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Hodis E, Triglia ET, Kwon JYH, Biancalani T, Zakka LR, Parkar S, Hütter JC, Buffoni L, Delorey TM, Phillips D, Dionne D, Nguyen LT, Schapiro D, Maliga Z, Jacobson CA, Hendel A, Rozenblatt-Rosen O, Mihm MC, Garraway LA, Regev A. Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment. Science 2022; 376:eabi8175. [PMID: 35482859 PMCID: PMC9427199 DOI: 10.1126/science.abi8175] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways, forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also affected tumor microenvironment composition and cell states. Our melanoma models shared genotype-associated expression programs with patient melanomas, and a deep learning model showed that these models partially recapitulated genotype-associated histopathological features as well. Thus, a progressive series of genome-edited human cancer models can causally connect genotypes carrying multiple mutations to phenotype.
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Affiliation(s)
- Eran Hodis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | | | - John Y. H. Kwon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Labib R. Zakka
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Saurabh Parkar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lorenzo Buffoni
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Toni M. Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Danielle Dionne
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lan T. Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Connor A. Jacobson
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ayal Hendel
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | - Martin C. Mihm
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Levi A. Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA 02139, USA
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Stover EH, Oh C, Keskula P, Choudhury AD, Tseng YY, Adalsteinsson VA, Lohr JG, Thorner AR, Ducar M, Kryukov GV, Ha G, Rosenberg M, Freeman SS, Zhang Z, Wu X, Van Allen EM, Takeda DY, Loda M, Wu CL, Taplin ME, Garraway LA, Boehm JS, Huang FW. Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate 2022; 82:584-597. [PMID: 35084050 PMCID: PMC8887817 DOI: 10.1002/pros.24305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Primary and metastatic prostate cancers have low mutation rates and recurrent alterations in a small set of genes, enabling targeted sequencing of prostate cancer-associated genes as an efficient approach to characterizing patient samples (compared to whole-exome and whole-genome sequencing). For example, targeted sequencing provides a flexible, rapid, and cost-effective method for genomic assessment of patient-derived cell lines to evaluate fidelity to initial patient tumor samples. METHODS We developed a prostate cancer-specific targeted next-generation sequencing (NGS) panel to detect alterations in 62 prostate cancer-associated genes as well as recurring gene fusions with ETS family members, representing the majority of common alterations in prostate cancer. We tested this panel on primary prostate cancer tissues and blood biopsies from patients with metastatic prostate cancer. We generated patient-derived cell lines from primary prostate cancers using conditional reprogramming methods and applied targeted sequencing to evaluate the fidelity of these cell lines to the original patient tumors. RESULTS The prostate cancer-specific panel identified biologically and clinically relevant alterations, including point mutations in driver oncogenes and ETS family fusion genes, in tumor tissues from 29 radical prostatectomy samples. The targeted panel also identified genomic alterations in cell-free DNA and circulating tumor cells (CTCs) from patients with metastatic prostate cancer, and in standard prostate cancer cell lines. We used the targeted panel to sequence our set of patient-derived cell lines; however, no prostate cancer-specific mutations were identified in the tumor-derived cell lines, suggesting preferential outgrowth of normal prostate epithelial cells. CONCLUSIONS We evaluated a prostate cancer-specific targeted NGS panel to detect common and clinically relevant alterations (including ETS family gene fusions) in prostate cancer. The panel detected driver mutations in a diverse set of clinical samples of prostate cancer, including fresh-frozen tumors, cell-free DNA, CTCs, and cell lines. Targeted sequencing of patient-derived cell lines highlights the challenge of deriving cell lines from primary prostate cancers and the importance of genomic characterization to credential candidate cell lines. Our study supports that a prostate cancer-specific targeted sequencing panel provides an efficient, clinically feasible approach to identify genetic alterations across a spectrum of prostate cancer samples and cell lines.
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Affiliation(s)
- Elizabeth H. Stover
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Coyin Oh
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Jens G. Lohr
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Gregory V. Kryukov
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Gavin Ha
- Fred Hutchinson Cancer Research Center, Seattle WA
| | | | | | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston MA
- University of Massachusetts Memorial Medical Center, Worcester MA
| | | | - Eliezer M. Van Allen
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Massimo Loda
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- New York-Presbyterian/Weill Cornell Medical Center, New York, NY
| | - Chin-Lee Wu
- Harvard Medical School, Boston MA
- Massachusetts General Hospital, Boston MA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
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3
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Affiliation(s)
- John D Carpten
- Department of Translational Genomics, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Lola Fashoyin-Aje
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, and Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, MD, USA.
| | | | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA.
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4
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Lo JA, Kawakubo M, Juneja VR, Su MY, Erlich TH, LaFleur MW, Kemeny LV, Rashid M, Malehmir M, Rabi SA, Raghavan R, Allouche J, Kasumova G, Frederick DT, Pauken KE, Weng QY, Pereira da Silva M, Xu Y, van der Sande AAJ, Silkworth W, Roider E, Browne EP, Lieb DJ, Wang B, Garraway LA, Wu CJ, Flaherty KT, Brinckerhoff CE, Mullins DW, Adams DJ, Hacohen N, Hoang MP, Boland GM, Freeman GJ, Sharpe AH, Manstein D, Fisher DE. Epitope spreading toward wild-type melanocyte-lineage antigens rescues suboptimal immune checkpoint blockade responses. Sci Transl Med 2021; 13:13/581/eabd8636. [PMID: 33597266 DOI: 10.1126/scitranslmed.abd8636] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
Although immune checkpoint inhibitors (ICIs), such as anti-programmed cell death protein-1 (PD-1), can deliver durable antitumor effects, most patients with cancer fail to respond. Recent studies suggest that ICI efficacy correlates with a higher load of tumor-specific neoantigens and development of vitiligo in patients with melanoma. Here, we report that patients with low melanoma neoantigen burdens who responded to ICI had tumors with higher expression of pigmentation-related genes. Moreover, expansion of peripheral blood CD8+ T cell populations specific for melanocyte antigens was observed only in patients who responded to anti-PD-1 therapy, suggesting that ICI can promote breakdown of tolerance toward tumor-lineage self-antigens. In a mouse model of poorly immunogenic melanomas, spreading of epitope recognition toward wild-type melanocyte antigens was associated with markedly improved anti-PD-1 efficacy in two independent approaches: introduction of neoantigens by ultraviolet (UV) B radiation mutagenesis or the therapeutic combination of ablative fractional photothermolysis plus imiquimod. Complete responses against UV mutation-bearing tumors after anti-PD-1 resulted in protection from subsequent engraftment of melanomas lacking any shared neoantigens, as well as pancreatic adenocarcinomas forcibly overexpressing melanocyte-lineage antigens. Our data demonstrate that somatic mutations are sufficient to provoke strong antitumor responses after checkpoint blockade, but long-term responses are not restricted to these putative neoantigens. Epitope spreading toward T cell recognition of wild-type tumor-lineage self-antigens represents a common pathway for successful response to ICI, which can be evoked in neoantigen-deficient tumors by combination therapy with ablative fractional photothermolysis and imiquimod.
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Affiliation(s)
- Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Masayoshi Kawakubo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Vikram R Juneja
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Mack Y Su
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Tal H Erlich
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Martin W LaFleur
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Lajos V Kemeny
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Mamunur Rashid
- Experimental Cancer Genetics, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Mohsen Malehmir
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - S Alireza Rabi
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Rumya Raghavan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard-MIT Health Sciences and Technology Program, Cambridge, MA 02139, USA
| | - Jennifer Allouche
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Gyulnara Kasumova
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Dennie T Frederick
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kristen E Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Qing Yu Weng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Marcelo Pereira da Silva
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Yu Xu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Anita A J van der Sande
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Whitney Silkworth
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Elisabeth Roider
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.,Department of Dermatology and Allergology, University of Szeged, Szeged 6727, Hungary.,Department of Dermatology, Venerology, and Allergology, Kantonsspital St. Gallen, St. Gallen 9000, Switzerland.,University of Zurich, Zurich 8006, Switzerland
| | - Edward P Browne
- Department of Medicine, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - David J Lieb
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Belinda Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Constance E Brinckerhoff
- Departments of Medicine and Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - David W Mullins
- Departments of Medical Education and Microbiology/Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Genevieve M Boland
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. .,Harvard Medical School, Boston, MA 02115, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA. .,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dieter Manstein
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. .,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
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5
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Wander SA, Cohen O, Johnson GN, Buendia J, Luo F, Geradts J, Winer EP, Lin NU, Garraway LA, Wagle N. Abstract B23: Genomic sequencing of metastatic hormone-receptor positive breast cancer implicates AKT1 in driving resistance to cyclin-dependent kinase 4/6 inhibitors. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.pi3k-mtor18-b23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The cyclin-dependent kinase 4/6 inhibitors (CDK4/6i), in combination with an antiestrogen, have emerged as standard-of-care options in both the first- and subsequent-line setting for patients with metastatic hormone-receptor positive (HR+)/HER2- breast cancer. Despite their widespread use, limited insight exists into the molecular pathways governing response and resistance to these agents.
Methods and Results: We performed whole-exome sequencing on metastatic tumor specimens from 59 patients with HR+/HER2- breast cancer who had received CDK4/6i-based therapy. Tumor biopsies were characterized as demonstrating sensitivity, intrinsic resistance, or acquired resistance based upon the timing of resistance, radiographic response, and duration of therapy. In contrast to prior reports indicating PIK3CA enrichment in patients receiving CDK4/6i-based therapy, alterations in PI3K were approximately evenly distributed in this cohort between sensitive and resistant biopsies (8/20, 40% vs. 21/40, 52.5%, respectively, p = 0.808 via Fisher's exact test). Activating alterations in AKT1, however, were identified in three resistant tumor specimens, including both point mutations and amplification. In two instances where matched pretreatment sensitive biopsies and post-treatment resistance biopsies were available, an AKT1 point mutation and an AKT1 amplification, respectively, were uniquely identified in the resistant biopsy. Immunohistochemical analysis of sensitive and resistance biopsy specimens in these patients confirmed upregulation of pAKT, pS6, and pRb, indicating upregulation of the AKT signaling axis. AKT1 was introduced into multiple HR+ breast cancer cell lines in vitro (T47D, MCF7, and CAMA1) via lentiviral overexpression. Overexpression of AKT1 in these cell lines provoked significant resistance to palbociclib, abemaciclib, fulvestrant, and estrogen deprivation (via charcoal-stripped serum, CSS). AKT1-expressing cells were also resistant to the various pairwise combinations of antiestrogen and CDK4/6i. Sensitivity to estrogen deprivation and CDK4/6i could be restored by treatment with the AKT inhibitor MK2206.
Conclusions: In contrast to prior reports, PIK3CA mutations did not correlate with resistance to CDK4/6 inhibition in our cohort of tumor specimens from 59 patients with metastatic HR+ breast cancer. AKT1 has emerged as a key potential mediator of resistance to both antiestrogens and CDK4/6i in vitro and in vivo. AKT1 pathway activation may serve as a potential biomarker of resistance to CDK4/6i, while novel strategies to target AKT1 may restore sensitivity to CDK4/6i-based therapy in HR+ metastatic breast cancer.
Citation Format: Seth A. Wander, Ofir Cohen, Gabriela N. Johnson, Jorge Buendia, Flora Luo, Joseph Geradts, Eric P. Winer, Nancy U. Lin, Levi A. Garraway, Nikhil Wagle. Genomic sequencing of metastatic hormone-receptor positive breast cancer implicates AKT1 in driving resistance to cyclin-dependent kinase 4/6 inhibitors [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B23.
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Affiliation(s)
- Seth A. Wander
- 1Massachusetts General Hospital Cancer Center, Boston, MA,
| | | | | | | | - Flora Luo
- 3Dana-Farber Cancer Institute, Boston, MA
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Shah P, Cuoco M, Su MJ, Melms J, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A, Jerby-Arnon L. Abstract PR01: A cancer cell program promotes T-cell exclusion and resistance to checkpoint blockade. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-pr01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune checkpoint inhibitors (ICI) 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-seq (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. This study will be published on Nov. 1st in Cell (Jerby-Arnon et al., Cell 2018).
This abstract is also being presented as Poster A25.
Citation Format: Parin Shah, Michael Cuoco, Mei-Ju Su, Johannes Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin, Shu Wang, Bokang Rabasha, David Liu, Alex K. Shalek, Itay Tirosh, Peter K. Sorger, Kai Wucherpfennig, Eliezer M. Van Allen, Dirk Schadendorf, Bruce E. Johnson, Asaf Rotem, Orit Rozenblatt-Rosen, Levi A. Garraway, Charles H. Yoon, Benjamin Izar, Aviv Regev, Livnat Jerby-Arnon. A cancer cell program promotes T-cell exclusion and resistance to checkpoint blockade [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR01.
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Affiliation(s)
- Parin Shah
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Mei-Ju Su
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | - Shaolin Mei
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jia-Ren Lin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Shu Wang
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - David Liu
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | - Asaf Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA
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7
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Li H, Bullock K, Gurjao C, Braun D, Shukla SA, Bosse D, Lalani AKA, Gopal S, Jin C, Horak C, Wind-Rotolo M, Signoretti S, McDermott DF, Freeman GJ, Van Allen EM, Schreiber SL, Hodi FS, Sellers WR, Garraway LA, Clish CB, Choueiri TK, Giannakis M. Abstract NG13: Metabolomic adaptations and correlates of survival to immune checkpoint blockade. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-ng13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Inhibition of immune-checkpoint targets including PD1 is clinically effective in a variety of cancers. However, only a subset of patients respond and complete response remains uncommon. To understand the mechanisms of response and resistance, recent studies have focused on neoantigens, copy-number alterations, and transcriptional signatures of tumor tissues collected from patients treated with immune-checkpoint inhibitors. Given the known role of metabolites in modulating immunity, we sought to understand how individual patients' metabolic activities adapt to PD1 immune checkpoint blockade and how they associate with therapeutic benefits. Methods: We profiled 106-202 metabolites in pre- and multiple on-treatment patient serum samples from three independent immunotherapy trials using liquid chromatography-mass spectrometry. These metabolites are involved in the metabolism of amino acids, nucleotides, nitrogen, and lipids, among others. Our study consisted of two Phase 1 trials (CA209-038 and -009) which included 78 patients with advanced melanoma and 91 patients with metastatic renal cell carcinoma (RCC) treated with nivolumab. RNASeq was performed on matched pre- and on-treatment tumor biopsies from the melanoma cohort. To investigate the generalizability of our results, we also performed metabolomics and serum specimens from a large randomized Phase 3 trial (CheckMate 025) with 743 RCC patients, among which 394 received nivolumab and 349 received everolimus. Results: During treatment with nivolumab, kynurenine, a product of tryptophan catabolism and the IDO/TDO genes, was the most significantly changed metabolite at week 4 and at week 6 compared to pre-treatment levels among melanoma patients (37% and 34% increase on average, q=1 × 10-10 and q=1 × 10-8 respectively, paired t-test). By using Kyn/Trp (Kynurenine/Tryptophan) as a metric indicating tryptophan-kynurenine conversion, we found that this ratio falls in a range spanning approximately 8-fold among these patients, suggesting prominent individual-to-individual differences. Specifically, 78% patients had any increases and 26.5% patients had increases above 50% at week 4. We confirmed this significant kynurenine up-regulation following nivolumab treatment in RCC patients in the phase 1 and phase 3 trials. In particular, the phase 3 cohort showed 23% and 24% increase on average at week 4 and week 8 respectively (q=1 × 10-10 and q=1 × 10-12, paired t-test). Additionally, 69.4% and 8.2% patients had Kyn/Trp increases above zero and 50% respectively at week 4. Notably, patients receiving everolimus control treatment had a decrease in kynurenine (q=1 × 10-5, t-test). Kynurenine is synthesized during tryptophan catabolism by indoleamine-2,3-dioxygenase (IDO) or tryptophan dioxygenase (TDO), and has been shown to suppress anti-tumor immune responses. To explore whether the circulating Kyn/Trp correlates with immune-suppression in the tumor microenvironment, we analyzed RNAseq data of matched tumor biopsies from the CA209-038 melanoma trial. We found a significant correlation between the Kyn/Trp ratio and PD-L1 expression, 4 weeks after starting nivolumab treatment (Pearson, p=0.01). We also discovered a correlation between Kyn/Trp and IDO1 but not TDO mRNA levels at the same time point. In contrast, Kyn/Trp was not associated with prior anti-CTLA4 treatment, or tumor mutational load. Moreover, compared to all other metabolites, increases of the Kyn/Trp ratio in the melanoma cohort (week 4 vs baseline) were consistently associated with greater risks for death (p=1.2*10-4, HR=2.71, 95% CI, 1.63-4.51). In particular, patients with a >50% increase in Kyn/Trp had a median OS of 15.7 months while those with decreases had a median survival time of > 38 months (p = 6.0*10-5, log-rank test). In contrast, the baseline Kyn/Trp ratio did not significantly associate with the melanoma patients' overall survival. To confirm this result, the association between Kyn/Trp ratios and overall survival in the larger phase 3 trial in RCC (CheckMate 025) was evaluated using serum samples collected at different time points. We found that at baseline, higher Kyn/Trp ratios associated with shorter overall survival both for the nivolumab- and the everolimus-treated patients (p = 3.6*10-4, HR=1.79, 95% CI, 1.30-2.47; p = 1.7*10-5, HR=2.06, 95% CI, 1.48-2.85; Cox model). However, at week 4, Kyn/Trp significantly associated with overall survival only in the nivolumab arm (p = 4.7*10-4, HR=2.81, 95% CI, 1.57-5.01; Cox model) but not in the everolimus arm (p = 0.53, HR=0.76, 95% CI, 0.32-1.78; Cox model). For nivolumab-treated RCC patients, those with a >50% increases of Kyn/Trp had a median survival of 16.7 months while those with any Kyn/Trp decreases had a median survival of 31.3 months (p = 4.3*10-4, log-rank test).Conclusions: We identified increased tryptophan to kynurenine conversion in response to PD1 blockade in a subset of melanoma and RCC patients. By using independent cohorts, we showed that Kyn/Trp temporal alterations robustly correlated with overall survival of patients receiving nivolumab. Our findings illustrate that checkpoint blockade in combination with IDO/TDO inhibitors might only benefit a selected group of patients with checkpoint-inhibition-triggered kynurenine pathway activation. Given the lack of improved therapeutic outcomes with PD1 and selective IDO1 inhibition among unselected patient populations in a recent phase 3 trial, our findings highlight the need and feasibility of patient stratification by monitoring serum Kyn/Trp alterations, show that kynurenine signaling may still be a relevant therapeutic target and more generally point to the relevance of metabolic adaptations in cancer immunotherapy. Our findings highlight the need and feasibility of patient stratification by monitoring serum Kyn/Trp alterations and point to the relevance of metabolic adaptations in cancer immunotherapy.
Citation Format: Haoxin Li, Kevin Bullock, Carino Gurjao, David Braun, Sachet A. Shukla, Dominick Bosse, Aly-Khan A. Lalani, Shuba Gopal, Chelsea Jin, Christine Horak, Megan Wind-Rotolo, Sabina Signoretti, David F. McDermott, Gordon J. Freeman, Eliezer M. Van Allen, Stuart L. Schreiber, Frank Stephen Hodi, William R. Sellers, Levi A. Garraway, Clary B. Clish, Toni K. Choueiri, Marios Giannakis. Metabolomic adaptations and correlates of survival to immune checkpoint blockade [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr NG13.
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Affiliation(s)
- Haoxin Li
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Kevin Bullock
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Carino Gurjao
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - David Braun
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Sachet A. Shukla
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Dominick Bosse
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Aly-Khan A. Lalani
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Shuba Gopal
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Chelsea Jin
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Christine Horak
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Megan Wind-Rotolo
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Sabina Signoretti
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - David F. McDermott
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Gordon J. Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Eliezer M. Van Allen
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Stuart L. Schreiber
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Frank Stephen Hodi
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - William R. Sellers
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Levi A. Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Toni K. Choueiri
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, Dana-Farber Cancer Institute, Boston, MA, Bristol-Myers Squibb, Princeton, NJ, Beth Israel Deaconess Medical Center, Boston, MA, Dana-Farber Cancer Institute, Boston, MA
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8
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Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su MJ, Shah P, Iwanicki M, Walker SR, Kanodia A, Melms JC, Mei S, Lin JR, Porter CBM, Slyper M, Waldman J, Jerby-Arnon L, Ashenberg O, Brinker TJ, Mills C, Rogava M, Vigneau S, Sorger PK, Garraway LA, Konstantinopoulos PA, Liu JF, Matulonis U, Johnson BE, Rozenblatt-Rosen O, Rotem A, Regev A. A single-cell landscape of high-grade serous ovarian cancer. Nat Med 2020; 26:1271-1279. [PMID: 32572264 PMCID: PMC7723336 DOI: 10.1038/s41591-020-0926-0] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 05/07/2020] [Indexed: 01/04/2023]
Abstract
Malignant abdominal fluid (ascites) frequently develops in women with advanced high-grade serous ovarian cancer (HGSOC) and is associated with drug resistance and a poor prognosis1. To comprehensively characterize the HGSOC ascites ecosystem, we used single-cell RNA sequencing to profile ~11,000 cells from 22 ascites specimens from 11 patients with HGSOC. We found significant inter-patient variability in the composition and functional programs of ascites cells, including immunomodulatory fibroblast sub-populations and dichotomous macrophage populations. We found that the previously described immunoreactive and mesenchymal subtypes of HGSOC, which have prognostic implications, reflect the abundance of immune infiltrates and fibroblasts rather than distinct subsets of malignant cells2. Malignant cell variability was partly explained by heterogeneous copy number alteration patterns or expression of a stemness program. Malignant cells shared expression of inflammatory programs that were largely recapitulated in single-cell RNA sequencing of ~35,000 cells from additionally collected samples, including three ascites, two primary HGSOC tumors and three patient ascites-derived xenograft models. Inhibition of the JAK/STAT pathway, which was expressed in both malignant cells and cancer-associated fibroblasts, had potent anti-tumor activity in primary short-term cultures and patient-derived xenograft models. Our work contributes to resolving the HSGOC landscape3-5 and provides a resource for the development of novel therapeutic approaches.
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Affiliation(s)
- Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Columbia University Medical Center, Columbia Center for Translational Immunology, New York, NY, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elizabeth H Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Idan Alter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Christopher Rodman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel Leeson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marcin Iwanicki
- Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Sarah R Walker
- Molecular, Cellular, and Biomedical Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Abhay Kanodia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johannes C Melms
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaolin Mei
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Caitlin Mills
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Meri Rogava
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sébastien Vigneau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | - Joyce F Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ursula Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ludwig Center for Cancer Research at MIT, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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9
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Wander SA, Cohen O, Gong X, Johnson GN, Buendia-Buendia JE, Lloyd MR, Kim D, Luo F, Mao P, Helvie K, Kowalski KJ, Nayar U, Waks AG, Parsons SH, Martinez R, Litchfield LM, Ye XS, Yu C, Jansen VM, Stille JR, Smith PS, Oakley GJ, Chu QS, Batist G, Hughes ME, Kremer JD, Garraway LA, Winer EP, Tolaney SM, Lin NU, Buchanan SG, Wagle N. The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor-Positive Metastatic Breast Cancer. Cancer Discov 2020; 10:1174-1193. [PMID: 32404308 PMCID: PMC8815415 DOI: 10.1158/2159-8290.cd-19-1390] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/29/2020] [Accepted: 05/08/2020] [Indexed: 11/16/2022]
Abstract
Mechanisms driving resistance to cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in hormone receptor-positive (HR+) breast cancer have not been clearly defined. Whole-exome sequencing of 59 tumors with CDK4/6i exposure revealed multiple candidate resistance mechanisms including RB1 loss, activating alterations in AKT1, RAS, AURKA, CCNE2, ERBB2, and FGFR2, and loss of estrogen receptor expression. In vitro experiments confirmed that these alterations conferred CDK4/6i resistance. Cancer cells cultured to resistance with CDK4/6i also acquired RB1, KRAS, AURKA, or CCNE2 alterations, which conferred sensitivity to AURKA, ERK, or CHEK1 inhibition. Three of these activating alterations-in AKT1, RAS, and AURKA-have not, to our knowledge, been previously demonstrated as mechanisms of resistance to CDK4/6i in breast cancer preclinically or in patient samples. Together, these eight mechanisms were present in 66% of resistant tumors profiled and may define therapeutic opportunities in patients. SIGNIFICANCE: We identified eight distinct mechanisms of resistance to CDK4/6i present in 66% of resistant tumors profiled. Most of these have a therapeutic strategy to overcome or prevent resistance in these tumors. Taken together, these findings have critical implications related to the potential utility of precision-based approaches to overcome resistance in many patients with HR+ metastatic breast cancer.This article is highlighted in the In This Issue feature, p. 1079.
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Affiliation(s)
- Seth A. Wander
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ofir Cohen
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Gabriela N. Johnson
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jorge E. Buendia-Buendia
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Maxwell R. Lloyd
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Dewey Kim
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Flora Luo
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Pingping Mao
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Karla Helvie
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kailey J. Kowalski
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Utthara Nayar
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Adrienne G. Waks
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | - Gerald Batist
- Segal Cancer Centre, Jewish General Hospital, McGill University, Montreal, Canada
| | - Melissa E. Hughes
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Levi A. Garraway
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA,Broad Institute of MIT and Harvard, Cambridge, MA,Eli Lilly and Co., Indianapolis, IN
| | - Eric P. Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,Harvard Medical School, Boston, MA
| | | | - Nikhil Wagle
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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10
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Wander SA, Cohen O, Gong X, Johnson GN, Buendia-Buendia J, Lloyd M, Kim D, Luo F, Mao P, Helvie K, Kowalski K, Nayar U, Parsons S, Martinez R, Litchfield L, Ye X, Yu CP, Jansen V, Garraway LA, Winer EP, Tolaney SM, Lin NU, Buchanan S, Wagle N. Abstract PD2-09: The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in patients with hormone receptor-positive (HR+)/HER2- metastatic breast cancer (MBC). Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-pd2-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The CDK4/6 inhibitors have emerged as standard first- or second-line regimens in combination with an antiestrogen for patients with HR+/HER2- MBC. While these agents convey significant clinical benefit in many patients, intrinsic resistance can occur and, in patients who respond, acquired resistance is unfortunately inevitable. Despite their widespread use, we have limited insight into the molecular mechanisms governing response and resistance to these agents.
Methods: Whole exome sequencing (WES) was performed on metastatic tumor biopsies from 58 patients (pts) with HR+/HER2- MBC who received a CDK4/6 inhibitor with or without an antiestrogen at the Dana-Farber Cancer Institute, including 7 pts with pre/post-exposure biopsy pairs. Among these biopsies, 69.5% were characterized as resistant (intrinsic or acquired) and 30.5% were characterized as sensitive. To validate putative resistance mediators identified in patient samples, HR+/HER2- breast cancer cells were modified via CRISPR knockout or lentiviral overexpression. Sensitivity of these cells to antiestrogens and CDK4/6i was interrogated via cell-titer-glo assay. In parallel, HR+/HER2- breast cancer cells were cultured to resistance in the presence of an escalating dose of CDK4/6i. Derivative cell lines were subjected to western blotting in an effort to interrogate the putative resistance mediators identified in pts. Novel dependencies were identified in these derivative cell lines via treatment with targeted therapeutic agents in vitro.
Results: WES of tumors with CDK4/6i exposure revealed candidate mechanisms of resistance including biallelic RB1 disruption (n=4, 10%) and activating events in AKT1 (n=5, 12.5%), RAS (n=4, 10%), aurora kinase A (AURKA, n=11, 27.5%), and cyclin E2 (CCNE2, n=6, 15%). Convergent evolution toward biallelic RB1 disruption was identified in a single patient with one pre- and two post-exposure biopsies, while acquisition of AKT1 mutation and amplification was identified in two separate instances. Knockout of RB1 and overexpression of AKT1, KRAS G12D, AURKA, and CCNE2 provoked CDK4/6i and antiestrogen resistance in vitro. Breast cancer cells cultured to resistance in CDK4/6i demonstrated concordant acquisition of RB1 downregulation, RAS/ERK activation, AURKA overexpression, and CCNE2 overexpression. Derivative resistant cell lines with RB1 loss or AURKA gain demonstrated enhanced sensitivity to a novel AURKA inhibitor (LY3295668), while cells with RAS activation were highly sensitive to ERK inhibition (via LY3214996). CCNE2-overexpressing cells were highly sensitive to prexasertib, a CHEK1 inhibitor.
Conclusions: The genomic landscape of resistance to CDK4/6i is heterogeneous with multiple potential mediators that play well-established roles in cell division and oncogenic signal transduction. We present novel mechanisms of clinical resistance including activation of AKT1 and RAS family oncogenes as well as amplification of AURKA and CCNE2. These drivers were able to provoke resistance to CDK4/6i in vitro. Finally, in each case, a novel dependency was identified which is readily translatable into the clinic. These results underscore the potential of next-generation sequencing as a critical tool to enable identification of resistance mediators, while also suggesting that the presence of specific genomic alterations may define new therapeutic opportunities in CDK4/6i-resistant HR+ MBC.
Citation Format: Seth A. Wander, Ofir Cohen, Xueqian Gong, Gabriela N. Johnson, Jorge Buendia-Buendia, Maxwell Lloyd, Dewey Kim, Flora Luo, Pingping Mao, Karla Helvie, Kailey Kowalski, Utthara Nayar, Stephen Parsons, Ricardo Martinez, Lacey Litchfield, Xiang Ye, Chun Ping Yu, Valerie Jansen, Levi A. Garraway, Eric P. Winer, Sara M. Tolaney, Nancy U. Lin, Sean Buchanan, Nikhil Wagle. The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in patients with hormone receptor-positive (HR+)/HER2- metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD2-09.
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Affiliation(s)
- Seth A. Wander
- 1Massachusetts General Hospital Cancer Center, Boston, MA
| | | | | | | | | | | | | | - Flora Luo
- 4Dana-Farber Cancer Institute, Boston, MA
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11
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Stover EH, Baco MB, Cohen O, Li YY, Christie EL, Bagul M, Goodale A, Lee Y, Pantel S, Rees MG, Wei G, Presser AG, Gelbard MK, Zhang W, Zervantonakis IK, Bhola PD, Ryan J, Guerriero JL, Montero J, Liang FJ, Cherniack AD, Piccioni F, Matulonis UA, Bowtell DDL, Sarosiek KA, Letai A, Garraway LA, Johannessen CM, Meyerson M. Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer. Mol Cancer Res 2019; 17:2281-2293. [PMID: 31462500 DOI: 10.1158/1541-7786.mcr-18-1243] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/07/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is often sensitive to initial treatment with platinum and taxane combination chemotherapy, but most patients relapse with chemotherapy-resistant disease. To systematically identify genes modulating chemotherapy response, we performed pooled functional genomic screens in HGSOC cell lines treated with cisplatin, paclitaxel, or cisplatin plus paclitaxel. Genes in the intrinsic pathway of apoptosis were among the top candidate resistance genes in both gain-of-function and loss-of-function screens. In an open reading frame overexpression screen, followed by a mini-pool secondary screen, anti-apoptotic genes including BCL2L1 (BCL-XL) and BCL2L2 (BCL-W) were associated with chemotherapy resistance. In a CRISPR-Cas9 knockout screen, loss of BCL2L1 decreased cell survival whereas loss of proapoptotic genes promoted resistance. To dissect the role of individual anti-apoptotic proteins in HGSOC chemotherapy response, we evaluated overexpression or inhibition of BCL-2, BCL-XL, BCL-W, and MCL1 in HGSOC cell lines. Overexpression of anti-apoptotic proteins decreased apoptosis and modestly increased cell viability upon cisplatin or paclitaxel treatment. Conversely, specific inhibitors of BCL-XL, MCL1, or BCL-XL/BCL-2, but not BCL-2 alone, enhanced cell death when combined with cisplatin or paclitaxel. Anti-apoptotic protein inhibitors also sensitized HGSOC cells to the poly (ADP-ribose) polymerase inhibitor olaparib. These unbiased screens highlight anti-apoptotic proteins as mediators of chemotherapy resistance in HGSOC, and support inhibition of BCL-XL and MCL1, alone or combined with chemotherapy or targeted agents, in treatment of primary and recurrent HGSOC. IMPLICATIONS: Anti-apoptotic proteins modulate drug resistance in ovarian cancer, and inhibitors of BCL-XL or MCL1 promote cell death in combination with chemotherapy.
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Affiliation(s)
- Elizabeth H Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Maria B Baco
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Mukta Bagul
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sasha Pantel
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew G Rees
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Guo Wei
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Adam G Presser
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Maya K Gelbard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Weiqun Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Patrick D Bhola
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jeremy Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer L Guerriero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Felice J Liang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Kristopher A Sarosiek
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Cory M Johannessen
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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12
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Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, Damato E, Aguirre AJ, Liang J, Liberzon A, Alexe G, Doench J, Ghandi M, Vazquez F, Weir BA, Tsherniak A, Subramanian A, Meneses-Cime K, Park J, Clemons P, Garraway LA, Thomas D, Boehm JS, Barbie DA, Hahn WC, Mesirov JP, Tamayo P. Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst 2019; 5:105-118.e9. [PMID: 28837809 DOI: 10.1016/j.cels.2017.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 05/01/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
Abstract
The systematic sequencing of the cancer genome has led to the identification of numerous genetic alterations in cancer. However, a deeper understanding of the functional consequences of these alterations is necessary to guide appropriate therapeutic strategies. Here, we describe Onco-GPS (OncoGenic Positioning System), a data-driven analysis framework to organize individual tumor samples with shared oncogenic alterations onto a reference map defined by their underlying cellular states. We applied the methodology to the RAS pathway and identified nine distinct components that reflect transcriptional activities downstream of RAS and defined several functional states associated with patterns of transcriptional component activation that associates with genomic hallmarks and response to genetic and pharmacological perturbations. These results show that the Onco-GPS is an effective approach to explore the complex landscape of oncogenic cellular states across cancers, and an analytic framework to summarize knowledge, establish relationships, and generate more effective disease models for research or as part of individualized precision medicine paradigms.
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Affiliation(s)
- Jong Wook Kim
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Omar O Abudayyeh
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Huwate Yeerna
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Chen-Hsiang Yeang
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Institute of Statistical Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Michelle Stewart
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Russell W Jenkins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David J Konieczkowski
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Radiation Oncology Program, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kate Medetgul-Ernar
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Taylor Cavazos
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Clarence Mah
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Stephanie Ting
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Eliezer M Van Allen
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ofir Cohen
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John Mcdermott
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Emily Damato
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew J Aguirre
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Jonathan Liang
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Arthur Liberzon
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gabriella Alexe
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | - John Doench
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mahmoud Ghandi
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Francisca Vazquez
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Barbara A Weir
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aviad Tsherniak
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aravind Subramanian
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Karina Meneses-Cime
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Jason Park
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Paul Clemons
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142, USA
| | - Levi A Garraway
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - David Thomas
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jesse S Boehm
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David A Barbie
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William C Hahn
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jill P Mesirov
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Pablo Tamayo
- Cancer Program, Eli and Edythe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA.
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13
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Izar B, Jerby-Arnon L, Tirosh I, Shah P, Cuoco MC, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Lin JR, Boland GM, Zhang G, Hodi FS, Sorger PK, Wucherpfennig KW, Allen EMV, Schadendorf D, Rozenblatt-Rosen O, Garraway LA, Rotem A, Yoon CH, Regev A. Abstract SY45-04: Development of therapeutic strategies by resolving the tumor ecosystem. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-sy45-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Solid tumors are complex ecosystem with inherent genetic and phenotypic variability, and interactions among cancer cells with the tumor microenvironment that shape the development, progression and the response or resistance to targeted- and immunotherapies. This heterogeneity is poorly captured with profiling of bulk tumor tissues that provides an average of these signals without recapitulating cellular interactions and phenotypes. Single-cell genomics technologies, such as single-cell RNA-sequencing (scRNA-seq), represent powerful tools to resolve tumor composition and dissect interactions within the ecosystem that may determine drug resistance and reveal vulnerabilities that can be therapeutically targeted. Using scRNA-seq we profiled thousands of malignant and non-malignant cells from patients with metastatic melanoma. We found that all tumors, irrespective of prior drug exposures, contained cells expressing a cell state characterized by high expression of AXL and low expression of MITF, the master regulator of the melanocytic lineage. The AXL-high/MITF-low cell state conferred intrinsic resistance to RAF/MEK inhibitor therapy in BRAF-mutated melanoma models, and led to the emergence of a small number of pre-existing AXL-high/MITF-low cells with treatment. Interrogation of tumor-infiltrating lymphocytes (TILs) provided insights into their diversity and expression of various immune checkpoints, such as PD-1, CTLA-4, LAG3, TIGIT and others, indicating their co-expression on CD8 and CD4 cells. While these markers indicated dysfunction of the T cells, we found concurrent expression of activating markers, including key cytokines such as interferon gamma. We dissected the relationship between activation, dysfunction, and clonality in these cells, and identified markers that saliently characterized the dysfunction state across different patients. Several complement factors, including C3, were predicted to modulate the infiltration and exclusion of T cells from the TME, and we validated the relationship of these in independent melanoma patient tissue sections.
We performed scRNA-seq on additional melanoma patients to assemble a total of 31 samples, of which 15 were isolated from patients with resistance to immune checkpoint inhibitors (ICI) (anti-PD-1 or anti-CTLA4 therapy or a combination of both). We performed a genome-scale inference of cancer cell-mediated drivers of T cell exclusion, a major mechanisms of ICI resistance. Next, we directly measured cell-intrinsic expression of pathways associated with immune evasion. Strikingly, the same cell state mediated both, T cell exclusion and immune evasion, indicating that one coherently regulated cancer cell program could be responsible for ICI resistance in patients. We validated the spatial impact of this resistance program by multiplexed immunofluorescence of immune infiltrates for predicted drivers of T cell exclusion in matching formalin-fixed, paraffin-embedded (FFPE) patient specimens. The signature was prognostic for survival in the melanoma TCGA cohort, indicating that the program can be intrinsically expressed. To test the predictive value of this signature, we compiled two validation cohorts, including one with 112 melanoma patients undergoing pre-treatment biopsies followed by anti-PD-1 therapy, and 26 additional patients of which some had sequential biopsies. RNA-sequencing of these cohorts revealed that the resistance program was predictive of progression-free survival, discriminated objective responders (OR), including complete response vs. partial response from patients progressive disease, and the duration of OR, supporting the possibility that the program captures both intrinsic and acquired resistance to ICI. Using an in silico prediction across >600 cell lines screened against 131 drugs, we found that cells with high expression of the resistance program were selectively susceptible to inhibition by CDK4/6 inhibitors, such as palbociclib or abemaciclib. We experimentally validated that abemaciclib reversed the resistance program in vitro, enhanced T cell responses in an ex vivo model of patient-derived melanoma cells and autologous T cells, and when combined with ICI, induced a high rate of complete responses in an otherwise ICI resistant syngeneic in vivo model of melanoma. Along with other studies in the field, our study suggest a potentially clinically active synergistic effect of combining CDK4/6 inhibitors with ICI.
Together, these studies highlight the possibility of developing rationale therapeutic strategies to overcome drug resistance by systematic assessment of patient tumor ecosystems.
Citation Format: Benjamin Izar, Livnat Jerby-Arnon, Itay Tirosh, Parin Shah, Michael C. Cuoco, Christopher Rodman, Mei-Ju Su, Johannes C. Melms, Rachel Leeson, Abhay Kanodia, Jia-Ren Lin, Genevieve M. Boland, Gao Zhang, F. Stephen Hodi, Peter K. Sorger, Kai W. Wucherpfennig, Eli M. Van Allen, Dirk Schadendorf, Orit Rozenblatt-Rosen, Levi A. Garraway, Asaf Rotem, Charles H. Yoon, Aviv Regev. Development of therapeutic strategies by resolving the tumor ecosystem [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY45-04.
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Affiliation(s)
| | | | - Itay Tirosh
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | - Parin Shah
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Mei-Ju Su
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Asaf Rotem
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Aviv Regev
- 2Broad Institute of Harvard and MIT, Cambridge, MA
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14
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Liu D, Abbosh P, Keliher D, Reardon B, Miao D, Mouw K, Weiner-Taylor A, Wankowicz S, Han G, Teo MY, Cipolla C, Kim J, Iyer G, Al-Ahmadie H, Dulaimi E, Chen DY, Alpaugh RK, Hoffman-Censits J, Garraway LA, Getz G, Carter SL, Bellmunt J, Plimack E, Rosenberg JE, Allen EMV. Abstract SY05-03: Dissecting genomic correlates of response and resistance to chemotherapy in bladder cancer through clinical computational oncology. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-sy05-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Approximately 20,000 new cases of muscle-invasive bladder cancer (MIBC), a localized but potentially lethal stage of disease, are diagnosed annually in the US alone. Standard-of-care therapy for MIBC includes neoadjuvant cisplatin-based chemotherapy followed by definitive bladder resection. In prior work, we identified and validated genomic alterations in DNA repair genes such as ERCC2, which predict response to cisplatin-based chemotherapy (Van Allen et al. Cancer Discovery 2014; Liu et al. JAMA Oncology 2016). However, the majority of patients have disease resistant to chemotherapy with a poor prognosis of <40% survival at 5 years, and the genomic basis of chemotherapy resistance has not been well-characterized. In this study, our goal was to analyze matched pre-treatment and resistant post-chemotherapy cystectomy tumor samples to identify genomic correlates of cisplatin-based chemotherapy exposure and resistance. We identified 56 MIBC patients with matched pre-chemotherapy biopsy samples and resistant tumor samples from cystectomy. Along with matched normal samples (blood), we performed whole exome sequencing (WES) on these “trios” of pre, post, and normal tissue, and called somatic variants using standardized pipelines including single nucleotide variants (SNVs), short insertions and deletions, allelic copy number alterations (CNAs), tumor purity and ploidy, and purity- and ploidy-corrected copy number variants. After quality control, including contamination estimation < 5%, mean target coverage > 50x, and a tumor purity minimum threshold of 10%, we had data from 30 trios available for analysis. We hypothesized that DNA-damaging chemotherapy may lead to increased mutational load in the post-treatment tumor. However, we observed that while some tumors gained mutations, others lost mutations, with no overall change (mean change = -17.3 mutations, paired t-test p = 0.20) in total mutational load. We found that clonal mutations (found in all tumor cells) were virtually unchanged from matched pre- to post-treatment tumors. In contrast, subclonal mutations (found only in a subset of tumor cells) were private to pre- and post-treatment tumors. These pre- and post-treatment mutation differences may reflect tumor sampling heterogeneity (i.e. taking from different parts of the tumor), but may be also due to selection pressure from therapy (e.g. loss of subclones) and cisplatin-induced mutations.To investigate the latter possibility, we adapted a non-negative matrix factorization (NMF) approach (Lee and Seung Nature 1999) to discover mutational signatures (Alexandrov et al Nature 2013) in the mutations unique to post-treatment tumors. Along with signatures known to be operant in bladder cancers, we discovered a mutational signature dissimilar to any other previously described mutational signature which accounted for ~15% of post-treatment mutations. This signature exhibited a transcriptional strand bias consistent with known mechanisms of cisplatin-induced DNA damage and repair, and was enriched in subclonal mutations consistent with the relatively short time frame between cisplatin exposure and cystectomy. This signature also exhibited similar activity to a cisplatin-induced mutational signature derived in a preclinical model (DT40) exposed to cisplatin therapy (Pearson rho = 0.95, empiric p = 0.004). Finally, we were able to validate this signature in a separate cohort of pre- and post-cisplatin treated bladder cancers (Faltas et al Nature Genetics 2016). We further hypothesized that the degree of tumor heterogeneity itself may be a prognostic factor. We calculated two different measures of intratumor heterogeneity: (1) the proportion of mutations in each tumor that was subclonal; and (2) the number of unique subclones in each tumor, and examined the association of survival with these measures of intratumor heterogeneity using Cox survival analyses. We found that overall survival was associated with heterogeneity, with a 6.6% increase in mortality rate for each 10% increase in post-treatment proportion of subclonal mutations (p=0.013), and 64% increase in mortality rate for each additional inferred subclone (p=0.02). Tumor heterogeneity continued to be associated with survival after adjusting for clinical covariates (p=0.03, p=0.014, respectively).Finally, we analyzed our tumors for genomic alterations associated with resistance. While we did not discover highly recurrent post-treatment mutations in specific genes, we found drivers of cell cycle progression (E2F3 amplification, JUN amplification), biallelic loss of FBXW7 (regulator of protein degradation of multiple onco-proteins including c-MYC, Notch, Cyclin E, and c-JUN), and focal amplification of PD-L1/2 in individual post-treatment resistant tumors.In this study, we found that cisplatin-based chemotherapy did not induce a large increase in the number of mutations. Thus, while there is good empiric data for the efficacy of combination of chemotherapy and immune checkpoint inhibition in specific tumor type and clinical settings (e.g. platinum-doublet therapy + ICB in first-line therapy of non-small cell lung cancer (NSCLC)), our data suggests that alternative mechanisms other than increased neoantigen burden are responsible. We discovered a cisplatin-induced mutational signature in post-treatment tumors which has subsequently been found in other cisplatin-treated tumors (e.g. NSCLC and ovarian cancer). Interestingly, the proportion of mutations inferred to be cisplatin-induced was quite different between resistant tumors, and an area for further inquiry is whether these differences could be associated with different mechanisms of resistance (e.g. upregulation of efflux pumps vs. anti-apoptotic adaptations). Tumor heterogeneity, which has been associated with worse outcomes and resistance in multiple contexts, was prognostic for survival in our cohort, suggesting that this may be clinically useful as part of a prognostic biomarker. We discovered additional association of drivers of cell-cycle progression with resistance, and further identified acquisition of a focal amplification in a region containing PD-L1/PD-L2, suggesting a potential biomarker for a subset of bladder cancers for response to immune checkpoint blockade. Broadly, this study represents the development of algorithms to dissect genomic features associated with survival and resistance in a carefully curated cohort of matched patient tumors within a specific clinical context. These types of approaches can be applied across tumor types, therapies, and clinical contexts to shed light onto biological mechanisms underpinning response and resistance and inform the development of biomarkers to guide clinical management.
Citation Format: David Liu, Philip Abbosh, Daniel Keliher, Brendan Reardon, Diana Miao, Kent Mouw, Amaro Weiner-Taylor, Stephanie Wankowicz, Garam Han, Min-Yuen Teo, Catharine Cipolla, Jaegil Kim, Gopa Iyer, Hikmat Al-Ahmadie, Essel Dulaimi, David Y.T. Chen, R. Katherine Alpaugh, Jean Hoffman-Censits, Levi A. Garraway, Gad Getz, Scott L. Carter, Joaquim Bellmunt, Elizabeth Plimack, Jonathan E. Rosenberg, Eliezer M. Van Allen. Dissecting genomic correlates of response and resistance to chemotherapy in bladder cancer through clinical computational oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY05-03.
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Affiliation(s)
- David Liu
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | - Diana Miao
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Kent Mouw
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Garam Han
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Min-Yuen Teo
- 4Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jaegil Kim
- 3Broad Institute of Harvard and MIT, Cambridge, MA
| | - Gopa Iyer
- 4Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Gad Getz
- 3Broad Institute of Harvard and MIT, Cambridge, MA
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15
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Li H, Ericsson M, Rabasha B, Budnik B, Chan SH, Freinkman E, Lewis CA, Doench JG, Wagner BK, Garraway LA, Schreiber SL. 6-Phosphogluconate Dehydrogenase Links Cytosolic Carbohydrate Metabolism to Protein Secretion via Modulation of Glutathione Levels. Cell Chem Biol 2019; 26:1306-1314.e5. [PMID: 31204288 DOI: 10.1016/j.chembiol.2019.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/26/2019] [Accepted: 05/13/2019] [Indexed: 12/15/2022]
Abstract
The proteinaceous extracellular matrix (ECM) is vital for the survival, proliferation, migration, and differentiation of many types of cancer. However, little is known regarding metabolic pathways required for ECM secretion. By using an unbiased computational approach, we searched for enzymes whose suppression may lead to disruptions in protein secretion. Here, we show that 6-phosphogluconate dehydrogenase (PGD), a cytosolic enzyme involved in carbohydrate metabolism, is required for ER structural integrity and protein secretion. Chemical inhibition or genetic suppression of PGD activity led to cell stress accompanied by significantly expanded ER volume and was rescued by compensating endogenous glutathione supplies. Our results also suggest that this characteristic ER-dilation phenotype may be a general marker indicating increased ECM protein congestion inside cells and decreased secretion. Thus, PGD serves as a link between cytosolic carbohydrate metabolism and protein secretion.
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Affiliation(s)
- Haoxin Li
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Maria Ericsson
- Electron Microscope Facility, Harvard Medical School, Boston, MA 02115, USA
| | - Bokang Rabasha
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Laboratory, Harvard University, Cambridge, MA 02138, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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16
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Amin-Mansour A, George S, Sioletic S, Carter SL, Rosenberg M, Taylor-Weiner A, Stewart C, Chevalier A, Seepo S, Tracy A, Getz G, Hornick JL, Nucci MR, Quade B, Demetri GD, Raut CP, Garraway LA, Van Allen EM, Wagner AJ. Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma. Clin Cancer Res 2019; 25:5135-5142. [PMID: 31164371 DOI: 10.1158/1078-0432.ccr-19-0271] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/27/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023]
Abstract
PURPOSE Leiomyosarcoma and liposarcoma are common subtypes of soft tissue sarcoma (STS). Patients with metastatic leiomyosarcoma or dedifferentiated liposarcoma (DDLPS) typically have worse outcomes compared with localized leiomyosarcoma or well-differentiated liposarcoma (WDLPS). A better understanding of genetic changes between primary/metastatic leiomyosarcoma and between WDLPS/DDLPS may provide insight into their genetic evolution. EXPERIMENTAL DESIGN We interrogated whole-exome sequencing (WES) from "trios" of normal tissue, primary tumor, and metastatic tumor from individual patients with leiomyosarcoma (n = 9), and trios of normal tissue, well-differentiated tumor, and dedifferentiated tumor from individual patients with liposarcoma (n = 19). Specifically, we performed mutational, copy number, and tumor evolution analyses on these cohorts and compared patterns among leiomyosarcoma and liposarcoma trios. RESULTS Leiomyosarcoma cases harbored shared drivers through a typical parent/child relationship where the metastatic tumor was derived from the primary tumor. In contrast, while all liposarcoma cases shared the characteristic focal chromosome 12 amplicon, most paired liposarcoma cases did not share additional mutations, suggesting a divergent evolutionary pattern from a common precursor. No highly recurrent genomic alterations from WES were identified that could be implicated as driving the progression of disease in either sarcoma subtype. CONCLUSIONS From a genomic perspective, leiomyosarcoma metastases contain genetic alterations that are also found in primary tumors. WDLPS and DDLPS, however, appear to divergently evolve from a common precursor harboring 12q amplification, rather than as a transformation to a higher-grade tumor. Further efforts to identify specific drivers of these distinct evolutionary patterns may inform future translational and clinical research in STS.
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Affiliation(s)
- Ali Amin-Mansour
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Suzanne George
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stefano Sioletic
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Scott L Carter
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Mara Rosenberg
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Chip Stewart
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aaron Chevalier
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sara Seepo
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Adam Tracy
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Marisa R Nucci
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley Quade
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J Wagner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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17
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Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet 2019; 51:1194. [PMID: 31152158 DOI: 10.1038/s41588-019-0451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie A M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Celine Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christopher E Barbieri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zafeiris Zafeiriou
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Susana Miranda
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Tolonen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Johann S de Bono
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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18
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Hayes TK, Luo F, Cohen O, Goodale AB, Lee Y, Pantel S, Bagul M, Piccioni F, Root DE, Garraway LA, Meyerson M, Johannessen CM. A Functional Landscape of Resistance to MEK1/2 and CDK4/6 Inhibition in NRAS-Mutant Melanoma. Cancer Res 2019; 79:2352-2366. [PMID: 30819666 PMCID: PMC7227487 DOI: 10.1158/0008-5472.can-18-2711] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/08/2019] [Accepted: 02/25/2019] [Indexed: 12/26/2022]
Abstract
Combinatorial inhibition of MEK1/2 and CDK4/6 is currently undergoing clinical investigation in NRAS-mutant melanoma. To prospectively map the landscape of resistance to this investigational regimen, we utilized a series of gain- and loss-of-function forward genetic screens to identify modulators of resistance to clinical inhibitors of MEK1/2 and CDK4/6 alone and in combination. First, we identified NRAS-mutant melanoma cell lines that were dependent on NRAS for proliferation and sensitive to MEK1/2 and CDK4/6 combination treatment. We then used a genome-scale ORF overexpression screen and a CRISPR knockout screen to identify modulators of resistance to each inhibitor alone or in combination. These orthogonal screening approaches revealed concordant means of achieving resistance to this therapeutic modality, including tyrosine kinases, RAF, RAS, AKT, and PI3K signaling. Activated KRAS was sufficient to cause resistance to combined MEK/CDK inhibition and to replace genetic depletion of oncogenic NRAS. In summary, our comprehensive functional genetic screening approach revealed modulation of resistance to the inhibition of MEK1/2, CDK4/6, or their combination in NRAS-mutant melanoma. SIGNIFICANCE: These findings reveal that NRAS-mutant melanomas can acquire resistance to genetic ablation of NRAS or combination MEK1/2 and CDK4/6 inhibition by upregulating activity of the RTK-RAS-RAF and RTK-PI3K-AKT signaling cascade.
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Affiliation(s)
- Tikvah K Hayes
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, Massachusetts
- Cancer Program, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Flora Luo
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, Massachusetts
- Cancer Program, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, Massachusetts
- Cancer Program, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Amy B Goodale
- Genetic Perturbation Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Yenarae Lee
- Genetic Perturbation Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Sasha Pantel
- Genetic Perturbation Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Mukta Bagul
- Genetic Perturbation Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Federica Piccioni
- Genetic Perturbation Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - David E Root
- Genetic Perturbation Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Levi A Garraway
- Eli Lilly Oncology, Eli Lilly Company, Indianapolis, Indiana
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, Massachusetts
- Cancer Program, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts
| | - Cory M Johannessen
- Cancer Program, The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts.
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19
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Li H, Ning S, Ghandi M, Kryukov GV, Gopal S, Deik A, Souza A, Pierce K, Keskula P, Hernandez D, Ann J, Shkoza D, Apfel V, Zou Y, Vazquez F, Barretina J, Pagliarini RA, Galli GG, Root DE, Hahn WC, Tsherniak A, Giannakis M, Schreiber SL, Clish CB, Garraway LA, Sellers WR. The landscape of cancer cell line metabolism. Nat Med 2019; 25:850-860. [PMID: 31068703 PMCID: PMC6629041 DOI: 10.1038/s41591-019-0404-8] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/20/2019] [Indexed: 02/08/2023]
Abstract
Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated dependencies remain uncommon. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) using liquid chromatography-mass spectrometry (LC-MS). This resource enables unbiased association analysis linking the cancer metabolome to genetic alterations, epigenetic features and gene dependencies. Additionally, by screening barcoded cell lines, we demonstrated that aberrant ASNS hypermethylation sensitizes subsets of gastric and hepatic cancers to asparaginase therapy. Finally, our analysis revealed distinct synthesis and secretion patterns of kynurenine, an immune-suppressive metabolite, in model cancer cell lines. Together, these findings and related methodology provide comprehensive resources that will help clarify the landscape of cancer metabolism.
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Affiliation(s)
- Haoxin Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaoyang Ning
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | | | | | - Shuba Gopal
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amy Deik
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amanda Souza
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kerry Pierce
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Paula Keskula
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Julie Ann
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Dojna Shkoza
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Verena Apfel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Yilong Zou
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jordi Barretina
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Giorgio G Galli
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Marios Giannakis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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20
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Maertens O, Kuzmickas R, Manchester HE, Emerson CE, Gavin AG, Guild CJ, Wong TC, De Raedt T, Bowman-Colin C, Hatchi E, Garraway LA, Flaherty KT, Pathania S, Elledge SJ, Cichowski K. MAPK Pathway Suppression Unmasks Latent DNA Repair Defects and Confers a Chemical Synthetic Vulnerability in BRAF-, NRAS-, and NF1-Mutant Melanomas. Cancer Discov 2019; 9:526-545. [PMID: 30709805 PMCID: PMC10151004 DOI: 10.1158/2159-8290.cd-18-0879] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/05/2018] [Accepted: 01/29/2019] [Indexed: 11/16/2022]
Abstract
Although the majority of BRAF-mutant melanomas respond to BRAF/MEK inhibitors, these agents are not typically curative. Moreover, they are largely ineffective in NRAS- and NF1-mutant tumors. Here we report that genetic and chemical suppression of HDAC3 potently cooperates with MAPK pathway inhibitors in all three RAS pathway-driven tumors. Specifically, we show that entinostat dramatically enhances tumor regression when combined with BRAF/MEK inhibitors, in both models that are sensitive or relatively resistant to these agents. Interestingly, MGMT expression predicts responsiveness and marks tumors with latent defects in DNA repair. BRAF/MEK inhibitors enhance these defects by suppressing homologous recombination genes, inducing a BRCA-like state; however, addition of entinostat triggers the concomitant suppression of nonhomologous end-joining genes, resulting in a chemical synthetic lethality caused by excessive DNA damage. Together, these studies identify melanomas with latent DNA repair defects, describe a promising drug combination that capitalizes on these defects, and reveal a tractable therapeutic biomarker. SIGNIFICANCE: BRAF/MEK inhibitors are not typically curative in BRAF-mutant melanomas and are ineffective in NRAS- and NF1-mutant tumors. We show that HDAC inhibitors dramatically enhance the efficacy of BRAF/MEK inhibitors in sensitive and insensitive RAS pathway-driven melanomas by coordinately suppressing two DNA repair pathways, and identify a clinical biomarker that predicts responsiveness.See related commentary by Lombard et al., p. 469.This article is highlighted in the In This Issue feature, p. 453.
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Affiliation(s)
- Ophélia Maertens
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Ryan Kuzmickas
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Haley E Manchester
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Chloe E Emerson
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Alessandra G Gavin
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Caroline J Guild
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Terence C Wong
- Department of Medical Oncology, Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Thomas De Raedt
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Christian Bowman-Colin
- Harvard Medical School, Boston, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elodie Hatchi
- Harvard Medical School, Boston, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Levi A Garraway
- Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Medical Oncology, Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Keith T Flaherty
- Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, Massachusetts
| | - Stephen J Elledge
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Genetics, Howard Hughes Medical Institute, Boston, Massachusetts
| | - Karen Cichowski
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
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21
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Jerby L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JM, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi S, Boland GM, Sullivan RJ, Frederick D, Miao B, Moll T, Flaherty K, Herlyn M, Jenkins RS, Thummalapalli R, Kowalczyk MS, Canadas I, Schilling B, Cartwright AN, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig KW, Allen EMV, Schadendorf D, Johnson BE, Rotem A, Rosenblatt-Rozen O, Garraway LA, Yoon CH, Izar B, Regev A. Abstract A082: Single-cell RNA-sequencing of metastatic melanoma identifies a cancer cell-intrinsic program associated with immune checkpoint inhibitor resistance. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune checkpoint inhibitors (ICI) produce durable responses in some melanoma patients, but many patients derive no clinical benefit. The molecular underpinnings of ICI resistance involve intricate cell-cell interactions that are yet elusive. To systematically map the interactions between malignant and immune cells in the tumor ecosystem, we applied single-cell RNA sequencing to 31 human melanoma tumors, profiling thousands of malignant, immune, and stromal cells. We identified a transcriptional program in malignanT-cells that is strongly associated with T-cell exclusion and immunotherapy resistance. Using highly multiplexed in situ imaging we first demonstrated that this program characterizes malignanT-cells in “cold” niches. Next, we showed that the program predicts clinical responses to ICI according to multiple independent validation cohorts, including a new cohort that we obtained from 112 melanoma patients treated with anti-PD-1 therapy. We then identified CDK4/6 as master regulators of this resistance program, and found that CDK4/6 inhibitors repress the program and shift melanoma cells into a senescence-associated secretory phenotype. Lastly, we showed that CDK4/6-inhibition leads to a substantial reduction in melanoma tumor outgrowth in a B16 mouse model when given in combination with immunotherapy. Taken together, our study provides a high-resolution landscape of ICI-resistant cell states, identifies clinically predictive signatures, and forms a basis for the development of novel therapeutic strategies that could overcome immunotherapy resistance.
Citation Format: Livnat Jerby, Parin Shah, Michael S. Cuoco, Christopher Rodman, Mei-Ju Su, Johannes M. Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin, Shu Wang, Bokang Rabasha, David Liu, Gao Zhang, Claire Margolais, Orr Ashenberg, Patrick A. Ott, Elizabeth I. Buchbinder, Riz Haq, Stephen Hodi, Genevieve M. Boland, Ryan J. Sullivan, Dennie Frederick, Benchun Miao, Tabea Moll, Keith Flaherty, Meenhard Herlyn, Russell S. Jenkins, Rohit Thummalapalli, Monika S. Kowalczyk, Israel Canadas, Bastian Schilling, Adam N.R Cartwright, Adrienne M. Luoma, Shruti Malu, Patrick Hwu, Chantale Bernatchez, Marie-Andree Forget, David A. Barbie, Alex K. Shalek, Itay Tirosh, Peter K. Sorger, Kai W. Wucherpfennig, Eliezer M. Van Allen, Dirk Schadendorf, Bruce E. Johnson, Asaf Rotem, Orit Rosenblatt-Rozen, Levi A. Garraway, Charles H. Yoon, Benjamin Izar, Aviv Regev. Single-cell RNA-sequencing of metastatic melanoma identifies a cancer cell-intrinsic program associated with immune checkpoint inhibitor resistance [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A082.
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Affiliation(s)
- Livnat Jerby
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Parin Shah
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Michael S. Cuoco
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Christopher Rodman
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Mei-Ju Su
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Johannes M. Melms
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Rachel Leeson
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Abhay Kanodia
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Shaolin Mei
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Jia-Ren Lin
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Shu Wang
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Bokang Rabasha
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - David Liu
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Gao Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Claire Margolais
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Patrick A. Ott
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Elizabeth I. Buchbinder
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Riz Haq
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Stephen Hodi
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Genevieve M. Boland
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Ryan J. Sullivan
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Dennie Frederick
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Benchun Miao
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Tabea Moll
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Keith Flaherty
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Meenhard Herlyn
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Russell S. Jenkins
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Rohit Thummalapalli
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Monika S. Kowalczyk
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Israel Canadas
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Bastian Schilling
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Adam N.R Cartwright
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Adrienne M. Luoma
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Shruti Malu
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Patrick Hwu
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Chantale Bernatchez
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Marie-Andree Forget
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - David A. Barbie
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Peter K. Sorger
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Kai W. Wucherpfennig
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Eliezer M. Van Allen
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Dirk Schadendorf
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Bruce E. Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Asaf Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Orit Rosenblatt-Rozen
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Levi A. Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Charles H. Yoon
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Benjamin Izar
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
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22
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2018; 565:E5-E6. [PMID: 30559381 DOI: 10.1038/s41586-018-0722-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Giordano Caponigro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam A Margolin
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Sage Bionetworks, 1100 Fairview Ave. N., Seattle, Washington, 98109, USA
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Christopher J Wilson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Lehár
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Gregory V Kryukov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Anupama Reddy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Manway Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Lauren Murray
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael F Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - John E Monahan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Paula Morais
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Jodi Meltzer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam Korejwa
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Judit Jané-Valbuena
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Felipa A Mapa
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Thibault
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Eva Bric-Furlong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Aaron Shipway
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Ingo H Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill Cheng
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Guoying K Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Peter Aspesi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Melanie de Silva
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Kalpana Jagtap
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Li Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Charles Hatton
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Supriya Gupta
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Scott Mahan
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Robert C Onofrio
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Wendy Winckler
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael Reich
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill P Mesirov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Stacey B Gabriel
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kristin Ardlie
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Vivien Chan
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Barbara L Weber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Markus Warmuth
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Peter Finan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jennifer L Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Todd R Golub
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Michael P Morrissey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - William R Sellers
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Robert Schlegel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA.
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA. .,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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23
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Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell 2018; 175:984-997.e24. [PMID: 30388455 PMCID: PMC6410377 DOI: 10.1016/j.cell.2018.09.006] [Citation(s) in RCA: 720] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/18/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022]
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.
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Affiliation(s)
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Mei-Ju Su
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johannes C Melms
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rachel Leeson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abhay Kanodia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaolin Mei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shu Wang
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bokang Rabasha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gao Zhang
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Claire Margolais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Benchun Miao
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tabea Moll
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Meenhard Herlyn
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Russell W Jenkins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Rohit Thummalapalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monika S Kowalczyk
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Celsius Therapeutics, Cambridge, MA, USA
| | - Israel Cañadas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bastian Schilling
- 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
| | - Adam N R Cartwright
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adrienne M Luoma
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shruti Malu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kai Wucherpfennig
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium, Essen, Germany
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- 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
| | | | - Levi A Garraway
- 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
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Brigham and Women's Hospital, Department of Surgical Oncology, Boston, MA, USA
| | - Benjamin Izar
- 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.
| | - Aviv Regev
- 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
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24
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Porter KM, Kauffman TL, Koenig BA, Lewis KL, Rehm HL, Richards CS, Strande NT, Tabor HK, Wolf SM, Yang Y, Amendola LM, Azzariti DR, Berg JS, Bergstrom K, Biesecker LG, Biswas S, Bowling KM, Chung WK, Clayton EW, Conlin LK, Cooper GM, Dulik MC, Garraway LA, Ghazani AA, Green RC, Hiatt SM, Jamal SM, Jarvik GP, Goddard KAB, Wilfond BS. Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience. Mol Genet Genomic Med 2018; 6:898-909. [PMID: 30133189 PMCID: PMC6305639 DOI: 10.1002/mgg3.453] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/23/2018] [Accepted: 06/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X‐linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed. Methods Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project‐specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects. Results The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results. Conclusion Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.
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Affiliation(s)
- Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, Seattle, Washington
| | - Tia L Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Barbara A Koenig
- Institute for Health and Aging, University of California, San Francisco, California
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch of the National Human Genome Research Institute, Bethesda, Maryland
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Partners Personalized Medicine, Boston, Massachusetts.,Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Carolyn Sue Richards
- Knight Diagnostic Laboratories and Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon
| | - Natasha T Strande
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Holly K Tabor
- Stanford Center for Biomedical Ethics, Palo Alto, California
| | - Susan M Wolf
- University of Minnesota Law School, Medical School and Consortium on Law and Values in Health, Environment & the Life Sciences, Minneapolis, Minnesota
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katie Bergstrom
- Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch of the National Human Genome Research Institute, Bethesda, Maryland
| | - Sawona Biswas
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kevin M Bowling
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University Medical Center, New York, New York
| | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Laura K Conlin
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Matthew C Dulik
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Arezou A Ghazani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robert C Green
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Partners Personalized Medicine, Boston, Massachusetts.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Susan M Hiatt
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama
| | - Seema M Jamal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington.,Department of Genome Sciences, University of Washington, Seattle, Washington
| | | | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
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25
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Sandoval GJ, Pulice JL, Pakula H, Schenone M, Takeda DY, Pop M, Boulay G, Williamson KE, McBride MJ, Pan J, St Pierre R, Hartman E, Garraway LA, Carr SA, Rivera MN, Li Z, Ronco L, Hahn WC, Kadoch C. Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. Mol Cell 2018; 71:554-566.e7. [PMID: 30078722 DOI: 10.1016/j.molcel.2018.06.040] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/04/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022]
Abstract
Chromosomal rearrangements resulting in the fusion of TMPRSS2, an androgen-regulated gene, and the ETS family transcription factor ERG occur in over half of prostate cancers. However, the mechanism by which ERG promotes oncogenic gene expression and proliferation remains incompletely understood. Here, we identify a binding interaction between ERG and the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which is conserved among other oncogenic ETS factors, including ETV1, ETV4, and ETV5. We find that ERG drives genome-wide retargeting of BAF complexes in a manner dependent on binding of ERG to the ETS DNA motif. Moreover, ERG requires intact BAF complexes for chromatin occupancy and BAF complex ATPase activity for target gene regulation. In a prostate organoid model, BAF complexes are required for ERG-mediated basal-to-luminal transition, a hallmark of ERG activity in prostate cancer. These observations suggest a fundamental interdependence between ETS transcription factors and BAF chromatin remodeling complexes in cancer.
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Affiliation(s)
- Gabriel J Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - John L Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hubert Pakula
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - David Y Takeda
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marius Pop
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gaylor Boulay
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kaylyn E Williamson
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matthew J McBride
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Chemical Biology Program, Harvard Medical School, Boston, MA, USA
| | - Joshua Pan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roodolph St Pierre
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Chemical Biology Program, Harvard Medical School, Boston, MA, USA
| | - Emily Hartman
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Miguel N Rivera
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Zhe Li
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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26
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Aguirre AJ, Nowak JA, Camarda ND, Moffitt RA, Ghazani AA, Hazar-Rethinam M, Raghavan S, Kim J, Brais LK, Ragon D, Welch MW, Reilly E, McCabe D, Marini L, Anderka K, Helvie K, Oliver N, Babic A, Da Silva A, Nadres B, Van Seventer EE, Shahzade HA, St Pierre JP, Burke KP, Clancy T, Cleary JM, Doyle LA, Jajoo K, McCleary NJ, Meyerhardt JA, Murphy JE, Ng K, Patel AK, Perez K, Rosenthal MH, Rubinson DA, Ryou M, Shapiro GI, Sicinska E, Silverman SG, Nagy RJ, Lanman RB, Knoerzer D, Welsch DJ, Yurgelun MB, Fuchs CS, Garraway LA, Getz G, Hornick JL, Johnson BE, Kulke MH, Mayer RJ, Miller JW, Shyn PB, Tuveson DA, Wagle N, Yeh JJ, Hahn WC, Corcoran RB, Carter SL, Wolpin BM. Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine. Cancer Discov 2018; 8:1096-1111. [PMID: 29903880 DOI: 10.1158/2159-8290.cd-18-0275] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/17/2018] [Accepted: 06/13/2018] [Indexed: 12/28/2022]
Abstract
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole-exome sequencing and RNA sequencing for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data. Twenty-six patients had germline and/or somatic alterations in DNA-damage repair genes, and 5 additional patients had mutational signatures of homologous recombination deficiency but no identified causal genomic alteration. Two patients had oncogenic in-frame BRAF deletions, and we report the first clinical evidence that this alteration confers sensitivity to MAPK pathway inhibition. Moreover, we identified tumor/stroma gene expression signatures with clinical relevance. Collectively, these data demonstrate the feasibility and value of real-time genomic characterization of advanced PDAC.Significance: Molecular analyses of metastatic PDAC tumors are challenging due to the heterogeneous cellular composition of biopsy specimens and rapid progression of the disease. Using an integrated multidisciplinary biopsy program, we demonstrate that real-time genomic characterization of advanced PDAC can identify clinically relevant alterations that inform management of this difficult disease. Cancer Discov; 8(9); 1096-111. ©2018 AACR.See related commentary by Collisson, p. 1062This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
- Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Nicholas D Camarda
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Richard A Moffitt
- Department of Biomedical Informatics, Department of Pathology, Stony Brook University, Stony Brook, New York
| | - Arezou A Ghazani
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Srivatsan Raghavan
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | | | | | - Emma Reilly
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Devin McCabe
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lori Marini
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Kristin Anderka
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Karla Helvie
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Nelly Oliver
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Ana Babic
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Annacarolina Da Silva
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Brandon Nadres
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | | | | | - Kelly P Burke
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Thomas Clancy
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - James M Cleary
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Leona A Doyle
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kunal Jajoo
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Nadine J McCleary
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Meyerhardt
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Janet E Murphy
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Kimmie Ng
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Anuj K Patel
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Kimberly Perez
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Michael H Rosenthal
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Douglas A Rubinson
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Marvin Ryou
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Stuart G Silverman
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rebecca J Nagy
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | | | | | - Matthew B Yurgelun
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Charles S Fuchs
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Levi A Garraway
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jason L Hornick
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Bruce E Johnson
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew H Kulke
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Robert J Mayer
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jeffrey W Miller
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Paul B Shyn
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Nikhil Wagle
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Jen Jen Yeh
- Departments of Surgery and Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Harvard Medical School, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Scott L Carter
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Brian M Wolpin
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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27
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Wander SA, Cohen O, Johnson GN, Kim D, Luo F, Mao P, Nayar U, Helvie K, Marini L, Freeman S, Getz G, Garraway LA, Winer EP, Lin NU, Wagle N. Whole exome sequencing (WES) in hormone-receptor positive (HR+) metastatic breast cancer (MBC) to identify mediators of resistance to cyclin-dependent kinase 4/6 inhibitors (CDK4/6i). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Ofir Cohen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Dewey Kim
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Flora Luo
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | |
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28
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Izar B, Jerby-Arnon L, Rotem A, Shah P, Liu D, Zhang G, Schilling B, Rozenblatt-Rosen O, Boland GM, Hodi FS, Flaherty K, Van Allen EM, Johnson BE, Schadendorf D, Yoon C, Garraway LA, Regev A. Single-cell RNA-sequencing and -imaging of melanoma ecosystems reveals sources of resistance to immune checkpoint blockade. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Asaf Rotem
- Dana-Farber Cancer Institute, Boston, MA
| | - Parin Shah
- Dana-Farber Cancer Institute, Boston, MA
| | - David Liu
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Bastian Schilling
- Department of Dermatology, University Hospital Wurzburg, Wurzburg, Germany
| | | | | | | | | | | | | | - Dirk Schadendorf
- Department of Dermatology, University of Duisburg-Essen, Essen, Germany
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29
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Abstract
Despite advances in cancer biology and therapeutics, drug resistance remains problematic. Resistance is often multifactorial, heterogeneous, and prone to undersampling. Nonetheless, many individual mechanisms of targeted therapy resistance may coalesce into a smaller number of convergences, including pathway reactivation (downstream re-engagement of original effectors), pathway bypass (recruitment of a parallel pathway converging on the same downstream output), and pathway indifference (development of a cellular state independent of the initial therapeutic target). Similar convergences may also underpin immunotherapy resistance. Such parsimonious, convergence-based frameworks may help explain resistance across tumor types and therapeutic categories and may also suggest strategies to overcome it.
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30
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Cascone T, McKenzie JA, Mbofung RM, Punt S, Wang Z, Xu C, Williams LJ, Wang Z, Bristow CA, Carugo A, Peoples MD, Li L, Karpinets T, Huang L, Malu S, Creasy C, Leahey SE, Chen J, Chen Y, Pelicano H, Bernatchez C, Gopal YNV, Heffernan TP, Hu J, Wang J, Amaria RN, Garraway LA, Huang P, Yang P, Wistuba II, Woodman SE, Roszik J, Davis RE, Davies MA, Heymach JV, Hwu P, Peng W. Increased Tumor Glycolysis Characterizes Immune Resistance to Adoptive T Cell Therapy. Cell Metab 2018; 27:977-987.e4. [PMID: 29628419 PMCID: PMC5932208 DOI: 10.1016/j.cmet.2018.02.024] [Citation(s) in RCA: 353] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 01/10/2018] [Accepted: 02/27/2018] [Indexed: 12/18/2022]
Abstract
Adoptive T cell therapy (ACT) produces durable responses in some cancer patients; however, most tumors are refractory to ACT and the molecular mechanisms underlying resistance are unclear. Using two independent approaches, we identified tumor glycolysis as a pathway associated with immune resistance in melanoma. Glycolysis-related genes were upregulated in melanoma and lung cancer patient samples poorly infiltrated by T cells. Overexpression of glycolysis-related molecules impaired T cell killing of tumor cells, whereas inhibition of glycolysis enhanced T cell-mediated antitumor immunity in vitro and in vivo. Moreover, glycolysis-related gene expression was higher in melanoma tissues from ACT-refractory patients, and tumor cells derived from these patients exhibited higher glycolytic activity. We identified reduced levels of IRF1 and CXCL10 immunostimulatory molecules in highly glycolytic melanoma cells. Our findings demonstrate that tumor glycolysis is associated with the efficacy of ACT and identify the glycolysis pathway as a candidate target for combinatorial therapeutic intervention.
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Affiliation(s)
- Tina Cascone
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rina M Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simone Punt
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhe Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leila J Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhiqiang Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher A Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alessandro Carugo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael D Peoples
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lerong Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lu Huang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara E Leahey
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiong Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuan Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Pelicano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peiying Yang
- Department of Palliative, Rehabilitation and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - R Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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31
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Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. The long tail of oncogenic drivers in prostate cancer. Nat Genet 2018; 50:645-651. [PMID: 29610475 PMCID: PMC6107367 DOI: 10.1038/s41588-018-0078-z] [Citation(s) in RCA: 523] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/26/2018] [Indexed: 01/05/2023]
Abstract
Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway. We find that the incidence of significantly mutated genes (SMGs) follows a long-tail distribution, with many genes mutated in less than 3% of cases. We identify a total of 97 SMGs, including 70 not previously implicated in prostate cancer, such as the ubiquitin ligase CUL3 and the transcription factor SPEN. Finally, comparing primary and metastatic prostate cancer identifies a set of genomic markers that may inform risk stratification.
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Affiliation(s)
- Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie A M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Celine Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christopher E Barbieri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zafeiris Zafeiriou
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Susana Miranda
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Tolonen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Johann S de Bono
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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32
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Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell 2018; 173:624-633.e8. [PMID: 29656892 DOI: 10.1016/j.cell.2018.03.026] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 12/11/2017] [Accepted: 03/13/2018] [Indexed: 02/07/2023]
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.
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Affiliation(s)
- Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Pavan Bachireddy
- 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
| | - Bastian Schilling
- 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
| | | | - Qian Zhan
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Clyde Bango
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Rupert Langer
- Department of Pathology, University of Bern, 3012 Bern, Switzerland
| | - Patrick C Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel Gusenleitner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Derin B Keskin
- 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
| | | | | | | | - Kendell Clement
- Broad Institute, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zachary J Cartun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Eliezer M Van Allen
- 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
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Ying Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alexandra Snyder
- Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA
| | - Taha Merghoub
- Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA
| | - Jedd D Wolchok
- Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA
| | - Levi A Garraway
- 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
| | - Alexander Meissner
- 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
| | - Jeffrey S Weber
- New York University Langone Medical Center, New York, NY 10016, USA
| | | | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Patrick R Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - George F Murphy
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christine G Lian
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany; German Cancer Consortium (DKTK), 69121 Heidelberg, Germany
| | - F Stephen Hodi
- 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
| | - Catherine J Wu
- 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.
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33
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Hamada T, Soong TR, Masugi Y, Kosumi K, Nowak JA, da Silva A, Mu XJ, Twombly TS, Koh H, Yang J, Song M, Liu L, Gu M, Shi Y, Nosho K, Morikawa T, Inamura K, Shukla SA, Wu CJ, Garraway LA, Zhang X, Wu K, Meyerhardt JA, Chan AT, Glickman JN, Rodig SJ, Freeman GJ, Fuchs CS, Nishihara R, Giannakis M, Ogino S. TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas. Oncoimmunology 2018; 7:e1442999. [PMID: 29900052 DOI: 10.1080/2162402x.2018.1442999] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/13/2018] [Accepted: 02/15/2018] [Indexed: 12/23/2022] Open
Abstract
Inhibitors targeting the PDCD1 (programmed cell death 1, PD-1) immune checkpoint pathway have revolutionized cancer treatment strategies. The TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PDCD1 ligand 1, PD-L1) expression and tumor-infiltrating lymphocytes (TIL) has been proposed to predict response to immunotherapy. It remains to be determined clinical, pathological, and molecular features of TIME subtypes of colorectal cancer. Using 812 colon and rectal carcinoma cases from the Nurses' Health Study and Health Professionals Follow-up Study, we examined the association of tumor characteristics and survival outcomes with four TIME subtypes (TIME 1, CD274low/TILabsent; TIME 2, CD274high/TILpresent; TIME 3, CD274low/TILpresent; and TIME 4, CD274high/TILabsent). In survival analyses, Cox proportional hazards models were adjusted for potential confounders, including microsatellite instability (MSI) status, CpG island methylator phenotype (CIMP) status, LINE-1 methylation level, and KRAS, BRAF, and PIK3CA mutation status. TIME subtypes 1, 2, 3 and 4 had 218 (27%), 117 (14%), 103 (13%), and 374 (46%) colorectal cancer cases, respectively. Compared with TIL-absent subtypes (TIME 1 and 4), TIL-present subtypes (TIME 2 and 3) were associated with high-level MSI, high-degree CIMP, BRAF mutation, and higher amounts of neoantigens (p < 0.001). TIME subtypes were not significantly associated with colorectal cancer-specific or overall survival. In conclusion, TIL-present TIME subtypes of colorectal cancer are associated with high levels of MSI and neoantigen load, supporting better responsiveness to cancer immunotherapy. Further studies examining tumor molecular alterations and additional factors in the tumor microenvironment may inform development of immunoprevention and immunotherapy strategies.
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Affiliation(s)
- Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Thing Rinda Soong
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yohei Masugi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Keisuke Kosumi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Annacarolina da Silva
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Xinmeng Jasmine Mu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler S Twombly
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Hideo Koh
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Juhong Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Hormone and Development, Ministry of Health, Metabolic Disease Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, P.R. China
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Li Liu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Huazhong University of Science and Technology, Hubei, P.R. China
| | - Mancang Gu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,College of Pharmacy, Zhejiang Chinese Medical University, Zhejiang, P.R. China
| | - Yan Shi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Chinese PLA General Hospital, Beijing, P.R. China
| | - Katsuhiko Nosho
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Teppei Morikawa
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Inamura
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan N Glickman
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Scott J Rodig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles S Fuchs
- Yale Cancer Center, New Haven, CT, USA.,Department of Medicine, Yale School of Medicine, New Haven, CT, USA.,Smilow Cancer Hospital, New Haven, CT, USA
| | - Reiko Nishihara
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shuji Ogino
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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34
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Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov 2018; 8:730-749. [PMID: 29510987 DOI: 10.1158/2159-8290.cd-17-1327] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/13/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
To understand the genetic drivers of immune recognition and evasion in colorectal cancer, we analyzed 1,211 colorectal cancer primary tumor samples, including 179 classified as microsatellite instability-high (MSI-high). This set includes The Cancer Genome Atlas colorectal cancer cohort of 592 samples, completed and analyzed here. MSI-high, a hypermutated, immunogenic subtype of colorectal cancer, had a high rate of significantly mutated genes in important immune-modulating pathways and in the antigen presentation machinery, including biallelic losses of B2M and HLA genes due to copy-number alterations and copy-neutral loss of heterozygosity. WNT/β-catenin signaling genes were significantly mutated in all colorectal cancer subtypes, and activated WNT/β-catenin signaling was correlated with the absence of T-cell infiltration. This large-scale genomic analysis of colorectal cancer demonstrates that MSI-high cases frequently undergo an immunoediting process that provides them with genetic events allowing immune escape despite high mutational load and frequent lymphocytic infiltration and, furthermore, that colorectal cancer tumors have genetic and methylation events associated with activated WNT signaling and T-cell exclusion.Significance: This multi-omic analysis of 1,211 colorectal cancer primary tumors reveals that it should be possible to better monitor resistance in the 15% of cases that respond to immune blockade therapy and also to use WNT signaling inhibitors to reverse immune exclusion in the 85% of cases that currently do not. Cancer Discov; 8(6); 730-49. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 663.
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Affiliation(s)
- Catherine S Grasso
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California. .,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xinmeng Jasmine Mu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael Quist
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Reiko Nishihara
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Zhi Rong Qian
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kentaro Inamura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Teppei Morikawa
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Katsuhiko Nosho
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Gabriel Abril-Rodriguez
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Charles Connolly
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Helena Escuin-Ordinas
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Milan S Geybels
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Siwen Hu-Lieskovan
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Yeon Joo Kim
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Paige Krystofinski
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Mark D M Leiserson
- Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Dennis J Montoya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California
| | - Brian B Nadel
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Cristina Puig-Saus
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Elleanor H Quist
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Ben J Raphael
- Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Daniel Sanghoon Shin
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Statistics, Iowa State University, Ames, Iowa
| | - Janet L Stanford
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jennifer Tsoi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California
| | - Alexander Upfill-Brown
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Jesse M Zaretsky
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.,AbbVie Inc., Redwood City, California
| | - Charles S Fuchs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Yale Cancer Center, New Haven, Connecticut.,Department of Medicine, Yale School of Medicine, New Haven, Connecticut.,Smilow Cancer Hospital, New Haven, Connecticut
| | - Antoni Ribas
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, and the Jonsson Comprehensive Cancer Center, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
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35
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Liu D, Abbosh P, Keliher D, Reardon B, Miao D, Mouw K, Weiner-Taylor A, Wankowicz S, Han G, Teo MY, Cipolla C, Kim J, Iyer G, Al-Ahmadie H, Dulaimi E, Chen DYT, Alpaugh RK, Hoffman-Censits J, Garraway LA, Getz G, Carter SL, Bellmunt J, Plimack ER, Rosenberg JE, Van Allen EM. Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer. Nat Commun 2017; 8:2193. [PMID: 29259186 PMCID: PMC5736752 DOI: 10.1038/s41467-017-02320-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022] Open
Abstract
Despite continued widespread use, the genomic effects of cisplatin-based chemotherapy and implications for subsequent treatment are incompletely characterized. Here, we analyze whole exome sequencing of matched pre- and post-neoadjuvant cisplatin-based chemotherapy primary bladder tumor samples from 30 muscle-invasive bladder cancer patients. We observe no overall increase in tumor mutational burden post-chemotherapy, though a significant proportion of subclonal mutations are unique to the matched pre- or post-treatment tumor, suggesting chemotherapy-induced and/or spatial heterogeneity. We subsequently identify and validate a novel mutational signature in post-treatment tumors consistent with known characteristics of cisplatin damage and repair. We find that post-treatment tumor heterogeneity predicts worse overall survival, and further observe alterations in cell-cycle and immune checkpoint regulation genes in post-treatment tumors. These results provide insight into the clinical and genomic dynamics of tumor evolution with cisplatin-based chemotherapy, suggest mechanisms of clinical resistance, and inform development of clinically relevant biomarkers and trials of combination therapies. The impact of cisplatin-based chemotherapy on tumor genomes is complex. Here, the authors study matched pre- and post-chemotherapy primary samples in muscle-invasive bladder cancer, finding a cisplatin-based mutational signature, and highlighting the impact of intratumor heterogeneity on survival.
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Affiliation(s)
- David Liu
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Philip Abbosh
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Daniel Keliher
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Brendan Reardon
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Diana Miao
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Kent Mouw
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Stephanie Wankowicz
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Garam Han
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Min Yuen Teo
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Jaegil Kim
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Gopa Iyer
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Essel Dulaimi
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | | | - Levi A Garraway
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Scott L Carter
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joaquim Bellmunt
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | | | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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36
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Brenan L, Andreev A, Cohen O, Pantel S, Kamburov A, Cacchiarelli D, Persky NS, Zhu C, Bagul M, Goetz EM, Burgin AB, Garraway LA, Getz G, Mikkelsen TS, Piccioni F, Root DE, Johannessen CM. Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants. Cell Rep 2017; 17:1171-1183. [PMID: 27760319 DOI: 10.1016/j.celrep.2016.09.061] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/01/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022] Open
Abstract
Tumor-specific genomic information has the potential to guide therapeutic strategies and revolutionize patient treatment. Currently, this approach is limited by an abundance of disease-associated mutants whose biological functions and impacts on therapeutic response are uncharacterized. To begin to address this limitation, we functionally characterized nearly all (99.84%) missense mutants of MAPK1/ERK2, an essential effector of oncogenic RAS and RAF. Using this approach, we discovered rare gain- and loss-of-function ERK2 mutants found in human tumors, revealing that, in the context of this assay, mutational frequency alone cannot identify all functionally impactful mutants. Gain-of-function ERK2 mutants induced variable responses to RAF-, MEK-, and ERK-directed therapies, providing a reference for future treatment decisions. Tumor-associated mutations spatially clustered in two ERK2 effector-recruitment domains yet produced mutants with opposite phenotypes. This approach articulates an allele-characterization framework that can be scaled to meet the goals of genome-guided oncology.
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Affiliation(s)
- Lisa Brenan
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ofir Cohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sasha Pantel
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Atanas Kamburov
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Davide Cacchiarelli
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nicole S Persky
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cong Zhu
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mukta Bagul
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eva M Goetz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alex B Burgin
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - David E Root
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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37
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Jenkins RW, Aref AR, Lizotte PH, Ivanova E, Stinson S, Zhou CW, Bowden M, Deng J, Liu H, Miao D, He MX, Walker W, Zhang G, Tian T, Cheng C, Wei Z, Palakurthi S, Bittinger M, Vitzthum H, Kim JW, Merlino A, Quinn M, Venkataramani C, Kaplan JA, Portell A, Gokhale PC, Phillips B, Smart A, Rotem A, Jones RE, Keogh L, Anguiano M, Stapleton L, Jia Z, Barzily-Rokni M, Cañadas I, Thai TC, Hammond MR, Vlahos R, Wang ES, Zhang H, Li S, Hanna GJ, Huang W, Hoang MP, Piris A, Eliane JP, Stemmer-Rachamimov AO, Cameron L, Su MJ, Shah P, Izar B, Thakuria M, LeBoeuf NR, Rabinowits G, Gunda V, Parangi S, Cleary JM, Miller BC, Kitajima S, Thummalapalli R, Miao B, Barbie TU, Sivathanu V, Wong J, Richards WG, Bueno R, Yoon CH, Miret J, Herlyn M, Garraway LA, Van Allen EM, Freeman GJ, Kirschmeier PT, Lorch JH, Ott PA, Hodi FS, Flaherty KT, Kamm RD, Boland GM, Wong KK, Dornan D, Paweletz CP, Barbie DA. Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids. Cancer Discov 2017; 8:196-215. [PMID: 29101162 DOI: 10.1158/2159-8290.cd-17-0833] [Citation(s) in RCA: 326] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022]
Abstract
Ex vivo systems that incorporate features of the tumor microenvironment and model the dynamic response to immune checkpoint blockade (ICB) may facilitate efforts in precision immuno-oncology and the development of effective combination therapies. Here, we demonstrate the ability to interrogate ex vivo response to ICB using murine- and patient-derived organotypic tumor spheroids (MDOTS/PDOTS). MDOTS/PDOTS isolated from mouse and human tumors retain autologous lymphoid and myeloid cell populations and respond to ICB in short-term three-dimensional microfluidic culture. Response and resistance to ICB was recapitulated using MDOTS derived from established immunocompetent mouse tumor models. MDOTS profiling demonstrated that TBK1/IKKε inhibition enhanced response to PD-1 blockade, which effectively predicted tumor response in vivo Systematic profiling of secreted cytokines in PDOTS captured key features associated with response and resistance to PD-1 blockade. Thus, MDOTS/PDOTS profiling represents a novel platform to evaluate ICB using established murine models as well as clinically relevant patient specimens.Significance: Resistance to PD-1 blockade remains a challenge for many patients, and biomarkers to guide treatment are lacking. Here, we demonstrate feasibility of ex vivo profiling of PD-1 blockade to interrogate the tumor immune microenvironment, develop therapeutic combinations, and facilitate precision immuno-oncology efforts. Cancer Discov; 8(2); 196-215. ©2017 AACR.See related commentary by Balko and Sosman, p. 143See related article by Deng et al., p. 216This article is highlighted in the In This Issue feature, p. 127.
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Affiliation(s)
- Russell W Jenkins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Amir R Aref
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick H Lizotte
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elena Ivanova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Chensheng W Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jiehui Deng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hongye Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Meng Xiao He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Graduate Program in Biophysics, Boston, Massachusetts
| | - William Walker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gao Zhang
- Melanoma Research Center and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Tian Tian
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Chaoran Cheng
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Sangeetha Palakurthi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark Bittinger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hans Vitzthum
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jong Wook Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ashley Merlino
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Max Quinn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Andrew Portell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prafulla C Gokhale
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Alicia Smart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert E Jones
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren Keogh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Maria Anguiano
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | | | - Michal Barzily-Rokni
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Israel Cañadas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marc R Hammond
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Raven Vlahos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eric S Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hua Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shuai Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Glenn J Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wei Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adriano Piris
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Jean-Pierre Eliane
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anat O Stemmer-Rachamimov
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lisa Cameron
- Confocal and Light Microscopy Core Facility, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mei-Ju Su
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Manisha Thakuria
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nicole R LeBoeuf
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Guilherme Rabinowits
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Viswanath Gunda
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sareh Parangi
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian C Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rohit Thummalapalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benchun Miao
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Thanh U Barbie
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vivek Sivathanu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Joshua Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William G Richards
- Division of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charles H Yoon
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Juan Miret
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Meenhard Herlyn
- Melanoma Research Center and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paul T Kirschmeier
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jochen H Lorch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keith T Flaherty
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Roger D Kamm
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Cloud Peter Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Fay AP, de Velasco G, Ho TH, Van Allen EM, Murray B, Albiges L, Signoretti S, Hakimi AA, Stanton ML, Bellmunt J, McDermott DF, Atkins MB, Garraway LA, Kwiatkowski DJ, Choueiri TK. Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma. J Natl Compr Canc Netw 2017; 14:820-4. [PMID: 27407122 DOI: 10.6004/jnccn.2016.0086] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/21/2016] [Indexed: 12/24/2022]
Abstract
Advances in next-generation sequencing have provided a unique opportunity to understand the biology of disease and mechanisms of sensitivity or resistance to specific agents. Renal cell carcinoma (RCC) is a heterogeneous disease and highly variable clinical responses have been observed with vascular endothelial growth factor (VEGF)-targeted therapy (VEGF-TT). We hypothesized that whole-exome sequencing analysis might identify genotypes associated with extreme response or resistance to VEGF-TT in metastatic (mRCC). Patients with mRCC who had received first-line sunitinib or pazopanib and were in 2 extreme phenotypes of response were identified. Extreme responders (ERs) were defined as those with partial response or complete response for 3 or more years (n=13) and primary refractory patients (PRPs) were defined as those with progressive disease within the first 3 months of therapy (n=14). International Metastatic RCC Database Consortium prognostic scores were not significantly different between the groups (P=.67). Considering the genes known to be mutated in RCC at significant frequency, PBRM1 mutations were identified in 7 ERs (54%) versus 1 PRP (7%) (P=.01). In addition, mutations in TP53 (n=4) were found only in PRPs (P=.09). Our data suggest that mutations in some genes in RCC may impact response to VEGF-TT.
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Affiliation(s)
- Andre P Fay
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Guillermo de Velasco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Thai H Ho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Boston, Massachusetts
| | - Bradley Murray
- Broad Institute of MIT and Harvard, Cambridge, Boston, Massachusetts
| | - Laurence Albiges
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - A Ari Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa L Stanton
- Department of Laboratory Medicine/Pathology, Mayo Clinic, Scottsdale, Arizona
| | - Joaquim Bellmunt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David F McDermott
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michael B Atkins
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts,Department of Medical Oncology, Georgetown-Lombardi Comprehensive Cancer Center, Washington, DC
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Boston, Massachusetts
| | | | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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39
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Hong AL, Tseng YY, Kynnap BD, Doshi MB, Sandoval G, Oh C, Sayeed A, Shubhroz G, Church AJ, Keskula P, Peng A, Clemons PA, Tsherniak A, Vazquez F, Rodriguez-Galindo C, Janeway KA, Garraway LA, Schreiber SL, Root DE, Mullen E, Stegmaier K, Kadoch C, Roberts CW, Boehm JS, Hahn WC. Abstract B17: Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-b17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Renal medullary carcinoma is a rare kidney cancer that is primarily seen in adolescent and young adult African American patients with sickle cell trait. Prognosis is poor and treatment options are limited. We have developed several cell line models that recapitulate the primary and relapsed metastatic samples from a patient who succumbed to this disease. We have confirmed by whole exome sequencing that our models have sickle cell trait and loss of heterozygosity of the SMARCB1 loci, both hallmarks of this disease. By RNA-sequencing, we see a lack of SMARCB1 transcription. We have further shown dependency of our models to SMARCB1 re-expression thus suggesting that this cancer is indeed driven by loss of SMARCB1 at a functional level. We performed pooled CRISPR-Cas9 and RNAi loss of function screens and a small molecule screen focused on druggable cancer targets based on our previous work in parallel to a genome-wide pooled CRISPR-Cas9 loss of function screen. Integrating these complementary and orthogonal methods, we identified a number of targets for further validation. These targets, when combined may provide a rational approach to therapeutic targeting for this rare kidney cancer.
Citation Format: Andrew L. Hong, Yuen-Yi Tseng, Bryan D. Kynnap, Mihir B. Doshi, Gabriel Sandoval, Coyin Oh, Abeer Sayeed, Gill Shubhroz, Alanna J. Church, Paula Keskula, Anson Peng, Paul A. Clemons, Aviad Tsherniak, Francisca Vazquez, Carlos Rodriguez-Galindo, Katherine A. Janeway, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Elizabeth Mullen, Kimberly Stegmaier, Cigall Kadoch, Charles W.M. Roberts, Jesse S. Boehm, William C. Hahn. Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B17.
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Affiliation(s)
| | | | | | | | | | - Coyin Oh
- 2Broad Institute, Cambridge, MA,
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Garraway LA, Sorger PK. Abstract PR17: Single-cell analysis reveals an adaptive, slowly-dividing, de-differentiated, drug-resistant cell state selectively inhibitable by drug combinations. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-pr17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Partial responsiveness of tumor cells due to drug adaptation (or tolerance) during the early phase of treatment with targeted therapeutics seems to be essential for creating a population of viable tumor cells from which resistant clones eventually arise. Thus, understanding transient drug adaptation is likely to be important for both improving the initial effectiveness of treatment and delaying or controlling acquired resistance. Despite the wealth of information available about the molecular events and feedback mechanisms leading to drug tolerance or adaptation, most of our knowledge in this area comes from studying drug response in bulk tumor cell populations. Furthermore, the phenotypic consequences of drug adaptation have been studied most frequently at a few fixed time-points, when drug-adapted cells exhibit a high population-average activity in multiple pro-growth or pro-survival signaling cascades. Therefore, it remains unclear how uniform or heterogeneous the early drug adaptation is across individual cells within a tumor cell population, and how the fate of drug-adapted cells is determined by a diversity of early drug-induced adaptive signaling responses. Uncovering the evolution of biochemical and phenotypic heterogeneity in drug-adapted cell populations is key to designing optimal combinations of drugs to overcome resistance and to achieve durable therapy.
In this study, we monitor the responses of BRAFV600E melanoma cells to RAF/MEK inhibitors at the single-cell level in real time using time-lapse live-cell imaging, and then analyze the resulting cell states using transcriptional, biochemical and phenotypic profiling. We found that exposure of tumor cells to RAF/MEK inhibitors elicits heterogeneous and time-variable responses in which some cells die, some arrest and a fraction of slowly-cycling cells adapts to drug, adopting a reversible drug-resistance phenotype characterized by up-regulation of markers of neural crest, a melanocyte precursor, including NGFR (the low affinity nerve growth factor receptor, also known as p75NTR or CD271). The slowly-cycling NFGRHigh state induced by RAF/MEK inhibitors is only transiently stable: after 1-2 weeks of outgrowth in drug-free medium, such cells reset to their initial state as measured by the restoration of RAF/MEK inhibitor sensitivity, accelerated rate of cell division and reduced expression of NGFR. Transcriptional and biochemical profiling of cell lines and human tumors implicates a role for the c-Jun/ECM/FAK/Src cascade in driving the de-differentiated (NGFRHigh) resistance program. We identify multiple drugs targeting this cascade as well as BET bromodomain inhibitors that block the slowly-cycling NGFRHigh state in cell lines and in a BRAFV600E melanoma xenograft model and increase sensitivity to RAF/MEK inhibitors. Our study reveals directly how drug adaptation happens in individual tumor cells leading to emergence of heterogeneous cell sub-populations with reduced drug-sensitivity that may be selectively targeted by drug combinations.
Citation Format: Mohammad Fallahi-Sichani, Verena Becker, Benjamin Izar, Gregory J. Baker, Jia-Ren Lin, Sarah A. Boswell, Levi A. Garraway, Peter K. Sorger. Single-cell analysis reveals an adaptive, slowly-dividing, de-differentiated, drug-resistant cell state selectively inhibitable by drug combinations [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR17.
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41
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Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA. Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov 2017; 7:973-983. [PMID: 28515055 PMCID: PMC5836784 DOI: 10.1158/2159-8290.cd-16-0960] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 02/22/2017] [Accepted: 05/04/2017] [Indexed: 12/25/2022]
Abstract
African-American men have the highest incidence of and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n = 102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3% to 5% of lethal castration-resistant prostate cancers. Knockdown of ERF confers increased anchorage-independent growth and generates a gene expression signature associated with oncogenic ETS activation and androgen signaling. Together, these results suggest that ERF is a prostate cancer tumor-suppressor gene. More generally, our findings support the application of systematic cancer genomic characterization in settings of broader ancestral diversity to enhance discovery and, eventually, therapeutic applications.Significance: Systematic genomic sequencing of prostate cancer in African-American men revealed new insights into prostate cancer, including the identification of ERF as a prostate cancer gene; somatic copy-number alteration differences; and uncommon PIK3CA and PTEN alterations. This study highlights the importance of inclusion of underrepresented minorities in cancer sequencing studies. Cancer Discov; 7(9); 973-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 920.
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Affiliation(s)
- Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian, New York, New York
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Andrea Garofalo
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Coyin Oh
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Maria Baco
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ali Amin-Mansour
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Bokang Rabasha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Samira Bahl
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Stephanie A Mullane
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Brian D Robinson
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian, New York, New York
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Saud Aldubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Francesca Khani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Beerinder Karir
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian, New York, New York
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Eejung Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jeremy Chimene-Weiss
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matan Hofree
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Joseph R Osborne
- Centre for Integrative Biology, University of Trento, Trento, Italy
- Department of Radiology, Weill Cornell Medicine, New York, New York
| | - Jong Wook Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gissou Azabdaftari
- Department of Pathology, Roswell Park Cancer Institute, Roswell Park, New York
| | - Anna Woloszynska-Read
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Roswell Park, New York
| | - Karen Sfanos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angelo M De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Francesca Demichelis
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian, New York, New York
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Stacey Gabriel
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jill Mesirov
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Medicine, University of California, San Diego, La Jolla, California
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Pablo Tamayo
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Medicine, University of California, San Diego, La Jolla, California
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Mark A Rubin
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian, New York, New York.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, New York
| | - Isaac J Powell
- Barbara Ann Karmanos Cancer Institute, Detroit, Michigan.
- Department of Urology, Wayne State University School of Medicine, Detroit, Michigan
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cancer Program, the Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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42
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Janouskova H, El Tekle G, Bellini E, Udeshi ND, Rinaldi A, Ulbricht A, Bernasocchi T, Civenni G, Losa M, Svinkina T, Bielski CM, Kryukov GV, Cascione L, Napoli S, Enchev RI, Mutch DG, Carney ME, Berchuck A, Winterhoff BJN, Broaddus RR, Schraml P, Moch H, Bertoni F, Catapano CV, Peter M, Carr SA, Garraway LA, Wild PJ, Theurillat JPP. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med 2017; 23:1046-1054. [PMID: 28805821 PMCID: PMC5592092 DOI: 10.1038/nm.4372] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations in the substrate recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancer. Their therapeutic implications remain incompletely understood. Here, we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer-specific SPOP mutants impaired degradation of BETs, promoting resistance against their pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations within the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat endometrial but not prostate cancer patients with SPOP mutations.
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Affiliation(s)
- Hana Janouskova
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Geniver El Tekle
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Elisa Bellini
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Namrata D Udeshi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anna Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Anna Ulbricht
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Tiziano Bernasocchi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Gianluca Civenni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Marco Losa
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Tanya Svinkina
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Craig M Bielski
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Luciano Cascione
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Radoslav I Enchev
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - David G Mutch
- Division of Gynecologic Oncology, Washington University, St. Louis, Missouri, USA
| | - Michael E Carney
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Duke Cancer Center, Durham, North Carolina, USA
| | - Boris J N Winterhoff
- Division of Gynecologic Oncology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Russell R Broaddus
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Matthias Peter
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Steven A Carr
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE, Golub TR, Boehm JS, Hahn WC. Defining a Cancer Dependency Map. Cell 2017; 170:564-576.e16. [PMID: 28753430 DOI: 10.1016/j.cell.2017.06.010] [Citation(s) in RCA: 1383] [Impact Index Per Article: 197.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/09/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
Most human epithelial tumors harbor numerous alterations, making it difficult to predict which genes are required for tumor survival. To systematically identify cancer dependencies, we analyzed 501 genome-scale loss-of-function screens performed in diverse human cancer cell lines. We developed DEMETER, an analytical framework that segregates on- from off-target effects of RNAi. 769 genes were differentially required in subsets of these cell lines at a threshold of six SDs from the mean. We found predictive models for 426 dependencies (55%) by nonlinear regression modeling considering 66,646 molecular features. Many dependencies fall into a limited number of classes, and unexpectedly, in 82% of models, the top biomarkers were expression based. We demonstrated the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC. Together, these observations provide a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
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Affiliation(s)
- Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Phil G Montgomery
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Gregory Kryukov
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Stanley Gill
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | | | - Sasha Pantel
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | | | - Robin M Meyers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Levi Ali
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Guozhi Jiang
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Jessica Hsiao
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | | | - Sara Howell
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Erin Merkel
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA.
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Garraway LA, Sorger PK. Abstract 5561: Single-cell analysis reveals an adaptive, transiently heritable, slowly-dividing, drug-resistant state inhibitable by drug combinations. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adaptation and fractional response of tumor cells to targeted inhibitors of oncogenic pathways creates a population of viable tumor cells from which fully resistant clones can ultimately arise. Thus, understanding transient drug adaptation is key for both improving the effectiveness of treatment and delaying/controlling acquired resistance. Despite the wealth of information available about feedback mechanisms associated with adaptive resistance, most of our knowledge in this area comes from studying drug response in bulk tumor cell populations. Furthermore, the phenotypic consequences of drug adaptation have been often studied at a few fixed time-points, when drug-adapted cells exhibit a high population-average activity in multiple pro-growth signaling cascades. It therefore remains unclear how the initial responses to drug relate to subsequent phenotypes such as cell death or adaptation. This is likely a key point for designing novel approaches to overcome fractional drug response in tumor cells and to achieve durable therapy.
We use real-time live-cell imaging, single-cell analysis and molecular profiling to show that exposure of BRAFV600E melanoma cells to RAF/MEK inhibitors elicits a time-variable and 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. The drug-induced slowly-cycling NFGRHigh state is only transiently stable, reverting to the drug-naïve state within two weeks of drug withdrawal as measured by the restoration of RAF/MEK inhibitor sensitivity, accelerated rate of cell division and reduced expression of NGFR. Transcriptional and biochemical profiling of cell lines and human tumors implicates a role for the c-Jun/ECM/FAK/Src cascade in driving the de-differentiated resistance program. We identify multiple drugs targeting this cascade as well as BET bromodomain inhibitors that block this resistance program in cell lines and in a BRAFV600E melanoma xenograft model and increase sensitivity and maximal effect (Emax) of RAF/MEK inhibitors. Our study reveals directly how drug adaptation happens in individual tumor cells leading to emergence of heterogeneous cell sub-populations with reduced drug-sensitivity that may be targeted by drug combinations.
Citation Format: Mohammad Fallahi-Sichani, Verena Becker, Benjamin Izar, Gregory J. Baker, Jia-Ren Lin, Sarah A. Boswell, Levi A. Garraway, Peter K. Sorger. Single-cell analysis reveals an adaptive, transiently heritable, slowly-dividing, drug-resistant state inhibitable by drug combinations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5561. doi:10.1158/1538-7445.AM2017-5561
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Smart AC, Margolis C, Miao D, Liu D, Park J, He MX, Reardon B, Mullane S, Schilling B, Garraway LA, Schadendorf D, Allen EMV. Abstract 5647: Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Development of immune checkpoint inhibitors has substantially improved outcomes in patients diagnosed with metastatic melanoma. However, only a minority of patients treated experience long-term clinical benefit, and clinicians have limited ability to predict which patients will respond. Recent studies have demonstrated that the burden of tumor neoantigens generated by expressed somatic mutations is predictive of response to immunotherapy. Intron retention, which is widespread in cancer transcriptomes, represents a putative source of tumor neoantigens by generating peptides that are available for presentation through the MHC I pathway.
Methods: We developed a neoantigen prediction pipeline to identify patient-specific neoantigens from transcriptome sequencing data, which enables identification of retained intron neoantigens from clinical cohorts receiving checkpoint inhibitor therapy. This pipeline incorporates published methods for detecting intron retention events from transcriptome data, detects open reading frames that extend from normal transcripts into intronic sequences, and identifies neoepitopes predicted as strong binders based on the patient’s HLA molecules. We applied this pipeline to a cohort of 41 melanoma patients receiving checkpoint inhibitor therapy and classified patient outcomes as receiving clinical benefit (CB) (n=14), no clinical benefit (NCB) (n=22), or long-term survival without clinical benefit (LS) (n=5).
Results: Our initial analysis identified a mean retained intron neoantigen burden of 7709 per sample, without significant difference between response groups. In one patient who derived clinical benefit from checkpoint inhibition, neoantigen load from nonsynonymous mutations was low (407, 0.34 standard deviations (SD) below a mean of 1,015 among CB patients), while retained intron neoantigen load was high (14579, 1.7 SDs above a mean of 7517 among CB patients), suggesting that retained intron neoantigen load may explain response in some patients with low mutational burden. Preliminary analysis of specific neoantigens suggests that a retained intron in ZNF880 identified in patients expressing HLA-A01:01 is present in 6 of 6 patients experiencing clinical benefit, but only 2 of 7 patients not experiencing clinical benefit. The same analysis was performed on two additional cohorts of melanoma tumor samples to assess whether a larger sample size could aid in the identification of recurrent neoepitopes generated by retained introns.
Conclusions: Application of this approach to data from patients receiving checkpoint blockade with selective response identifies response-associated neoantigens that may warrant further investigation. Identification of a novel source of neoantigens associated with immunotherapy response will provide valuable prognostic information to patients and inform the development of next generation immunotherapeutics.
Citation Format: Alicia C. Smart, Claire Margolis, Diana Miao, David Liu, Jihye Park, Meng Xiao He, Brendan Reardon, Stephanie Mullane, Bastian Schilling, Levi A. Garraway, Dirk Schadendorf, Eliezer M. Van Allen. Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5647. doi:10.1158/1538-7445.AM2017-5647
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Affiliation(s)
| | | | - Diana Miao
- 1Dana Farber Cancer Institute, Boston, MA
| | - David Liu
- 1Dana Farber Cancer Institute, Boston, MA
| | - Jihye Park
- 1Dana Farber Cancer Institute, Boston, MA
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46
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Sun Y, Alberta JA, Pilarz C, Calligaris D, Chadwick EJ, Ramkissoon SH, Ramkissoon LA, Garcia VM, Mazzola E, Goumnerova L, Kane M, Yao Z, Kieran MW, Ligon KL, Hahn WC, Garraway LA, Rosen N, Gray NS, Agar NY, Buhrlage SJ, Segal RA, Stiles CD. A brain-penetrant RAF dimer antagonist for the noncanonical BRAF oncoprotein of pediatric low-grade astrocytomas. Neuro Oncol 2017; 19:774-785. [PMID: 28082416 PMCID: PMC5464455 DOI: 10.1093/neuonc/now261] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Activating mutations or structural rearrangements in BRAF are identified in roughly 75% of all pediatric low-grade astrocytomas (PLGAs). However, first-generation RAF inhibitors approved for adult melanoma have poor blood-brain penetrance and are only effective on tumors that express the canonical BRAFV600E oncoprotein, which functions as a monomer. These drugs (type I antagonists that target the "DFG-in" conformation of the kinase) fail to block signaling via KIAA1549:BRAF, a truncation/fusion BRAF oncoprotein which functions as a dimer and is found in the most common form of PLGA. Methods A panel of small molecule RAF inhibitors (including type II inhibitors, targeting the "DFG-out" conformation of the kinase) was screened for drugs showing efficacy on murine models of PLGA and on authentic human PLGA cells expressing KIAA1549:BRAF. Results We identify a type II RAF inhibitor that serves as an equipotent antagonist of BRAFV600E, KIAA1549:BRAF, and other noncanonical BRAF oncoproteins that function as dimers. This drug (MLN2480, also known as TAK-580) has good brain penetrance and is active on authentic human PLGA cells in brain organotypic cultures. Conclusion MLN2480 may be an effective therapeutic for BRAF mutant pediatric astrocytomas.
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Affiliation(s)
- Yu Sun
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John A Alberta
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Catherine Pilarz
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David Calligaris
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily J Chadwick
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shakti H Ramkissoon
- Center for Molecular Oncologic Pathology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lori A Ramkissoon
- Center for Molecular Oncologic Pathology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Veronica Matia Garcia
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Emanuele Mazzola
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Liliana Goumnerova
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Kane
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Zhan Yao
- Program in Molecular Pharmacology, Department of Medicine, and Center for Mechanism Based Therapeutics Memorial Sloan Kettering Cancer Center, New York, USA
| | - Mark W Kieran
- Division of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Keith L Ligon
- Center for Molecular Oncologic Pathology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Department of Medicine, and Center for Mechanism Based Therapeutics Memorial Sloan Kettering Cancer Center, New York, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathalie Y Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Departments of Neurosurgery and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosalind A Segal
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Charles D Stiles
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Giannakis M, Li H, Jin C, Gopal S, Desai K, Horak C, Wind-Rotolo M, Van Allen EM, Clish C, Hodi FS, Garraway LA, Choueiri TK. Metabolomic correlates of response in nivolumab-treated renal cell carcinoma and melanoma patients. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.3036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3036 Background: Immune-checkpoint inhibition has been shown to be effective in a variety of cancers, including renal cell carcinoma (RCC) and melanoma. However, only a subset of patients with RCC and melanoma respond to anti-PD1 therapy. Given the importance of metabolism in the tumor immune microenvironment, we performed serum metabolomics in nivolumab-treated patients towards identifying novel non-invasive correlates of response and progression-free survival in immunotherapy-treated patients. Methods: We performed liquid chromatography-mass spectrometry on pre- and on-treatment serum samples from 79 patients with advanced melanoma (CA209-038 study) and 82 patients with metastatic RCC (CA209-009 study) receiving nivolumab. We precisely measured more than one-hundred named metabolites at baseline (prior to starting nivolumab), at 4 weeks and at 6 (melanoma) or 9 weeks (RCC) after initiation of treatment and correlated these with best overall response as well as progression-free survival (PFS). Results: In melanoma patients treated with nivolumab, the difference in mean levels of kynurenine (the product of IDO / TDO activity in tryptophan catabolism) between weeks 4 and 6 compared to baseline was significantly different between responders and non-responders (t-test with unequal variance p-value = 0.043 and p-value = 0.044 respectively). In RCC patients, we observed that patients with no response to nivolumab had significantly higher adenosine levels, than those who responded, at baseline and at 4 weeks after initiation of treatment (158% and 138% higher, t-test p-value = 0.0019 and p-value = 0.0011 respectively). RCC nivolumab-treated patients with higher (top quartile) baseline adenosine levels also had a significantly worse PFS (log rank test p-value = 0.004). Conclusions: In this first-of-its kind metabolomic analysis of peripheral blood from nivolumab-treated patients, we find that the change in kynurenine levels in melanoma patients correlates to response. In addition, higher baseline levels of adenosine in RCC patients are associated with worse PFS and lack of response to nivolumab. These results suggest a possible role for serum metabolites as biomarkers of benefit to PD1 inhibition.
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Affiliation(s)
| | - Haoxin Li
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Shuba Gopal
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Toni K. Choueiri
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
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Rohanizadegan M, Aldubayan SH, Giannakis M, Mu XJ, Nishihara R, Qian ZR, Nowak J, Cao Y, Liu L, Song M, Chan AT, Garraway LA, Ogino S, Fuchs CS, Van Allen EM. Clinical actionability of germline testing in patients with limited colorectal polyps. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e13027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13027 Background: As classic adenoma-carcinoma sequence is the main process underlying most colorectal cancer (CRC), early detection and removal of colorectal adenomas is crucial in preventing CRC. Although adenomatous polyps are usually sporadic, several inherited CRC syndromes such as Familial adenomatous polyposis, MUTYH-associated polyposis and Lynch syndrome can present initially with colon polyps. The identification of germline defects in patients with colon polyps is thus critical for proper cancer risk counseling and CRC prevention. Current guidelines recommend germline testing for patients with more than 20 polyps or those with more than 10 polyps and a family history of CRC. However, the diagnostic yield of germline testing on otherwise healthy individuals with 10 or fewer colon polyps has not been well studied. Here, we performed a pilot study to evaluate the clinical actionability of germline genetic testing on these patients. Methods: A total of 13 cancer-free adults, who presented with colon polyps (n < 10) and who otherwise were not selected based on age of onset or family history underwent germline Exome Sequencing. Variants in 13 well-established CRC risk genes ( APC, CHEK2, MYH, MLH1, MSH2, MSH6, PMS2, NTHL1, BMPR1A, SMAD4, PTEN, STK11, TP53) were evaluated for pathogenicity. Results: A total of 13 patients (12 male, 1 female) were evaluated. The median age of presentation was 69 (range 49 to 88). The median number of adenomatous colon polyps was 1 (range 1 to 8). Two (15.4%, 95% CI = 1.9 - 45.4, Binomial Exact) patients had at least one disruptive mutation in the examined genes. One of these patients had a truncating mutation in APC (p.Arg216*) and presented with two tubulovillous adenomas at age 49. The second patient had 8 adenomas in distal colon and rectum at age 64, and harbored a known pathogenic mutation in MSH6(p.Arg1035*). Conclusions: This pilot study provides evidence that a relatively high percentage of patients presenting with a few colon polyps may have inherited defects in highly actionable genes. If validated in larger cohorts with appropriate population controls, these findings may influence the clinical care of such patients and their families and suggest germline molecular testing in those patients.
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Affiliation(s)
| | | | | | - Xinmeng Jasmine Mu
- Dana-Farber Cancer Institute/Harvard Medical School and Broad Institute, Cambridge, MA
| | | | | | | | - Yin Cao
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Li Liu
- Dana-Farber Cancer Institute, Boston, MA
| | - Mingyang Song
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Andrew T. Chan
- Massachusetts General Hospital and Harvard Medical School, Boston, MA
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Aldubayan SH, Giannakis M, Moore N, Mu XJ, Han GC, Nishihara R, Qian ZR, Liu L, Ogino S, Garraway LA, Fuchs CS, Van Allen EM. Enrichment of germline DNA-repair gene mutations in patients with colorectal cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.1500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1500 Background: Twin studies showed that 30% of all colorectal cancer (CRC) patients have an inherited genetic susceptibility. Several CRC predisposition genes have been described to date. However, mutations in these genes explain the risk in only 5-10% of CRC cases. In this study, we hypothesized that some of the CRC heritability may be explained by excess disruptive germline mutations in DNA repair genes (DRGs). Methods: Exome sequencing data of 716 in the discovery cohort (CanSeq and NHS/HPFS studies) and 1609 CRC patients in the validation cohort (TCGA and NSCCG studies) were used to evaluate germline variants in a pre-selected group of 42 DRGs and 12 known CRC risk genes. Frequencies of disruptive mutations in our cohorts were examined relative to 27173 non-Finnish European cancer-free adults from the ExAC cohort to evaluate for enrichment. Results: Of 716 patients in the discovery cohort, 27 (3.8%) patients harbored germline mutations in APC (n = 11), MSH6 (n = 2), MUTYH (n = 11), CHEK2 (n = 1) and TP53 (n = 2). Interestingly, germline mutations in ATM and PALB2 were significantly enriched in our CRC discovery cohort (OR = 2.7; P = 0.044; and OR = 4.8; P = 0.026, respectively). Evaluation of germline data from another 1609 CRC patients (validation cohort) also showed significantly higher rates of ATM mutations (5; 0.7%; OR = 2.1; P = 0.044), and a trend for enrichment of PALB2 mutations (3; 0.4%; OR = 2.8; P = 0.056). Secondary analysis of actionable germline mutations in a highly penetrant cancer risk gene set ( ATM, BRCA1, BRCA2, BRIP1 and PALB2) suggest a broader enrichment trend in CRC patients for these genes (Discovery: OR = 1.7; P = 0.06; Validation: OR = 2; P = 1.96e-04). Conclusions: Our analysis of germline variants in 2325 CRC patients showed the first robust evidence for germline ATM mutations to confer a higher risk of developing CRC. We also presented evidence to support PALB2 as a potential novel CRC risk gene. Overall, our study shows that mutations in some DRGs may explain some of the missing CRC heritability. It also indicates that a significant percentage of CRC patients, who carry mutations in highly actionable genes where cancer screening recommendations for patients and families do exist, are not captured with current testing recommendations.
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Affiliation(s)
| | | | | | - Xinmeng Jasmine Mu
- Dana-Farber Cancer Institute/Harvard Medical School and Broad Institute, Cambridge, MA
| | | | | | | | - Li Liu
- Dana-Farber Cancer Institute, Boston, MA
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50
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Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F. Erratum to: Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol 2017; 18:80. [PMID: 28464947 PMCID: PMC5412043 DOI: 10.1186/s13059-017-1183-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 02/27/2017] [Indexed: 12/02/2022] Open
Affiliation(s)
- Davide Prandi
- Centre for Integrative Biology, University of Trento, Povo Trento, 38123, Italy
| | - Sylvan C Baca
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Alessandro Romanel
- Centre for Integrative Biology, University of Trento, Povo Trento, 38123, Italy
| | - Christopher E Barbieri
- Department of Urology, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, 10065, USA
| | - Juan-Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, 10065, USA
| | - Jacqueline Fontugne
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Himisha Beltran
- Department of Medicine, Division of Hematology and Oncology, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, 10065, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, 10065, USA.,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Mark A Rubin
- Department of Urology, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, 10065, USA
| | - Francesca Demichelis
- Centre for Integrative Biology, University of Trento, Povo Trento, 38123, Italy. .,Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, 10065, USA. .,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, 10065, USA.
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