|
1
|
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.
Collapse
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.
| |
Collapse
|