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Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet 2023; 55:807-819. [PMID: 37024582 PMCID: PMC10181943 DOI: 10.1038/s41588-023-01355-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023]
Abstract
Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.
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Affiliation(s)
- Arvind Ravi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Monica B Arniella
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Mark Holton
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for the AIDS Programme for Research in South Africa, Durban, South Africa
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aaron T Griffin
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie I Vokes
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Mustafa Sakhi
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Vashine Kamesan
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Patrick M Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Don L Gibbons
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Nathan A Pennell
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Vamsidhar Velcheti
- Department of Hematology and Oncology, NYU Langone Health, New York, NY, USA
| | - Subba R Digumarthy
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, New York, NY, USA
| | - John V Heymach
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Roy S Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Julie R Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kurt A Schalper
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Victor E Velculescu
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian S Henick
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrew Chow
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marta Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice T Shaw
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA.
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Freeman SS, Sade-Feldman M, Kim J, Stewart C, Gonye AL, Ravi A, Arniella MB, Gushterova I, LaSalle TJ, Blaum EM, Yizhak K, Frederick DT, Sharova T, Leshchiner I, Elagina L, Spiro OG, Livitz D, Rosebrock D, Aguet F, Carrot-Zhang J, Ha G, Lin Z, Chen JH, Barzily-Rokni M, Hammond MR, Vitzthum von Eckstaedt HC, Blackmon SM, Jiao YJ, Gabriel S, Lawrence DP, Duncan LM, Stemmer-Rachamimov AO, Wargo JA, Flaherty KT, Sullivan RJ, Boland GM, Meyerson M, Getz G, Hacohen N. Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma. Cell Rep Med 2022; 3:100500. [PMID: 35243413 PMCID: PMC8861826 DOI: 10.1016/j.xcrm.2021.100500] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 05/03/2021] [Revised: 09/26/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Immune checkpoint blockade (CPB) improves melanoma outcomes, but many patients still do not respond. Tumor mutational burden (TMB) and tumor-infiltrating T cells are associated with response, and integrative models improve survival prediction. However, integrating immune/tumor-intrinsic features using data from a single assay (DNA/RNA) remains underexplored. Here, we analyze whole-exome and bulk RNA sequencing of tumors from new and published cohorts of 189 and 178 patients with melanoma receiving CPB, respectively. Using DNA, we calculate T cell and B cell burdens (TCB/BCB) from rearranged TCR/Ig sequences and find that patients with TMBhigh and TCBhigh or BCBhigh have improved outcomes compared to other patients. By combining pairs of immune- and tumor-expressed genes, we identify three gene pairs associated with response and survival, which validate in independent cohorts. The top model includes lymphocyte-expressed MAP4K1 and tumor-expressed TBX3. Overall, RNA or DNA-based models combining immune and tumor measures improve predictions of melanoma CPB outcomes.
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Affiliation(s)
- Samuel S. Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Moshe Sade-Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna L.K. Gonye
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Arvind Ravi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Irena Gushterova
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Thomas J. LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily M. Blaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 2611001, Israel
| | - Dennie T. Frederick
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tatyana Sharova
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ignaty Leshchiner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Oliver G. Spiro
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dimitri Livitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jian Carrot-Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle 98109, WA, USA
| | - Ziao Lin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard University, Cambridge MA, 02138
| | - Jonathan H. Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Massachusetts General Hospital, Boston 02114, MA, USA
| | - Michal Barzily-Rokni
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marc R. Hammond
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Shauna M. Blackmon
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yunxin J. Jiao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Donald P. Lawrence
- Department of Medical Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lyn M. Duncan
- Department of Pathology, Massachusetts General Hospital, Boston 02114, MA, USA
| | | | - Jennifer A. Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keith T. Flaherty
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ryan J. Sullivan
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Genevieve M. Boland
- Department of Surgery, Massachusetts General Hospital, Boston 02115, MA, USA
| | - Matthew Meyerson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston 02115, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard University, Cambridge MA, 02138
- Department of Pathology, Harvard Medical School, Boston 02115, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston 02115, MA, USA
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Arniella MB, Ravi A, Gainor J, Stewart C, Freeman S, Awad M, Forde P, Anagnostou V, Henick B, Riess JW, Gibbons D, Pennell N, Velcheti V, Leshchiner I, Kim J, Digumarthy S, Mino-Kenudson M, Heymach J, Hacohen N, Rizvi N, Herbst R, Velculescu VE, Brahmer J, Schalper K, Jänne P, Wolchok J, Shaw A, Getz G, Hellman MD. Abstract LB197: An SU2C-Mark Foundation Lung collaborative update: integrative genomics identifies distinct transcriptional states associated with checkpoint blockade resistance. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb197] [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
The advent of PD-1/PD-L1 agents has transformed the therapeutic landscape of many advanced cancers, including non-small cell lung cancer (NSCLC). However, our understanding of the genomic biomarkers underlying effective treatment response remain limited. Here we provide updated results from our ongoing effort, the Stand Up To Cancer Lung (SU2C-Lung)/Mark Foundation EXTOLConsortium, a multi-institution collaboration to expand our understanding of the molecular determinants of immunotherapy response in NSCLC. Comprising a set of nearly 400 patients, this cohort enables evaluation of both genomic and transcriptomic factors associated with checkpoint blockade response. In addition to validating previously known associations including TMB and neoantigen burden, we examined transcriptional predictors associated with response. We generated a list of differentially expressed genes with respect to best overall response (BOR), and performed dimensionality reduction using semi-supervised Bayesian Non-Negative Factorization (ssBNMF). We identified 3 distinct clusters with strong sample membership. Characterization of these subtypes revealed varying levels of immune infiltrate, histologic composition, and response rates to checkpoint blockade. Of these three subtypes, two were associated with low response rates to PD-1/PD-L1 blockade, suggesting the existence of distinct avenues toward resistance. To further characterize these transcriptional subtypes, we used ssBNMF marker genes to classify publicly available NSCLC samples from The Cancer Genome Atlas (TCGA), along with gene expression from a smaller cohort of large-cell neuroendocrine (LCNE) samples. Histologic composition showed good concordance with our SU2C samples, and redemonstrated observations within our smaller SU2C cohort of distinct immuno-suppressive and immuno-depleted milieus associated with resistance.
Citation Format: Monica B. Arniella, Arvind Ravi, Justin Gainor, Chip Stewart, Sam Freeman, Mark Awad, Patrick Forde, Valsamo Anagnostou, Brian Henick, Jonathan W. Riess, Don Gibbons, Nathan Pennell, Vamsidhar Velcheti, Ignaty Leshchiner, Jaegil Kim, Subba Digumarthy, Mari Mino-Kenudson, John Heymach, Nir Hacohen, Naiyer Rizvi, Roy Herbst, Victor E. Velculescu, Julie Brahmer, Kurt Schalper, Pasi Jänne, Jedd Wolchok, Alice Shaw, Gad Getz, Matthew D. Hellman. An SU2C-Mark Foundation Lung collaborative update: integrative genomics identifies distinct transcriptional states associated with checkpoint blockade resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB197.
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Affiliation(s)
| | - Arvind Ravi
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Chip Stewart
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Sam Freeman
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Mark Awad
- 3Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Brian Henick
- 5Columbia University Medical Center, New York City, NY
| | | | | | | | | | | | - Jaegil Kim
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | - Nir Hacohen
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Naiyer Rizvi
- 5Columbia University Medical Center, New York City, NY
| | | | | | | | | | - Pasi Jänne
- 3Dana-Farber Cancer Institute, Boston, MA
| | - Jedd Wolchok
- 10Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Alice Shaw
- 2Massachusetts General Hospital, Boston, MA
| | - Gad Getz
- 1Broad Institute of MIT and Harvard, Cambridge, MA
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