.edu. · Melanoma Institute Australia, Sydney, NSW, Australia; Centre for Cancer Research, The University of Sydney at The Westmead Millennium Institute, Westmead, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia. · Department of Dermatology, University Hospital, University Duisburg-Essen, Essen, Germany. · Department of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA. · Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. · Centre for Cancer Research, The University of Sydney at The Westmead Millennium Institute, Westmead, NSW, Australia; Macquarie University, Sydney, NSW, Australia. · Melanoma Institute Australia, Sydney, NSW, Australia; Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia. · Department of Dermatology and Allergy, Skin Cancer Center Hannover, Hannover Medical School, Hannover, Germany. · First Department of Medicine, University of Athens Medical School, Athens, Greece. · Melanoma Institute Australia, Sydney, NSW, Australia; Centre for Cancer Research, The University of Sydney at The Westmead Millennium Institute, Westmead, NSW, Australia; Macquarie University, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia. · Translational Skin Cancer Research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany. · Department of Dermatology, Ludwig-Maximilians-University, Munich, Germany. · Department of Dermatology, University Hospital of Schleswig-Holstein, Kiel, Germany. · Department of Dermatology, University Medical Center, Mainz, Germany. · Department of Dermatology, University Hospital Zürich, Switzerland. · Centre for Cancer Research, The University of Sydney at The Westmead Millennium Institute, Westmead, NSW, Australia. · Department of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA. · Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. ·Eur J Cancer · Pubmed #26608120.

ABSTRACT: BACKGROUND: Acquired resistance to BRAF inhibitors (BRAFi) is a near-universal phenomenon caused by numerous genetic and non-genetic alterations. In this study, we evaluated the spectrum, onset, pattern of progression, and subsequent clinical outcomes associated with specific mechanisms of resistance. METHODS: We compiled clinical and genetic data from 100 patients with 132 tissue samples obtained at progression on BRAFi therapy from 3 large, previously published studies of BRAFi resistance. These samples were subjected to whole-exome sequencing and/or polymerase chain reaction-based genetic testing. RESULTS: Among 132 samples, putative resistance mechanisms were identified in 58%, including NRAS or KRAS mutations (20%), BRAF splice variants (16%), BRAF(V600E/K) amplifications (13%), MEK1/2 mutations (7%), and non-mitogen-activated protein kinase pathway alterations (11%). Marked heterogeneity was observed within tumors and patients; 18 of 19 patients (95%) with more than one progression biopsy had distinct/unknown drivers of resistance between samples. NRAS mutations were associated with vemurafenib use (p = 0.045) and intracranial metastases (p = 0.036), and MEK1/2 mutations correlated with hepatic progression (p = 0.011). Progression-free survival and overall survival were similar across resistance mechanisms. The median survival after disease progression was 6.9 months, and responses to subsequent BRAF and MEK inhibition were uncommon (2 of 15; 13%). Post-progression outcomes did not correlate with specific acquired BRAFi-resistance mechanisms. CONCLUSIONS: This is the first study to systematically characterise the clinical implications of particular acquired BRAFi-resistance mechanisms in patients with BRAF-mutant melanoma largest study to compile the landscape of resistance. Despite marked heterogeneity of resistance mechanisms within patients, NRAS mutations correlated with vemurafenib use and intracranial disease involvement.

16 Article Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. 2015

Van Allen, Eliezer M / Miao, Diana / Schilling, Bastian / Shukla, Sachet A / Blank, Christian / Zimmer, Lisa / Sucker, Antje / Hillen, Uwe / Foppen, Marnix H Geukes / Goldinger, Simone M / Utikal, Jochen / Hassel, Jessica C / Weide, Benjamin / Kaehler, Katharina C / Loquai, Carmen / Mohr, Peter / Gutzmer, Ralf / Dummer, Reinhard / Gabriel, Stacey / Wu, Catherine J / Schadendorf, Dirk / Garraway, Levi A. ·Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. · Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. · Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA. · Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany. · German Cancer Consortium (DKTK), 69121 Heidelberg, Germany. · Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands. · Department of Dermatology, University Hospital Zurich, 8091 Zurich, Switzerland. · Skin Cancer Unit, German Cancer Research Center(DKTK), 69121 Heidelberg, Germany. · Department of Dermatology, Venerology, and Allergology, University Medical Center, Ruprecht-Karls University of Heidelberg, 68167 Mannheim, Germany. · Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany. · Department of Dermatology, University Hospital Tübingen, 72076 Tübingen, Germany. · Department of Dermatology, University Hospital Kiel, 24105 Kiel, Germany. · Department of Dermatology, University Medical Center, 55131 Mainz, Germany. · Department of Dermatology, Elbe-Kliniken, 21614 Buxtehude, Germany. · Department of Dermatology and Allergy, Skin Cancer Center Hannover, Hannover Medical School, 30625 Hannover, Germany. ·Science · Pubmed #26359337.

ABSTRACT: Monoclonal antibodies directed against cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), such as ipilimumab, yield considerable clinical benefit for patients with metastatic melanoma by inhibiting immune checkpoint activity, but clinical predictors of response to these therapies remain incompletely characterized. To investigate the roles of tumor-specific neoantigens and alterations in the tumor microenvironment in the response to ipilimumab, we analyzed whole exomes from pretreatment melanoma tumor biopsies and matching germline tissue samples from 110 patients. For 40 of these patients, we also obtained and analyzed transcriptome data from the pretreatment tumor samples. Overall mutational load, neoantigen load, and expression of cytolytic markers in the immune microenvironment were significantly associated with clinical benefit. However, no recurrent neoantigen peptide sequences predicted responder patient populations. Thus, detailed integrated molecular characterization of large patient cohorts may be needed to identify robust determinants of response and resistance to immune checkpoint inhibitors.

17 Article ERK mutations confer resistance to mitogen-activated protein kinase pathway inhibitors. 2014

Goetz, Eva M / Ghandi, Mahmoud / Treacy, Daniel J / Wagle, Nikhil / Garraway, Levi A. ·Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute, Cambridge, Massachusetts. · Broad Institute, Cambridge, Massachusetts. · Dana-Farber Cancer Institute, Boston, Massachusetts. · Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute, Cambridge, Massachusetts. Levi_Garraway@dfci.harvard.edu. ·Cancer Res · Pubmed #25320010.

ABSTRACT: The use of targeted therapeutics directed against BRAF(V600)-mutant metastatic melanoma improves progression-free survival in many patients; however, acquired drug resistance remains a major medical challenge. By far, the most common clinical resistance mechanism involves reactivation of the MAPK (RAF/MEK/ERK) pathway by a variety of mechanisms. Thus, targeting ERK itself has emerged as an attractive therapeutic concept, and several ERK inhibitors have entered clinical trials. We sought to preemptively determine mutations in ERK1/2 that confer resistance to either ERK inhibitors or combined RAF/MEK inhibition in BRAF(V600)-mutant melanoma. Using a random mutagenesis screen, we identified multiple point mutations in ERK1 (MAPK3) and ERK2 (MAPK1) that could confer resistance to ERK or RAF/MEK inhibitors. ERK inhibitor-resistant alleles were sensitive to RAF/MEK inhibitors and vice versa, suggesting that the future development of alternating RAF/MEK and ERK inhibitor regimens might help circumvent resistance to these agents.

18 Article Unraveling the clonal hierarchy of somatic genomic aberrations. 2014

Prandi, Davide / Baca, Sylvan C / Romanel, Alessandro / Barbieri, Christopher E / Mosquera, Juan-Miguel / Fontugne, Jacqueline / Beltran, Himisha / Sboner, Andrea / Garraway, Levi A / Rubin, Mark A / Demichelis, Francesca. · ·Genome Biol · Pubmed #25160065.

ABSTRACT: Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations. Comparative analysis across 100 sequenced genomes from prostate, melanoma, and lung cancers established diverse evolutionary hierarchies, demonstrating the early disruption of tumor-specific pathways. The analyses highlight the diversity of clonal evolution within and across tumor types that might be informative for risk stratification and patient selection for targeted therapies. CLONET addresses heterogeneous clinical samples seen in the setting of precision medicine.

19 Article A Notch for noncoding RNA in melanoma. 2014

Garraway, Levi A. · ·N Engl J Med · Pubmed #24827041.

ABSTRACT: -- No abstract --

20 Article A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. 2014

Konieczkowski, David J / Johannessen, Cory M / Abudayyeh, Omar / Kim, Jong Wook / Cooper, Zachary A / Piris, Adriano / Frederick, Dennie T / Barzily-Rokni, Michal / Straussman, Ravid / Haq, Rizwan / Fisher, David E / Mesirov, Jill P / Hahn, William C / Flaherty, Keith T / Wargo, Jennifer A / Tamayo, Pablo / Garraway, Levi A. ·Authors' Affiliations:Broad Institute of Harvard and MIT, Cambridge; Department of Medical Oncology, Dana-Farber Cancer Institute; Divisions of. · Authors' Affiliations:Broad Institute of Harvard and MIT, Cambridge; · Surgical Oncology, and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. · Dermatopathology and. · Surgical Oncology. · Massachusetts General Hospital Cancer Center, and Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts; Departments of. · Massachusetts General Hospital Cancer Center, and. · Authors' Affiliations:Broad Institute of Harvard and MIT, Cambridge; Department of Medical Oncology, Dana-Farber Cancer Institute; Divisions of levi_garraway@dfci.harvard.edu. ·Cancer Discov · Pubmed #24771846.

ABSTRACT: SIGNIFICANCE: Although most BRAF(V600)-mutant melanomas are sensitive to RAF and/or MEK inhibitors, a subset fails to respond to such treatment. This study characterizes a transcriptional cell state distinction linked to MITF and NF-κB that may modulate intrinsic sensitivity of melanomas to MAPK pathway inhibitors.

21 Article The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. 2014

Van Allen, Eliezer M / Wagle, Nikhil / Sucker, Antje / Treacy, Daniel J / Johannessen, Cory M / Goetz, Eva M / Place, Chelsea S / Taylor-Weiner, Amaro / Whittaker, Steven / Kryukov, Gregory V / Hodis, Eran / Rosenberg, Mara / McKenna, Aaron / Cibulskis, Kristian / Farlow, Deborah / Zimmer, Lisa / Hillen, Uwe / Gutzmer, Ralf / Goldinger, Simone M / Ugurel, Selma / Gogas, Helen J / Egberts, Friederike / Berking, Carola / Trefzer, Uwe / Loquai, Carmen / Weide, Benjamin / Hassel, Jessica C / Gabriel, Stacey B / Carter, Scott L / Getz, Gad / Garraway, Levi A / Schadendorf, Dirk / Anonymous3490776. ·1Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School; 2Department of Pathology, Massachusetts General Hospital Cancer Center, Boston; 3Broad Institute of MIT and Harvard; 4Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts; 5Department of Dermatology, University Hospital, West German Cancer Center, University Duisburg-Essen, Essen; 6German Cancer Consortium (DKTK); 7Department of Dermatology, Heidelberg University Hospital, Heidelberg; 8Department of Dermatology and Allergy, Hannover Medical School, Hannover; 9Department of Dermatology, University of Wuerzburg, Wuerzburg; 10Department of Dermatology, Venerology and Allergology, University of Schleswig-Holstein Hospital, Kiel; 11Department of Dermatology and Allergology, Ludwig-Maximilian University, Munich; 12Department of Dermatology, Venerology and Allergy, Charité Universitätsmedizin Berlin, Humboldt University, Berlin; 13Department of Dermatology, University of Mainz, Mainz; 14University Medical Center, University of Tübingen, Tübingen, Germany; 15Department of Genome Sciences, University of Washington, Seattle, Washington; 16Department of Dermatology, University Hospital Zurich, Zurich, Switzerland; and 17First Department of Medicine, Medical School, University of Athens, Athens, Greece. ·Cancer Discov · Pubmed #24265153.

ABSTRACT: Most patients with BRAF(V600)-mutant metastatic melanoma develop resistance to selective RAF kinase inhibitors. The spectrum of clinical genetic resistance mechanisms to RAF inhibitors and options for salvage therapy are incompletely understood. We performed whole-exome sequencing on formalin-fixed, paraffin-embedded tumors from 45 patients with BRAF(V600)-mutant metastatic melanoma who received vemurafenib or dabrafenib monotherapy. Genetic alterations in known or putative RAF inhibitor resistance genes were observed in 23 of 45 patients (51%). Besides previously characterized alterations, we discovered a "long tail" of new mitogen-activated protein kinase (MAPK) pathway alterations (MAP2K2, MITF) that confer RAF inhibitor resistance. In three cases, multiple resistance gene alterations were observed within the same tumor biopsy. Overall, RAF inhibitor therapy leads to diverse clinical genetic resistance mechanisms, mostly involving MAPK pathway reactivation. Novel therapeutic combinations may be needed to achieve durable clinical control of BRAF(V600)-mutant melanoma. Integrating clinical genomics with preclinical screens may model subsequent resistance studies.

22 Article A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. 2013

Johannessen, Cory M / Johnson, Laura A / Piccioni, Federica / Townes, Aisha / Frederick, Dennie T / Donahue, Melanie K / Narayan, Rajiv / Flaherty, Keith T / Wargo, Jennifer A / Root, David E / Garraway, Levi A. ·1] The Broad Institute of Harvard University and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA. ·Nature · Pubmed #24185007.

ABSTRACT: Malignant melanomas harbouring point mutations (Val600Glu) in the serine/threonine-protein kinase BRAF (BRAF(V600E)) depend on RAF-MEK-ERK signalling for tumour cell growth. RAF and MEK inhibitors show remarkable clinical efficacy in BRAF(V600E) melanoma; however, resistance to these agents remains a formidable challenge. Global characterization of resistance mechanisms may inform the development of more effective therapeutic combinations. Here we carried out systematic gain-of-function resistance studies by expressing more than 15,500 genes individually in a BRAF(V600E) melanoma cell line treated with RAF, MEK, ERK or combined RAF-MEK inhibitors. These studies revealed a cyclic-AMP-dependent melanocytic signalling network not previously associated with drug resistance, including G-protein-coupled receptors, adenyl cyclase, protein kinase A and cAMP response element binding protein (CREB). Preliminary analysis of biopsies from BRAF(V600E) melanoma patients revealed that phosphorylated (active) CREB was suppressed by RAF-MEK inhibition but restored in relapsing tumours. Expression of transcription factors activated downstream of MAP kinase and cAMP pathways also conferred resistance, including c-FOS, NR4A1, NR4A2 and MITF. Combined treatment with MAPK-pathway and histone-deacetylase inhibitors suppressed MITF expression and cAMP-mediated resistance. Collectively, these data suggest that oncogenic dysregulation of a melanocyte lineage dependency can cause resistance to RAF-MEK-ERK inhibition, which may be overcome by combining signalling- and chromatin-directed therapeutics.

23 Article C-RAF mutations confer resistance to RAF inhibitors. 2013

Antony, Rajee / Emery, Caroline M / Sawyer, Allison M / Garraway, Levi A. ·Department of Medical Oncology, Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA 02115, USA. ·Cancer Res · Pubmed #23737487.

ABSTRACT: Melanomas that contain B-RAF(V600E) mutations respond transiently to RAF and MEK inhibitors; however, resistance to these agents remains a formidable challenge. Although B- or C-RAF dysregulation represents prominent resistance mechanisms, resistance-associated point mutations in RAF oncoproteins are surprisingly rare. To gain insights herein, we conducted random mutagenesis screens to identify B- or C-RAF mutations that confer resistance to RAF inhibitors. Whereas bona fide B-RAF(V600E) resistance alleles were rarely observed, we identified multiple C-RAF mutations that produced biochemical and pharmacologic resistance. Potent C-RAF resistance alleles localized to a 14-3-3 consensus binding site or a separate site within the P loop. These mutations elicited paradoxical upregulation of RAF kinase activity in a dimerization-dependent manner following exposure to RAF inhibitors. Knowledge of resistance-associated C-RAF mutations may enhance biochemical understanding of RAF-dependent signaling, anticipate clinical resistance to novel RAF inhibitors, and guide the design of "next-generation" inhibitors for deployment in RAF- or RAS-driven malignancies.

24 Article BCL2A1 is a lineage-specific antiapoptotic melanoma oncogene that confers resistance to BRAF inhibition. 2013

Haq, Rizwan / Yokoyama, Satoru / Hawryluk, Elena B / Jönsson, Göran B / Frederick, Dennie Tompers / McHenry, Kevin / Porter, Dale / Tran, Thanh-Nga / Love, Kevin T / Langer, Robert / Anderson, Daniel G / Garraway, Levi A / Duncan, Lyn McDivitt / Morton, Donald L / Hoon, Dave S B / Wargo, Jennifer A / Song, Jun S / Fisher, David E. ·Division of Medical Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA. ·Proc Natl Acad Sci U S A · Pubmed #23447565.

ABSTRACT: Although targeting oncogenic mutations in the BRAF serine/threonine kinase with small molecule inhibitors can lead to significant clinical responses in melanoma, it fails to eradicate tumors in nearly all patients. Successful therapy will be aided by identification of intrinsic mechanisms that protect tumor cells from death. Here, we used a bioinformatics approach to identify drug-able, "driver" oncogenes restricted to tumor versus normal tissues. Applying this method to 88 short-term melanoma cell cultures, we show that the antiapoptotic BCL2 family member BCL2A1 is recurrently amplified in ∼30% of melanomas and is necessary for melanoma growth. BCL2A1 overexpression also promotes melanomagenesis of BRAF-immortalized melanocytes. We find that high-level expression of BCL2A1 is restricted to melanoma due to direct transcriptional control by the melanoma oncogene MITF. Although BRAF inhibitors lead to cell cycle arrest and modest apoptosis, we find that apoptosis is significantly enhanced by suppression of BCL2A1 in melanomas with BCL2A1 or MITF amplification. Moreover, we find that BCL2A1 expression is associated with poorer clinical responses to BRAF pathway inhibitors in melanoma patients. Cotreatment of melanomas with BRAF inhibitors and obatoclax, an inhibitor of BCL2A1 and other BCL2 family members, overcomes intrinsic resistance to BRAF inhibitors in BCL2A1-amplified cells in vitro and in vivo. These studies identify MITF-BCL2A1 as a lineage-specific oncogenic pathway in melanoma and underscore its role for improved response to BRAF-directed therapy.

25 Article Highly recurrent TERT promoter mutations in human melanoma. 2013

Huang, Franklin W / Hodis, Eran / Xu, Mary Jue / Kryukov, Gregory V / Chin, Lynda / Garraway, Levi A. ·Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. ·Science · Pubmed #23348506.

ABSTRACT: Systematic sequencing of human cancer genomes has identified many recurrent mutations in the protein-coding regions of genes but rarely in gene regulatory regions. Here, we describe two independent mutations within the core promoter of telomerase reverse transcriptase (TERT), the gene coding for the catalytic subunit of telomerase, which collectively occur in 50 of 70 (71%) melanomas examined. These mutations generate de novo consensus binding motifs for E-twenty-six (ETS) transcription factors, and in reporter assays, the mutations increased transcriptional activity from the TERT promoter by two- to fourfold. Examination of 150 cancer cell lines derived from diverse tumor types revealed the same mutations in 24 cases (16%), with preliminary evidence of elevated frequency in bladder and hepatocellular cancer cells. Thus, somatic mutations in regulatory regions of the genome may represent an important tumorigenic mechanism.

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