1
|
Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol 2024; 25:644-658. [PMID: 38503922 DOI: 10.1038/s41590-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7+PD-1+CD8+ T cells, activated CCR7+LAMP3+ dendritic cells and CCL19+ fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10+ macrophages and TCF7-CD8+ T cells as well as between mature regulatory dendritic cells and TCF7+CD4+ and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
Collapse
Affiliation(s)
- Jonathan H Chen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Department of Pathology, MGH, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Linda T Nieman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Maxwell Spurrell
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Liad Elmelech
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Peter Richieri
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Katherine H Xu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Roopa Madhu
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA
| | - Milan Parikh
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Izabella Zamora
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Christopher S Nabel
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua D Pirl
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chenyue Lu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Catherine B Meador
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Hematology/Oncology, MGH, HMS, Boston, MA, USA
| | | | | | - Alexander L Tang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Matan Hofree
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Lautenberg Center for Immunology and Cancer Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Angela Shih
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, MGH, Boston, MA, USA
| | - Karin Pelka
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, Gladstone Institutes, San Francisco, CA, USA
| | - Martin J Aryee
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mari Mino-Kenudson
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Center for Thoracic Cancers, MGH, Boston, MA, USA.
| | - Ilya Korsunsky
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA.
| | - Nir Hacohen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
2
|
Ceglia N, Sethna Z, Freeman SS, Uhlitz F, Bojilova V, Rusk N, Burman B, Chow A, Salehi S, Kabeer F, Aparicio S, Greenbaum BD, Shah SP, McPherson A. Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector. Nat Commun 2023; 14:4400. [PMID: 37474509 PMCID: PMC10359421 DOI: 10.1038/s41467-023-39985-2] [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] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/04/2023] [Indexed: 07/22/2023] Open
Abstract
Deciphering individual cell phenotypes from cell-specific transcriptional processes requires high dimensional single cell RNA sequencing. However, current dimensionality reduction methods aggregate sparse gene information across cells, without directly measuring the relationships that exist between genes. By performing dimensionality reduction with respect to gene co-expression, low-dimensional features can model these gene-specific relationships and leverage shared signal to overcome sparsity. We describe GeneVector, a scalable framework for dimensionality reduction implemented as a vector space model using mutual information between gene expression. Unlike other methods, including principal component analysis and variational autoencoders, GeneVector uses latent space arithmetic in a lower dimensional gene embedding to identify transcriptional programs and classify cell types. In this work, we show in four single cell RNA-seq datasets that GeneVector was able to capture phenotype-specific pathways, perform batch effect correction, interactively annotate cell types, and identify pathway variation with treatment over time.
Collapse
Affiliation(s)
- Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Zachary Sethna
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel S Freeman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florian Uhlitz
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viktoria Bojilova
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bharat Burman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Chow
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab Salehi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Farhia Kabeer
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - 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
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
3
|
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
|
4
|
Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N. Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response. bioRxiv 2023:2023.04.04.535379. [PMID: 37066412 PMCID: PMC10104028 DOI: 10.1101/2023.04.04.535379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially-localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens, and found that they were associated with beneficial responses to PD-1-blockade. Immunity hubs were enriched for many interferon-stimulated genes, T cells in multiple differentiation states, and CXCL9/10/11 + macrophages that preferentially interact with CD8 T cells. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcomes, distinct from mature tertiary lymphoid structures, and enriched for stem-like TCF7+PD-1+ CD8 T cells and activated CCR7 + LAMP3 + dendritic cells, as well as chemokines that organize these cells. These results elucidate the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
Collapse
|
5
|
Gonye ALK, LaSalle TJ, Freeman SS, Reyes M, Hacohen N, Villani AC, Sade-Feldman M. Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity. STAR Protoc 2023; 4:102125. [PMID: 36853705 PMCID: PMC9946790 DOI: 10.1016/j.xpro.2023.102125] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/25/2023] Open
Abstract
Although neutrophils are the most abundant leukocyte in healthy individuals and impact outcomes of diseases ranging from sepsis to cancer, they remain understudied due to technical constraints of isolation, preservation, and sequencing. We present a modified Smart-Seq2 protocol for bulk RNA sequencing of neutrophils enriched from whole blood. We describe steps for neutrophil isolation, cDNA generation, library preparation, and sample purity estimation via a bioinformatic approach. Our approach permits the collection of large cohorts and enables detection of neutrophil transcriptomic subtypes. For complete details on the use and execution of this protocol, please refer to LaSalle et al. (2022)1 and Boribong et al. (2022).2.
Collapse
Affiliation(s)
- Anna L K Gonye
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Thomas J LaSalle
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Samuel S Freeman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Miguel Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nir Hacohen
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Cowan A, Ferrari F, Freeman SS, Redd R, El-Khoury H, Perry J, Patel V, Kaur P, Barr H, Lee DJ, Lightbody E, Downey K, Argyelan D, Theodorakakou F, Fotiou D, Liacos CI, Kanellias N, Chavda SJ, Ainley L, Sandecká V, Pospíšilová L, Minarik J, Jungova A, Radocha J, Spicka I, Nadeem O, Yong K, Hájek R, Kastritis E, Marinac CR, Dimopoulos MA, Get G, Trippa L, Ghobrial IM. Personalised progression prediction in patients with monoclonal gammopathy of undetermined significance or smouldering multiple myeloma (PANGEA): a retrospective, multicohort study. Lancet Haematol 2023; 10:e203-e212. [PMID: 36858677 PMCID: PMC9991855 DOI: 10.1016/s2352-3026(22)00386-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 09/07/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 03/03/2023]
Abstract
BACKGROUND Patients with precursors to multiple myeloma are dichotomised as having monoclonal gammopathy of undetermined significance or smouldering multiple myeloma on the basis of monoclonal protein concentrations or bone marrow plasma cell percentage. Current risk stratifications use laboratory measurements at diagnosis and do not incorporate time-varying biomarkers. Our goal was to develop a monoclonal gammopathy of undetermined significance and smouldering multiple myeloma stratification algorithm that utilised accessible, time-varying biomarkers to model risk of progression to multiple myeloma. METHODS In this retrospective, multicohort study, we included patients who were 18 years or older with monoclonal gammopathy of undetermined significance or smouldering multiple myeloma. We evaluated several modelling approaches for predicting disease progression to multiple myeloma using a training cohort (with patients at Dana-Farber Cancer Institute, Boston, MA, USA; annotated from Nov, 13, 2019, to April, 13, 2022). We created the PANGEA models, which used data on biomarkers (monoclonal protein concentration, free light chain ratio, age, creatinine concentration, and bone marrow plasma cell percentage) and haemoglobin trajectories from medical records to predict progression from precursor disease to multiple myeloma. The models were validated in two independent validation cohorts from National and Kapodistrian University of Athens (Athens, Greece; from Jan 26, 2020, to Feb 7, 2022; validation cohort 1), University College London (London, UK; from June 9, 2020, to April 10, 2022; validation cohort 1), and Registry of Monoclonal Gammopathies (Czech Republic, Czech Republic; Jan 5, 2004, to March 10, 2022; validation cohort 2). We compared the PANGEA models (with bone marrow [BM] data and without bone marrow [no BM] data) to current criteria (International Myeloma Working Group [IMWG] monoclonal gammopathy of undetermined significance and 20/2/20 smouldering multiple myeloma risk criteria). FINDINGS We included 6441 patients, 4931 (77%) with monoclonal gammopathy of undetermined significance and 1510 (23%) with smouldering multiple myeloma. 3430 (53%) of 6441 participants were female. The PANGEA model (BM) improved prediction of progression from smouldering multiple myeloma to multiple myeloma compared with the 20/2/20 model, with a C-statistic increase from 0·533 (0·480-0·709) to 0·756 (0·629-0·785) at patient visit 1 to the clinic, 0·613 (0·504-0·704) to 0·720 (0·592-0·775) at visit 2, and 0·637 (0·386-0·841) to 0·756 (0·547-0·830) at visit three in validation cohort 1. The PANGEA model (no BM) improved prediction of smouldering multiple myeloma progression to multiple myeloma compared with the 20/2/20 model with a C-statistic increase from 0·534 (0·501-0·672) to 0·692 (0·614-0·736) at visit 1, 0·573 (0·518-0·647) to 0·693 (0·605-0·734) at visit 2, and 0·560 (0·497-0·645) to 0·692 (0·570-0·708) at visit 3 in validation cohort 1. The PANGEA models improved prediction of monoclonal gammopathy of undetermined significance progression to multiple myeloma compared with the IMWG rolling model at visit 1 in validation cohort 2, with C-statistics increases from 0·640 (0·518-0·718) to 0·729 (0·643-0·941) for the PANGEA model (BM) and 0·670 (0·523-0·729) to 0·879 (0·586-0·938) for the PANGEA model (no BM). INTERPRETATION Use of the PANGEA models in clinical practice will allow patients with precursor disease to receive more accurate measures of their risk of progression to multiple myeloma, thus prompting for more appropriate treatment strategies. FUNDING SU2C Dream Team and Cancer Research UK.
Collapse
Affiliation(s)
- Annie Cowan
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Federico Ferrari
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Biostatistics and Research Decision Sciences, Merck & Co, Rahway, NJ, USA
| | - Samuel S Freeman
- Bioinformatics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert Redd
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Habib El-Khoury
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Vidhi Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Priya Kaur
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hadley Barr
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David J Lee
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Katelyn Downey
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Argyelan
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Foteini Theodorakakou
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Despina Fotiou
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Christine Ivy Liacos
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Kanellias
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Louise Ainley
- UCL Cancer Institute, University College London, London, UK
| | - Viera Sandecká
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | | | - Jiri Minarik
- Department of Hemato-Oncology, University Hospital Olomouc, Olomouc, Czech Republic
| | - Alexandra Jungova
- Department of Hematology and Oncology, University Hospital Pilsen, Pilsen, Czech Republic
| | - Jakub Radocha
- Fourth Department of Internal Medicine Hematology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Czech Republic
| | - Ivan Spicka
- First Department of Medicine, Department of Hematology, First Faculty of Medicine, Charles University and General Hospital in Prague, Czech Republic
| | - Omar Nadeem
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kwee Yong
- UCL Cancer Institute, University College London, London, UK
| | - Roman Hájek
- Fourth Department of Internal Medicine-Hematology, University Hospital in Ostrava, Ostrava, Czech Republic
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Gad Get
- Bioinformatics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lorenzo Trippa
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Irene M Ghobrial
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
7
|
LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Revach OY, Mehta A, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients. Cell Rep Med 2022; 3:100779. [PMID: 36208629 PMCID: PMC9510054 DOI: 10.1016/j.xcrm.2022.100779] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 08/02/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2023]
Abstract
Mechanisms of neutrophil involvement in severe coronavirus disease 2019 (COVID-19) remain incompletely understood. Here, we collect longitudinal blood samples from 306 hospitalized COVID-19+ patients and 86 controls and perform bulk RNA sequencing of enriched neutrophils, plasma proteomics, and high-throughput antibody profiling to investigate relationships between neutrophil states and disease severity. We identify dynamic switches between six distinct neutrophil subtypes. At days 3 and 7 post-hospitalization, patients with severe disease display a granulocytic myeloid-derived suppressor cell-like gene expression signature, while patients with resolving disease show a neutrophil progenitor-like signature. Humoral responses are identified as potential drivers of neutrophil effector functions, with elevated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulin G1 (IgG1)-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirm that while patient-derived IgG antibodies induce phagocytosis in healthy donor neutrophils, IgA antibodies predominantly induce neutrophil cell death. Overall, our study demonstrates a dysregulated myelopoietic response in severe COVID-19 and a potential role for IgA-dominant responses contributing to mortality.
Collapse
Affiliation(s)
- Thomas J LaSalle
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.
| | - Anna L K Gonye
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Irena Gushterova
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyle R Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F Thomas
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M Lilly
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N Mckaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole C Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily M Blaum
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola B Lirofonis
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Or-Yam Revach
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arnav Mehta
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abraham Sonny
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Roby P Bhattacharyya
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marcia B Goldberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael R Filbin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Moshe Sade-Feldman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
8
|
Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Nat Immunol 2022; 23:1495-1506. [PMID: 36151395 DOI: 10.1038/s41590-022-01315-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/15/2022] [Indexed: 02/04/2023]
Abstract
The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1b/HLA-E. Surprisingly, loss of tumor interferon-γ (IFNγ) signaling sensitizes many models to immunity. The immune inhibitory effects of tumor IFN sensing are mediated through two mechanisms. First, tumor upregulation of classical MHC class I inhibits natural killer cells. Second, IFN-induced expression of Qa-1b inhibits CD8+ T cells via the NKG2A/CD94 receptor, which is induced by ICB. Finally, we show that strong IFN signatures are associated with poor response to ICB in individuals with renal cell carcinoma or melanoma. This study reveals that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints can facilitate immune escape.
Collapse
Affiliation(s)
- Juan Dubrot
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Peter P Du
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Samuel S Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Peter M Allen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Clara H Wolfe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nelson H Knudsen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | - Ian C Kohnle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hans W Pope
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Austin Ayer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gargi Mishra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sarah Y Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Dennie T Frederick
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - W Nicholas Haining
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- ArsenalBio, South San Francisco, CA, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen B Yates
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Robert T Manguso
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
9
|
Cowan A, El-Khoury H, Ferrari F, Freeman SS, Redd R, Perry J, Patel V, Kaur P, Barr H, Downey K, Argyelan D, Justis AV, Lee DJ, Lightbody ED, Theodorakakou F, Fotiou D, Kanellias N, Liacos C, Getz G, Trippa L, Marinac C, Kastritis E, Meletios D, Ghobrial I. Abstract 2259: Predictive modeling of smoldering multiple myeloma progression to multiple myeloma by continuous variable analysis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2259] [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
Introduction: Multiple myeloma (MM) is consistently preceded by two precursor conditions, monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). The distinctions between MGUS, SMM, and MM rely on clinical values with inherent variation relating to tumor burden quantified from bone marrow biopsies, a measure subject to inconsistencies in location, timing, and pathologist interpretation. These challenges limit the potential of current standardized risk criteria and advocate for models that examine precursor disease kinetics. We thus developed a risk model that leverages dynamic changes in markers of precursor disease to improve clinical ability to predict time to disease progression.
Methods: To model the evolution of progression risk, we built PANGEA, an international retrospective cohort of precursor patients with baseline and serial time points of clinical and biological variables. This cohort comprises 1095 SMM patients, 254 (23%) of which progressed to MM. Using this cohort, we modeled progression to MM with Cox regression using time-dependent and continuous clinical variables. The model was trained on a subset of data restricted to patients of the Dana-Farber Cancer Institute (DFCI) and validated its performance by computing the c-statistic in a sub-cohort independent from the DFCI training cohort.
Results: The PANGEA cohort was first used to validate current models of SMM disease progression. We validated the 20/2/20 International Myeloma Working Group criteria for SMM patients using binary cutoffs of initial measurements (baseline model), and then extended this model, allowing for re-stratification by the 20/2/20 criteria over time (dynamic model). We then assessed whether rates of change in a set of myeloma-specific clinical variables unrestricted to those of the 20/2/20 criteria improved the predictive ability of the model. This improved our progression prediction as indicated by a c-statistic increase of more than 10% with respect to both 20/2/20 models (baseline and dynamic). Specifically, changes in disease indicators such as age and creatinine are highly predictive of imminent disease progression (p-value < 0.01). Finally, we clustered patients based on latent trajectories of these time-varying clinical variables and included the trajectory classes in the Cox regression. The resulting multivariable, dynamic algorithm is a dramatic improvement over current clinical standards in predicting progression from SMM to MM disease.
Conclusion: The PANGEA multivariable algorithm’s use of continuous clinical variables enhances progression risk predictions in SMM. These findings demonstrate that disease progression from SMM to MM, which likely occurs by the acquisition of sequential changes to the plasma cell clone, can be tracked by trends in clinical values, thus improving prognostication for precursor patients.
Citation Format: Annie Cowan, Habib El-Khoury, Federico Ferrari, Samuel S. Freeman, Robert Redd, Jacqueline Perry, Vidhi Patel, Priya Kaur, Hadley Barr, Katelyn Downey, David Argyelan, Anna V. Justis, David J. Lee, Elizabeth D. Lightbody, Foteini Theodorakakou, Despina Fotiou, Nikolaos Kanellias, Christine Liacos, Gad Getz, Lorenzo Trippa, Catherine Marinac, Efstathios Kastritis, Dimopoulos Meletios, Irene Ghobrial. Predictive modeling of smoldering multiple myeloma progression to multiple myeloma by continuous variable analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2259.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Priya Kaur
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | - Despina Fotiou
- 4National and Kapodistrian University of Athens, Athens, Greece
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. Abstract 3610: In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3610] [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 immune system can eliminate tumors, but checkpoints enable tumors to escape immune destruction. Here, we report the systematic identification of immune evasion mechanisms using genome-scale in vivo CRISPR screens in eight murine cancer models treated with immune checkpoint blockade (ICB). We identify and validate previously unreported immune evasion genes and identify key immune inhibitory checkpoints that have a conserved role across several cancer models, such as the non-classical MHC-I molecule Qa-1b/HLA-E, which scores as the top overall sensitizing hit across all screens. Surprisingly, we find that loss of IFNγ signaling by tumor cells sensitizes 6 of 8 cancer models to ICB. While IFN-mediated inflammation has been associated with response to ICB, there have also been reports of ICB-resistance driven by IFN sensing. However, several divergent mechanisms have been proposed to explain the inhibitory effect of tumor IFN sensing, leading to uncertainty about how this key immune signaling pathway is regulating anti-tumor immunity in different contexts. Using in vivo screening data, transcriptional profiling, and genetic interaction studies, we reveal that the immune-inhibitory effects of tumor IFN sensing are the direct result of tumor upregulation of classical and non-classical MHC-I genes. The interferon-MHC-I axis can inhibit anti-tumor immunity through two mechanisms: first, upregulation of classical MHC-I inhibits the cytotoxicity of natural killer cells, which are activated by ICB. Second, IFN-mediated upregulation of Qa-1b directly inhibits cytotoxicity by effector CD8+ T cells via the NKG2A/CD94 receptor, which is induced on CD8+ T cells by ICB. Finally, we show that high interferon-stimulated gene expression in patients is associated with decreased survival in RCC and poor response to ICB in melanoma. Our study establishes a unifying mechanism to explain the inhibitory role of tumor IFN sensing, revealing that IFN-mediated upregulation of classical and non-classical MHC-I inhibitory checkpoints can facilitate immune escape.
Citation Format: Juan Dubrot, Peter P. Du, Sarah Kate Lane-Reticker, Emily A. Kessler, Audrey J. Muscato, Arnav Mehta, Samuel S. Freeman, Peter M. Allen, Kira E. Olander, Kyle M. Ockerman, Clara H. Wolfe, Fabius Wiesmann, Nelson H. Knudsen, Hsiao-Wei Tsao, Arvin Iracheta-Vellve, Emily M. Schneider, Andrea N. Rivera-Rosario, Ian C. Kohnle, Hans W. Pope, Austin Ayer, Gargi Mishra, Margaret D. Zimmer, Sarah Y. Kim, Animesh Mahapatra, Hakimeh Ebrahimi-Nik, Dennie T. Frederick, Genevieve M. Boland, W. Nicholas Haining, David E. Root, John G. Doench, Nir Hacohen, Kathleen B. Yates, Robert T. Manguso. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3610.
Collapse
|
11
|
Oliveira G, Stromhaug K, Cieri N, Iorgulescu JB, Klaeger S, Wolff JO, Rachimi S, Chea V, Krause K, Freeman SS, Zhang W, Li S, Braun DA, Neuberg D, Carr SA, Livak KJ, Frederick DT, Fritsch EF, Wind-Rotolo M, Hacohen N, Sade-Feldman M, Yoon CH, Keskin DB, Ott PA, Rodig SJ, Boland GM, Wu CJ. Landscape of helper and regulatory antitumour CD4 + T cells in melanoma. Nature 2022; 605:532-538. [PMID: 35508657 PMCID: PMC9815755 DOI: 10.1038/s41586-022-04682-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [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: 07/23/2021] [Accepted: 03/23/2022] [Indexed: 01/11/2023]
Abstract
Within the tumour microenvironment, CD4+ T cells can promote or suppress antitumour responses through the recognition of antigens presented by human leukocyte antigen (HLA) class II molecules1,2, but how cancers co-opt these physiologic processes to achieve immune evasion remains incompletely understood. Here we performed in-depth analysis of the phenotype and tumour specificity of CD4+ T cells infiltrating human melanoma specimens, finding that exhausted cytotoxic CD4+ T cells could be directly induced by melanoma cells through recognition of HLA class II-restricted neoantigens, and also HLA class I-restricted tumour-associated antigens. CD4+ T regulatory (TReg) cells could be indirectly elicited through presentation of tumour antigens via antigen-presenting cells. Notably, numerous tumour-reactive CD4+ TReg clones were stimulated directly by HLA class II-positive melanoma and demonstrated specificity for melanoma neoantigens. This phenomenon was observed in the presence of an extremely high tumour neoantigen load, which we confirmed to be associated with HLA class II positivity through the analysis of 116 melanoma specimens. Our data reveal the landscape of infiltrating CD4+ T cells in melanoma and point to the presentation of HLA class II-restricted neoantigens and direct engagement of immunosuppressive CD4+ TReg cells as a mechanism of immune evasion that is favoured in HLA class II-positive melanoma.
Collapse
Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Kari Stromhaug
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacquelyn O Wolff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Vipheaviny Chea
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kate Krause
- Department of surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Samuel S Freeman
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennie T Frederick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Edward F Fritsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nir Hacohen
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Surgical Oncology, Brigham and Women's Hospital Boston, Boston, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
12
|
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.
Collapse
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
| | | | | | | |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients. bioRxiv 2021. [PMID: 34642692 DOI: 10.1101/2021.10.04.463121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Multiple studies have identified an association between neutrophils and COVID-19 disease severity; however, the mechanistic basis of this association remains incompletely understood. Here we collected 781 longitudinal blood samples from 306 hospitalized COVID-19 + patients, 78 COVID-19 âˆ' acute respiratory distress syndrome patients, and 8 healthy controls, and performed bulk RNA-sequencing of enriched neutrophils, plasma proteomics, cfDNA measurements and high throughput antibody profiling assays to investigate the relationship between neutrophil states and disease severity or death. We identified dynamic switches between six distinct neutrophil subtypes using non-negative matrix factorization (NMF) clustering. At days 3 and 7 post-hospitalization, patients with severe disease had an enrichment of a granulocytic myeloid derived suppressor cell-like state gene expression signature, while non-severe patients with resolved disease were enriched for a progenitor-like immature neutrophil state signature. Severe disease was associated with gene sets related to neutrophil degranulation, neutrophil extracellular trap (NET) signatures, distinct metabolic signatures, and enhanced neutrophil activation and generation of reactive oxygen species (ROS). We found that the majority of patients had a transient interferon-stimulated gene signature upon presentation to the emergency department (ED) defined here as Day 0, regardless of disease severity, which persisted only in patients who subsequently died. Humoral responses were identified as potential drivers of neutrophil effector functions, as enhanced antibody-dependent neutrophil phagocytosis and reduced NETosis was associated with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirmed that while patient-derived IgG antibodies mostly drove neutrophil phagocytosis and ROS production in healthy donor neutrophils, patient-derived IgA antibodies induced a predominant NETosis response. Overall, our study demonstrates neutrophil dysregulation in severe COVID-19 and a potential role for IgA-dominant responses in driving neutrophil effector functions in severe disease and mortality.
Collapse
|
15
|
Sheffer M, Lowry E, Beelen N, Borah M, Amara SNA, Mader CC, Roth JA, Tsherniak A, Freeman SS, Dashevsky O, Gandolfi S, Bender S, Bryan JG, Zhu C, Wang L, Tariq I, Kamath GM, Simoes RDM, Dhimolea E, Yu C, Hu Y, Dufva O, Giannakis M, Syrgkanis V, Fraenkel E, Golub T, Romee R, Mustjoki S, Culhane AC, Wieten L, Mitsiades CS. Genome-scale screens identify factors regulating tumor cell responses to natural killer cells. Nat Genet 2021; 53:1196-1206. [PMID: 34253920 DOI: 10.1038/s41588-021-00889-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 04/03/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022]
Abstract
To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we quantified the NK cell responsiveness of hundreds of molecularly annotated 'DNA-barcoded' solid tumor cell lines in multiplexed format and applied genome-scale CRISPR-based gene-editing screens in several solid tumor cell lines, to functionally interrogate which genes in tumor cells regulate the response to NK cells. In these orthogonal studies, NK cell-sensitive tumor cells tend to exhibit 'mesenchymal-like' transcriptional programs; high transcriptional signature for chromatin remodeling complexes; high levels of B7-H6 (NCR3LG1); and low levels of HLA-E/antigen presentation genes. Importantly, transcriptional signatures of NK cell-sensitive tumor cells correlate with immune checkpoint inhibitor (ICI) resistance in clinical samples. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies.
Collapse
MESH Headings
- Allogeneic Cells/physiology
- Animals
- B7 Antigens/genetics
- Cell Line, Tumor
- Chromatin Assembly and Disassembly/physiology
- Cytotoxicity Tests, Immunologic/methods
- Cytotoxicity, Immunologic/genetics
- Cytotoxicity, Immunologic/physiology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genome, Human
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Killer Cells, Natural/physiology
- Mice, Inbred NOD
- Xenograft Model Antitumor Assays
- HLA-E Antigens
- Mice
Collapse
Affiliation(s)
- Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
| | - Emily Lowry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicky Beelen
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Minasri Borah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Chris C Mader
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jennifer A Roth
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aviad Tsherniak
- 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
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Samantha Bender
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Cong Zhu
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Li Wang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ifrah Tariq
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Channing Yu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Sichuan University, Chengdu, China
| | - Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Ernest Fraenkel
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Todd Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Aedin C Culhane
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
16
|
Bhatt RS, Berjis A, Konge JC, Mahoney KM, Klee AN, Freeman SS, Chen CH, Jegede OA, Catalano PJ, Pignon JC, Sticco-Ivins M, Zhu B, Hua P, Soden J, Zhu J, McDermott DF, Arulanandam AR, Signoretti S, Freeman GJ. KIR3DL3 Is an Inhibitory Receptor for HHLA2 that Mediates an Alternative Immunoinhibitory Pathway to PD1. Cancer Immunol Res 2020; 9:156-169. [PMID: 33229411 DOI: 10.1158/2326-6066.cir-20-0315] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/16/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
Blockade of the PD1 pathway is a broadly effective cancer therapy, but additional immune-inhibitory pathways contribute to tumor immune evasion. HERV-H LTR-associating 2 (HHLA2; also known as B7H5 and B7H7) is a member of the B7 family of immunoregulatory ligands that mediates costimulatory effects through its interaction with the CD28 family member transmembrane and immunoglobulin domain containing 2 (TMIGD2). However, HHLA2 has also been known to have inhibitory effects on T cells. Here, we report that we have identified killer cell immunoglobulin-like receptor, three immunoglobulin domains and long cytoplasmic tail 3 (KIR3DL3) as an inhibitory receptor for HHLA2 in T cells and natural killer (NK) cells and have generated HHLA2 and KIR3DL3 antibodies that block the immune-inhibitory activity of HHLA2, preserving the costimulatory signal. It is known that HHLA2 is frequently expressed in several tumor types, including clear cell renal cell carcinoma (ccRCC). We found that HHLA2 expression was nonoverlapping with PDL1 expression in ccRCC, suggesting that HHLA2 mediates a mechanism of tumor immune evasion that is independent from PDL1. Blockade of both the PD1 and KIR3DL3 pathways may be a more effective way to reverse tumor immune evasion.See related Spotlight on p. 128.
Collapse
Affiliation(s)
- Rupal S Bhatt
- Department of Medicine, Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
| | - Abdulla Berjis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Julie C Konge
- Department of Medicine, Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kathleen M Mahoney
- Department of Medicine, Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alyssa N Klee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Samuel S Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Chun-Hau Chen
- Department of Medicine, Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Opeyemi A Jegede
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paul J Catalano
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jean-Christophe Pignon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maura Sticco-Ivins
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Baogong Zhu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ping Hua
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jo Soden
- Retrogenix, Chinley, High Peak, United Kingdom
| | - Jie Zhu
- BPS Bioscience, San Diego, California
| | - David F McDermott
- Department of Medicine, Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Antonio R Arulanandam
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|
17
|
Hong X, Roh W, Sullivan RJ, Wong KHK, Wittner BS, Guo H, Dubash TD, Sade-Feldman M, Wesley B, Horwitz E, Boland GM, Marvin DL, Bonesteel T, Lu C, Aguet F, Burr R, Freeman SS, Parida L, Calhoun K, Jewett MK, Nieman LT, Hacohen N, Näär AM, Ting DT, Toner M, Stott SL, Getz G, Maheswaran S, Haber DA. The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis. Cancer Discov 2020; 11:678-695. [PMID: 33203734 DOI: 10.1158/2159-8290.cd-19-1500] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [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: 12/18/2019] [Revised: 09/22/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Circulating tumor cells (CTC) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastasis. We show that single CTCs from patients with melanoma coordinately upregulate lipogenesis and iron homeostasis pathways. These are correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant CTCs. The lipogenesis regulator SREBP2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species, and lipid peroxidation, thereby conferring resistance to inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic antioxidants ferrostatin-1 and vitamin E. In a prospective melanoma cohort, presence of CTCs with high lipogenic and iron metabolic RNA signatures is correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBP2-driven iron homeostatic pathways contribute to cancer progression, drug resistance, and metastasis. SIGNIFICANCE: Through single-cell analysis of primary and cultured melanoma CTCs, we have uncovered intrinsic cancer cell heterogeneity within lipogenic and iron homeostatic pathways that modulates resistance to BRAF inhibitors and to ferroptosis inducers. Activation of these pathways within CTCs is correlated with adverse clinical outcome, pointing to therapeutic opportunities.This article is highlighted in the In This Issue feature, p. 521.
Collapse
Affiliation(s)
- Xin Hong
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Whijae Roh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Keith H K Wong
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Shriners Hospitals for Children, Boston, Massachusetts
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Hongshan Guo
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Taronish D Dubash
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Benjamin Wesley
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Elad Horwitz
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dieuwke L Marvin
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Todd Bonesteel
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - François Aguet
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Risa Burr
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | | | - Laxmi Parida
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Katherine Calhoun
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michelle K Jewett
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Linda T Nieman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Anders M Näär
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mehmet Toner
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Shriners Hospitals for Children, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shannon L Stott
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Bethesda, Maryland
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- IBM Research, Yorktown Heights, New York
| |
Collapse
|
18
|
Hong X, Roh W, Sullivan RJ, Wong KH, Wittner BS, Guo H, Dubash TD, Sade-Feldman M, Wesley BK, Boland GM, Marvin DL, Bonesteel T, Lu C, Horwitz E, Aguet F, Freeman SS, Calhoun K, Jewett MK, Nieman LT, Hacohen N, Näär AM, Ting DT, Toner M, Stott SL, Getz G, Maheswaran S, Haber DA. Abstract 6073: The lipogenic regulator SREBP induces Transferrin in circulating melanoma cells, suppressing their susceptibility to ferroptosis. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6073] [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
Circulating tumor cells (CTCs) are shed by cancers into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastatic outgrowth. Clonally derived cultured CTCs from patients with BRAF-mutant melanoma reveal upregulation of lipogenesis and iron homeostasis pathways, correlated with their baseline and acquired drug resistance. In CTCs, the lipogenesis regulator SREBP directly induces transcription of the iron carrier Transferrin (TF), thereby reducing intracellular reactive oxygen species (ROS) and lipid peroxidation, and conferring resistance to BRAF inhibitors and inducers of ferroptosis. Knockdown of endogenous TF impairs tumorigenesis by melanoma CTCs; their associated soft agar clonogenic defect is rescued by the lipophilic anti-oxidants Ferrostatin-1 or Vitamin E, and by cholesterol. Single cell RNA-seq of patient-derived melanoma CTCs identifies a subset with high lipogenic, iron metabolic and proliferative signatures, correlated with adverse clinical outcome. Together, the coordinated regulation of these SREBP-driven pathways contributes to cancer progression, drug resistance and metastasis.
Citation Format: Xin Hong, Whijae Roh, Ryan J. Sullivan, Keith H. Wong, Ben S. Wittner, HongShan Guo, Taronish D. Dubash, Moshe Sade-Feldman, Ben K. Wesley, Genevieve M. Boland, Dieuwke L. Marvin, Todd Bonesteel, Chenyue Lu, Elad Horwitz, François Aguet, Samuel S. Freeman, Katherine Calhoun, Michelle K. Jewett, Linda T. Nieman, Nir Hacohen, Anders M. Näär, David T. Ting, Mehmet Toner, Shannon L. Stott, Gad Getz, Shyamala Maheswaran, Daniel A. Haber. The lipogenic regulator SREBP induces Transferrin in circulating melanoma cells, suppressing their susceptibility to ferroptosis [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 6073.
Collapse
Affiliation(s)
- Xin Hong
- 1MGH/Harvard Medical School, Charlestown, MA
| | - Whijae Roh
- 2Broad Institute of Harvard and MIT, Charlestown, MA
| | | | | | | | | | | | | | | | | | | | | | - Chenyue Lu
- 1MGH/Harvard Medical School, Charlestown, MA
| | | | | | | | - Katherine Calhoun
- 3Center for Engineering in Medicine/Harvard Medical School, Charlestown, MA
| | - Michelle K. Jewett
- 3Center for Engineering in Medicine/Harvard Medical School, Charlestown, MA
| | | | - Nir Hacohen
- 1MGH/Harvard Medical School, Charlestown, MA
| | | | | | - Mehmet Toner
- 3Center for Engineering in Medicine/Harvard Medical School, Charlestown, MA
| | | | - Gad Getz
- 2Broad Institute of Harvard and MIT, Charlestown, MA
| | | | | |
Collapse
|
19
|
Freeman SS, Sade-Feldman M, Kim J, Stewart C, Ravi A, Arniella M, Yizhak K, Leshchiner I, Elagina L, Spiro O, Livitz D, Rosebrock D, Aguet F, Carrot-Zhang J, Gonye A, Ha G, Lin Z, Chen JH, Frederick DT, Barzily-Rokni M, Hammond MR, Vitzthum H, Blackmon SM, Jiao YJ, Lawrence DP, Duncan LM, Stemmer-Rachamimov A, Wargo JA, Flaherty KT, Boland GM, Sullivan RJ, Meyerson M, Getz G, Hacohen N. Abstract 6670: Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6670] [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
Cancer immunotherapy with checkpoint blockade has improved survival and outcomes in melanoma, but still a majority of patients do not respond. Both high tumor mutation burden (TMB) and high T cell infiltration have been associated with response, but integrative models based on DNA or RNA assays have not been comprehensively explored and validated. Focusing on melanomas from patients receiving checkpoint blockade, we generated new and aggregated existing datasets of whole exome sequencing (WES) (n = 189 total) and bulk RNA sequencing (n = 154 total) to derive genomic and transcriptomic factors that predict survival and response to immunotherapy in melanoma.
We quantified T and B cell infiltrates using rearranged T cell receptor (TCR) and immunoglobulin (Ig) sequences, respectively, from DNA or RNA sequencing. High levels of rearranged TCR reads or rearranged Ig reads in RNA-seq were associated with survival (P = 0.0046, P = 0.015) and response (P = 0.0034, P = 0.047). We created RNA-based metrics of T and B cell burden (TCBRNA or BCBRNA) by normalizing the number of rearranged TCR reads by the total number of mapped reads. When we analyzed WES data in patients for whom DNA and RNA were extracted from the same region, we found that the TCBDNA correlated with TCBRNA (rho = 0.73) and BCBDNA with BCBRNA (rho = 0.41), demonstrating that the level of lymphocyte infiltration can be estimated using rearranged TCR or Ig reads from tumor WES alone.
We found that TCBDNA and BCBDNA both associated with survival (P = 0.0023 and 0.0089). In a combined model, patients with high TMB and high TCB DNA survived longer (P = 2.4e-4, HR = 2.68) and had a higher response rate (Fisher P = 0.028). This combined model was superior to models with TMB or TCBDNA alone. Similarly, patients with high TMB and high BCBDNA had longer survival and higher response rates (log-rank P = 0.0029, HR = 2.64, Fisher P = 0.015). We reanalyzed stage III/IV melanomas from TCGA and found that the TMB high, TCBDNA high subgroup had increased survival (P = 0.007).
Next, clustering of tumor transcriptomes identified 5 tumor subtypes based on melanocyte differentiation, immune infiltration and keratin levels. These melanoma subtypes were associated with survival outcomes after immunotherapy (P = 0.019). We found that TBX3, a tumor-expressed transcription factor enriched in poorly differentiated melanomas, was over-expressed among non-responders within the immune-infiltrated subtype and among all patients (P = 3.9e-4, P = 8.7e-5). Patients whose tumors had high immune infiltrate and low expression of TBX3 had longer survival (P = 1.6e-5, HR = 3.39), however this subgroup did not have longer survival in an independent cohort (n = 73, P = 0.10, HR = 2.63). In conclusion, we demonstrate both RNA-based (immune infiltrate and tumor subtype) and DNA-based metrics (TMB/TCB or TMB/BCB) can be used as pre-treatment predictors of survival after checkpoint blockade in melanoma.
Citation Format: Samuel S. Freeman, Moshe Sade-Feldman, Jaegil Kim, Chip Stewart, Arvind Ravi, Monica Arniella, Keren Yizhak, Ignaty Leshchiner, Liudmila Elagina, Oliver Spiro, Dimitri Livitz, Daniel Rosebrock, François Aguet, Jian Carrot-Zhang, Anna Gonye, Gavin Ha, Ziao Lin, Jonathan H. Chen, Dennie T. Frederick, Michal Barzily-Rokni, Marc R. Hammond, Hans Vitzthum, Shauna M. Blackmon, Yunxin J. Jiao, Donald P. Lawrence, Lyn M. Duncan, Anat Stemmer-Rachamimov, Jennifer A. Wargo, Keith T. Flaherty, Genevieve M. Boland, Ryan J. Sullivan, Matthew Meyerson, Gad Getz, Nir Hacohen. Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma [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 6670.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anna Gonye
- 2Massachusetts General Hospital, Boston, MA
| | - Gavin Ha
- 3Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Getz
- 2Massachusetts General Hospital, Boston, MA
| | | |
Collapse
|
20
|
Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson VA. Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer. Clin Cancer Res 2020; 26:2556-2564. [PMID: 32170028 DOI: 10.1158/1078-0432.ccr-19-3005] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/26/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing. EXPERIMENTAL DESIGN We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2- metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative. We performed whole-exome sequencing of tumors and designed individualized MRD tests, which we applied to serial cfDNA samples. RESULTS Our approach was 100-fold more sensitive than ddPCR when tracking 488 mutations, but most patients had fewer identifiable tumor mutations to track in cfDNA (median = 57; range = 2-346). Clinical sensitivity was 81% (n = 13/16) in newly diagnosed MBC, 23% (n = 7/30) at postoperative and 19% (n = 6/32) at 1 year in early-stage disease, and highest in patients with the most tumor mutations available to track. MRD detection at 1 year was strongly associated with distant recurrence [HR = 20.8; 95% confidence interval, 7.3-58.9]. Median lead time from first positive sample to recurrence was 18.9 months (range = 3.4-39.2 months). CONCLUSIONS Tracking large numbers of individualized tumor mutations in cfDNA can improve MRD detection, but its sensitivity is driven by the number of tumor mutations available to track.
Collapse
Affiliation(s)
- Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Priyanka Ram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pedro Exman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher C Lo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Boston University School of Public Health, Boston, Massachusetts
| | - Tianyu Li
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark Fleharty
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gregory J Kirkner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shoshana M Rosenberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura C Collins
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Kathy D Miller
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | | | - Lorenzo Trippa
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Donna S Neuberg
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gavin Ha
- Division of Public Health Services, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel G Stover
- Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ian Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
| | - G Mike Makrigiorgos
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Erica L Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Viktor A Adalsteinsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
| |
Collapse
|
21
|
Waks AG, Cohen O, Kochupurakkal B, Kim D, Dunn CE, Buendia Buendia J, Wander S, Helvie K, Lloyd MR, Marini L, Hughes ME, Freeman SS, Ivy SP, Geradts J, Isakoff S, LoRusso P, Adalsteinsson VA, Tolaney SM, Matulonis U, Krop IE, D'Andrea AD, Winer EP, Lin NU, Shapiro GI, Wagle N. Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer. Ann Oncol 2020; 31:590-598. [PMID: 32245699 DOI: 10.1016/j.annonc.2020.02.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [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: 09/11/2019] [Revised: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Little is known about mechanisms of resistance to poly(adenosine diphosphate-ribose) polymerase inhibitors (PARPi) and platinum chemotherapy in patients with metastatic breast cancer and BRCA1/2 mutations. Further investigation of resistance in clinical cohorts may point to strategies to prevent or overcome treatment failure. PATIENTS AND METHODS We obtained tumor biopsies from metastatic breast cancer patients with BRCA1/2 deficiency before and after acquired resistance to PARPi or platinum chemotherapy. Whole exome sequencing was carried out on each tumor, germline DNA, and circulating tumor DNA. Tumors underwent RNA sequencing, and immunohistochemical staining for RAD51 foci on tumor sections was carried out for functional assessment of intact homologous recombination (HR). RESULTS Pre- and post-resistance tumor samples were sequenced from eight patients (four with BRCA1 and four with BRCA2 mutation; four treated with PARPi and four with platinum). Following disease progression on DNA-damaging therapy, four patients (50%) acquired at least one somatic reversion alteration likely to result in functional BRCA1/2 protein detected by tumor or circulating tumor DNA sequencing. Two patients with germline BRCA1 deficiency acquired genomic alterations anticipated to restore HR through increased DNA end resection: loss of TP53BP1 in one patient and amplification of MRE11A in another. RAD51 foci were acquired post-resistance in all patients with genomic reversion, consistent with reconstitution of HR. All patients whose tumors demonstrated RAD51 foci post-resistance were intrinsically resistant to subsequent lines of DNA-damaging therapy. CONCLUSIONS Genomic reversion in BRCA1/2 was the most commonly observed mechanism of resistance, occurring in four of eight patients. Novel sequence alterations leading to increased DNA end resection were seen in two patients, and may be targetable for therapeutic benefit. The presence of RAD51 foci by immunohistochemistry was consistent with BRCA1/2 protein functional status from genomic data and predicted response to later DNA-damaging therapy, supporting RAD51 focus formation as a clinically useful biomarker.
Collapse
Affiliation(s)
- A G Waks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Broad Institute of MIT and Harvard, Cambridge, USA; Harvard Medical School, Boston, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA
| | - O Cohen
- Broad Institute of MIT and Harvard, Cambridge, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA
| | - B Kochupurakkal
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, USA
| | - D Kim
- Broad Institute of MIT and Harvard, Cambridge, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA
| | - C E Dunn
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, USA
| | - J Buendia Buendia
- Broad Institute of MIT and Harvard, Cambridge, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA
| | - S Wander
- Broad Institute of MIT and Harvard, Cambridge, USA; Harvard Medical School, Boston, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, USA
| | - K Helvie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA
| | - M R Lloyd
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; University of Massachusetts Medical School, Worcester, USA
| | - L Marini
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA
| | - M E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - S S Freeman
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - S P Ivy
- Investigational Drug Branch, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, USA
| | - J Geradts
- City of Hope Comprehensive Cancer Center, Duarte, USA
| | - S Isakoff
- Harvard Medical School, Boston, USA; Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, USA
| | | | | | - S M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA
| | - U Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA
| | - I E Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA
| | - A D D'Andrea
- Harvard Medical School, Boston, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - E P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA
| | - N U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA
| | - G I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Harvard Medical School, Boston, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, USA
| | - N Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Brigham and Women's Hospital, Boston, USA; Broad Institute of MIT and Harvard, Cambridge, USA; Harvard Medical School, Boston, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, USA.
| |
Collapse
|
22
|
Chen H, Carrot-Zhang J, Zhao Y, Hu H, Freeman SS, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, Zhang J, Ramachandran A, Zheng Q, Pan Y, Zheng D, Zheng S, Cheng C, Kuang M, Zhou X, Zhang Y, Li H, Ye T, Ma Y, Gao Z, Tao X, Han H, Shang J, Yu Y, Bao D, Huang Y, Li X, Zhang Y, Xiang J, Sun Y, Li Y, Cherniack AD, Campbell JD, Shi L, Meyerson M. Genomic and immune profiling of pre-invasive lung adenocarcinoma. Nat Commun 2019; 10:5472. [PMID: 31784532 PMCID: PMC6884501 DOI: 10.1038/s41467-019-13460-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [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: 11/30/2018] [Accepted: 10/31/2019] [Indexed: 12/30/2022] Open
Abstract
Adenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these lesions are poorly understood. Here we report exome and transcriptome sequencing of 98 lung adenocarcinoma precursor lesions and 99 invasive adenocarcinomas. We have identified EGFR, RBM10, BRAF, ERBB2, TP53, KRAS, MAP2K1 and MET as significantly mutated genes in the pre/minimally invasive group. Classes of genome alterations that increase in frequency during the progression to malignancy are revealed. These include mutations in TP53, arm-level copy number alterations, and HLA loss of heterozygosity. Immune infiltration is correlated with copy number alterations of chromosome arm 6p, suggesting a link between arm-level events and the tumor immune environment.
Collapse
Grants
- T32 HG002295 NHGRI NIH HHS
- U2C CA233238 NCI NIH HHS
- National Natural Science Foundation of China (National Science Foundation of China)
- Shanghai Shen Kang Hospital Development Center
- This study is supported by the National Natural Science Foundation of China (81330056, 81572253, 31720103909, 31471239, and 31671368), Shanghai Shen Kang Hospital Development Center City Hospital Emerging Cutting-edge Technology Joint Research Project (SHDC12017102), National Key Research and Development Plan (2016YFC0902302), Chinese Minister of Science and Technology grant (2016YFA0501800, 2017YFC1311004, 2016YFC1201701 and 2017YFA0505501), the National Key R&D Project of China (2016YFC0901704, 2017YFC0907502, and 2017YFF0204600), Shanghai Municipal Science and Technology Major Project (2017SHZDZX01), the National Human Genetic Resources Sharing Service Platform (2005DKA21300), and Shanghai R&D Public Service Platform Project (12DZ2295100). M.M. receives a grant from Stand Up to Cancer (SU2C-AACR-DT23-17) and the Pre-Cancer Genome Atlas 2.0 (1U2CCA233238-01). J.C.-Z. has a Canadian Institutes of Health Research (CIHR) fellowship. J.D.C. is funded by the LUNGevity Career Development award.
Collapse
Affiliation(s)
- Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Institute of Thoracic Oncology, Fudan University, Shanghai, China.
| | - Jian Carrot-Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haichuan Hu
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Samuel S Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Su Yu
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gavin Ha
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alison M Taylor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Aruna Ramachandran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yunjian Pan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Difan Zheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shanbo Zheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao Cheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Muyu Kuang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyan Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yang Zhang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hang Li
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Ye
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan Ma
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhendong Gao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoting Tao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Han Han
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Yechao Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiangnan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Yawei Zhang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqing Xiang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D Campbell
- Division of Computational Biomedicine, Department of Medicine, Boston University, Boston, MA, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
23
|
Hassounah NB, Malladi VS, Huang Y, Freeman SS, Beauchamp EM, Koyama S, Souders N, Martin S, Dranoff G, Wong KK, Pedamallu CS, Hammerman PS, Akbay EA. Identification and characterization of an alternative cancer-derived PD-L1 splice variant. Cancer Immunol Immunother 2019; 68:407-420. [PMID: 30564890 PMCID: PMC6428600 DOI: 10.1007/s00262-018-2284-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [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: 05/25/2018] [Accepted: 12/06/2018] [Indexed: 12/17/2022]
Abstract
Therapeutic blockade of the PD-1/PD-L1 axis is recognized as an effective treatment for numerous cancer types. However, only a subset of patients respond to this treatment, warranting a greater understanding of the biological mechanisms driving immune evasion via PD-1/PD-L1 signaling and other T-cell suppressive pathways. We previously identified a head and neck squamous cell carcinoma with human papillomavirus integration in the PD-L1 locus upstream of the transmembrane domain-encoding region, suggesting expression of a truncated form of PD-L1 (Parfenov et al., Proc Natl Acad Sci USA 111(43):15544-15549, 2014). In this study, we extended this observation by performing a computational analysis of 33 other cancer types as well as human cancer cell lines, and identified additional PD-L1 isoforms with an exon 4 enrichment expressed in 20 cancers and human cancer cell lines. We demonstrate that cancer cell lines with high expression levels of exon 4-enriched PD-L1 generate a secreted form of PD-L1. Further biochemical studies of exon 4-enriched PD-L1 demonstrated that this form is secreted and maintains the capacity to bind PD-1 as well as to serve as a negative regulator on T cell function, as measured by inhibition of IL-2 and IFNg secretion. Overall, we have demonstrated that truncated forms of PD-L1 exist in numerous cancer types, and have validated that truncated PD-L1 can be secreted and negatively regulate T cell function.
Collapse
Affiliation(s)
- Nadia B Hassounah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Venkat S Malladi
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yi Huang
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
- Simmons Comprehensive Cancer Center, Dallas, TX, USA
| | - Samuel S Freeman
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ellen M Beauchamp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shohei Koyama
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas Souders
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sunil Martin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Glenn Dranoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology and Cancer Vaccine Center, Dana Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Ludwig Institute for Cancer, Boston, MA, USA
- Belfer Institute for Applied Cancer Science, Boston, MA, USA
| | - Chandra S Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter S Hammerman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Esra A Akbay
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.
- Simmons Comprehensive Cancer Center, Dallas, TX, USA.
| |
Collapse
|
24
|
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2019; 176:404. [PMID: 30633907 DOI: 10.1016/j.cell.2018.12.034] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
25
|
Choudhury AD, Werner L, Francini E, Wei XX, Ha G, Freeman SS, Rhoades J, Reed SC, Gydush G, Rotem D, Lo C, Taplin ME, Harshman LC, Zhang Z, O'Connor EP, Stover DG, Parsons HA, Getz G, Meyerson M, Love JC, Hahn WC, Adalsteinsson VA. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight 2018; 3:122109. [PMID: 30385733 DOI: 10.1172/jci.insight.122109] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [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: 05/07/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tumor content in circulating cell-free DNA (cfDNA) is a promising biomarker, but longitudinal dynamics of tumor-derived and non-tumor-derived cfDNA through multiple courses of therapy have not been well described. METHODS CfDNA from 663 plasma samples from 140 patients with castration-resistant prostate cancer (CRPC) was subject to sparse whole genome sequencing. Tumor fraction (TFx) estimated using the computational tool ichorCNA was correlated with clinical features and responses to therapy. RESULTS TFx associated with the number of bone metastases (median TFx = 0.014 with no bone metastases, 0.047 with 1-3 bone metastases, 0.190 for 4+ bone metastases; P < 0.0001) and with visceral metastases (P < 0.0001). In multivariable analysis, TFx remained associated with metastasis location (P = 0.042); TFx was positively correlated with alkaline phosphatase (P = 0.0227) and negatively correlated with hemoglobin (Hgb) (P < 0.001), but it was not correlated with prostate specific antigen (PSA) (P = 0.75). Tumor-derived and non-tumor-derived cfDNA track together and do not increase with generalized tissue damage from chemotherapy or radiation at the time scales examined. All new treatments that led to ≥30% PSA decline at 6 weeks were associated with TFx decline when baseline TFx was >7%; however, TFx in patients being subsequently maintained on secondary hormonal therapy was quite dynamic. CONCLUSION TFx correlates with clinical features associated with overall survival in CRPC, and TFx decline is a promising biomarker for initial therapeutic response. TRIAL REGISTRATION Dana-Farber/Harvard Cancer Center (DF/HCC) protocol no. 18-135. FUNDING Wong Family Award in Translational Oncology, Dana Farber Cancer Institute Medical Oncology grant, Gerstner Family Foundation, Janssen Pharmaceuticals Inc., and Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute (NCI).
Collapse
Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lillian Werner
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Edoardo Francini
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Sapienza University of Rome, Rome, Italy
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samuel S Freeman
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justin Rhoades
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah C Reed
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory Gydush
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Denisse Rotem
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher Lo
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren C Harshman
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | - Heather A Parsons
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gad Getz
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - J Christopher Love
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Viktor A Adalsteinsson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
26
|
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2018; 175:998-1013.e20. [PMID: 30388456 PMCID: PMC6641984 DOI: 10.1016/j.cell.2018.10.038] [Citation(s) in RCA: 998] [Impact Index Per Article: 166.3] [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] [Received: 01/17/2018] [Revised: 07/07/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023]
Abstract
Treatment of cancer has been revolutionized by immune checkpoint blockade therapies. Despite the high rate of response in advanced melanoma, the majority of patients succumb to disease. To identify factors associated with success or failure of checkpoint therapy, we profiled transcriptomes of 16,291 individual immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors. Two distinct states of CD8+ T cells were defined by clustering and associated with patient tumor regression or progression. A single transcription factor, TCF7, was visualized within CD8+ T cells in fixed tumor samples and predicted positive clinical outcome in an independent cohort of checkpoint-treated patients. We delineated the epigenetic landscape and clonality of these T cell states and demonstrated enhanced antitumor immunity by targeting novel combinations of factors in exhausted cells. Our study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy.
Collapse
MESH Headings
- Animals
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/pharmacology
- Antigens, CD/immunology
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/pharmacology
- Apyrase/antagonists & inhibitors
- Apyrase/immunology
- CD8-Positive T-Lymphocytes/immunology
- Cell Line, Tumor
- Humans
- Immunotherapy/methods
- Leukocyte Common Antigens/antagonists & inhibitors
- Leukocyte Common Antigens/immunology
- Melanoma/immunology
- Melanoma/therapy
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- T Cell Transcription Factor 1/metabolism
- Transcriptome
Collapse
Affiliation(s)
- Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Keren Yizhak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Stacey L Bjorgaard
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - John P Ray
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Carl G de Boer
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Russell W Jenkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - David J Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jonathan H Chen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Dennie T Frederick
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Michal Barzily-Rokni
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, HMS, Boston, MA, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul J Hoover
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Brigham & Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Elena Ivanova
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Andrew Portell
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Patrick H Lizotte
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Amir R Aref
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Jean-Pierre Eliane
- Department of Pathology, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Marc R Hammond
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Hans Vitzthum
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Shauna M Blackmon
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Bo Li
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Virology, Harvard Medical School, Boston, MA, USA
| | | | - Sangeetha M Reddy
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary A Cooper
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cloud P Paweletz
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - David A Barbie
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | | | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Surgery, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, HMS, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA.
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA.
| |
Collapse
|
27
|
Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell 2018; 174:433-447.e19. [PMID: 29909985 PMCID: PMC6046279 DOI: 10.1016/j.cell.2018.05.036] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [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: 12/13/2017] [Revised: 03/09/2018] [Accepted: 05/16/2018] [Indexed: 01/17/2023]
Abstract
Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS) studies of this disease state. We performed linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing data from 86 patients with mCRPC. In addition to frequent rearrangements affecting known prostate cancer genes, we observed complex rearrangements of the AR locus in most cases. Unexpectedly, these rearrangements include highly recurrent tandem duplications involving an upstream enhancer of AR in 70%-87% of cases compared with <2% of primary prostate cancers. A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.
Collapse
Affiliation(s)
- Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Gavin Ha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Andreas M Hoff
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Jeremiah A Wala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jian Carrot-Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas J Haradhvala
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Samuel S Freeman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sarah C Reed
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Justin Rhoades
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paz Polak
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Stephanie A Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alicia Wong
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tushar Kamath
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Zhenwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory J Gydush
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Denisse Rotem
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J Christopher Love
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Stacey Gabriel
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cheng-Zhong Zhang
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Cambridge, MA, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 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
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Viktor A Adalsteinsson
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Brigham and Women's Hospital, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
28
|
Getz G, Cibulskis C, Leshchiner I, Hanna M, Livitz D, Slowik K, Levovitz C, Utro F, Rhrissorrakrai K, Rotem D, Gydush G, Reed SC, Rhoades J, Ha G, Freeman SS, Lo C, Fleharty M, Abreu J, Larkin K, Cipicchio M, Blumenstiel B, DeFelice M, Grimsby J, Hamilton S, Lennon N, Adalsteinsson VA, Parida L. Abstract 3001: Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3001] [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 Broad/IBM Cancer Resistance Project has partnered with Broad Genomics to pilot the use of cutting edge sequencing technology for the analysis of cell free DNA in blood biopsies. Working closely with the Broad's Cancer Program, Broad Genomics has developed a suite of liquid biopsy sequencing products designed to provide optimal flexibility in conducting research studies with a broad range of applications including; biomarker discovery, treatment resistance monitoring, and detection of minimal residual disease (MRD) post-surgery. Cell-free DNA is extracted from the blood, and a dual unique-molecular-indexed library is created. From this library, low coverage whole genome (ultra-low-pass 0.1x coverage) data is generated to survey sample quality and evaluate the tumor fraction in the liquid specimen. Utilizing the same library, additional assays can be selected for processing based on the research aim (Targeted Panel Assays, MRD Detection or Whole Exomes). Since our approach utilizes the same genomic material for whole genome and targeted sequencing assays, it is possible to maximize the information learned from each valuable and limited liquid biopsy specimen. Our study design takes advantage of the discovery potential of combined tissue-based sequencing and serial liquid biopsy analysis to elucidate mechanisms of cancer resistance by tracking the evolution of clonal and subclonal populations in patients samples over time. This collaboration will utilize the ultra-low-pass sequencing and whole exome sequencing together with custom analysis pipelines to correlate the genomic events with patient clinical data. We aim to process 3,000 samples from 1,000 patients over the next 3 years. To date we have processed close to 500 samples through the ultra-low-pass pipeline and 100 samples through the whole exome sequencing pipeline (results to be provided).The ability to successfully investigate treatment resistant cancers from non-invasive liquid biopsies presents new opportunities for identifying markers, understanding dynamics and monitoring tumor dissemination and clonal evolution.
Citation Format: Gad Getz, Carrie Cibulskis, Ignaty Leshchiner, Megan Hanna, Dimitri Livitz, Kara Slowik, Chaya Levovitz, Filippo Utro, Kahn Rhrissorrakrai, Denisse Rotem, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Gavin Ha, Samuel S. Freeman, Christopher Lo, Mark Fleharty, Justin Abreu, Katie Larkin, Michelle Cipicchio, Brendan Blumenstiel, Matt DeFelice, Jonna Grimsby, Susanna Hamilton, Niall Lennon, Viktor A. Adalsteinsson, Laxmi Parida. Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3001.
Collapse
Affiliation(s)
- Gad Getz
- 1MGH Cancer Center and Broad Institute, Charlestown, MA
| | | | | | | | | | | | | | - Filippo Utro
- 3IBM T. J. Watson Research, Yorktown Heights, NY
| | | | | | | | | | | | - Gavin Ha
- 4Broad Institute, Harvard University, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Laxmi Parida
- 3IBM T. J. Watson Research, Yorktown Heights, NY
| |
Collapse
|
29
|
Freeman SS, Lin Z, Ha G, Leshchiner I, Rhoades J, Livitz D, Rosebrock D, Reed SC, Gydush G, Lo C, Rotem D, Choudhury AD, Stover DG, Parsons HA, Boehm JS, Love JC, Meyerson M, Grandgenett P, Hollingsworth MA, Adalsteinsson VA, Getz G. Abstract LB-225: Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-225] [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
Introduction: Precision medicine approaches to guide therapy selection require routine sampling of tumors. However, tumor biopsies are not always accessible and may be confounded by spatial heterogeneity. Liquid biopsies, including analysis of cell-free DNA (cfDNA), present a non-invasive alternative which may reflect multiple tumors in the body. Previous studies have demonstrated exome-wide concordance between single-site tumor biopsies and cfDNA, but little is known about how cfDNA reflects multiple lesions within a patient. Here we sought to determine how cfDNA reflects the body-wide tumor phylogeny, which will inform the use of cfDNA for cancer precision medicine.
Methods: We identified 20 patients with pancreatic cancer who had undergone rapid autopsy. We then screened cfDNA tumor fraction and performed whole-exome sequencing of cfDNA and multiple tumor biopsies for 3 patients with cfDNA tumor fraction >10%. We inferred the tumor phylogeny and then developed a statistical approach to deconvolute the contributions to cfDNA from tumor phylogenetic nodes. Finally, we determined whether shared trunk mutations could be detected in cfDNA and tumor biopsies.
Results: For each patient, we found mutations shared between all sites and cfDNA, including putative driver mutations. We found mutations which were clonal in multiple regions were detectable in cfDNA, whereas mutations private to individual sites were never clonal in cfDNA. Through our deconvolution analysis, we found that cfDNA could not be modeled as a simple linear combination of individual sites, but rather that cfDNA represented multiple nodes in the inferred phylogeny. For two pancreatic adenocarcinoma patients, the inferred ancestor of the metastases had high estimated contribution (>70%) to cfDNA, while the ancestors of the primaries had lower contributions (<10%). Next, we considered trunk mutations, which originate earliest in the tumor phylogenetic tree. When we analyzed precision for detection of trunk mutations, we found on average, 71% of clonal mutations in metastases were truncal, while only 55% of clonal mutations in primary tumors were truncal. Due to copy number deletions, not all trunk mutations were detected in metastases. Finally, on average, cfDNA had equal or better precision than 83% of primaries and 88% of metastases, suggesting cfDNA may provide more accurate trunk SSNV calls than tumor biopsies.
Conclusions: Through analyzing cfDNA and synchronous tumor biopsies from the same patient, we find trunk mutations are enriched in cfDNA as compared to the average single-site biopsy. We also predict that cfDNA represents multiple nodes in the inferred phylogeny. In cases where tumor biopsies are inaccessible, we demonstrate that cfDNA might be a promising alternative to detect trunk SSNVs. These results suggest that cfDNA may be complementary to tumor biopsies for disease monitoring and treatment selection in personalized medicine.
Citation Format: Samuel S. Freeman, Ziao Lin, Gavin Ha, Ignaty Leshchiner, Justin Rhoades, Dimitri Livitz, Daniel Rosebrock, Sarah C. Reed, Gregory Gydush, Christopher Lo, Denisse Rotem, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Jesse S. Boehm, J Christopher Love, Matthew Meyerson, Paul Grandgenett, Michael A. Hollingsworth, Viktor A. Adalsteinsson, Gad Getz. Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-225.
Collapse
Affiliation(s)
| | | | - Gavin Ha
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | | | - Daniel G. Stover
- 3Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | | | | | | | - Gad Getz
- 6Massachusetts General Hospital, Boston, MA
| |
Collapse
|
30
|
Manier S, Park J, Capelletti M, Bustoros M, Freeman SS, Ha G, Rhoades J, Liu CJ, Huynh D, Reed SC, Gydush G, Salem KZ, Rotem D, Freymond C, Yosef A, Perilla-Glen A, Garderet L, Van Allen EM, Kumar S, Love JC, Getz G, Adalsteinsson VA, Ghobrial IM. Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun 2018; 9:1691. [PMID: 29703982 PMCID: PMC5923255 DOI: 10.1038/s41467-018-04001-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [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: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 12/29/2022] Open
Abstract
Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM. Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) enables characterization of a patient’s cancer. Here, the authors analyse CTCs, cfDNA, and tumor biopsies from multiple myeloma patients to show these approaches are complementary for mutation detection, together enabling a greater fraction of patient tumors to be profiled.
Collapse
Affiliation(s)
- S Manier
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Hematology Department, CHU, Univ. Lille, 59000, Lille, France.,INSERM UMR-S1172, 59000, Lille, France
| | - J Park
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - M Capelletti
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - M Bustoros
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - S S Freeman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Ha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - J Rhoades
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - C J Liu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - D Huynh
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - S C Reed
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Gydush
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - K Z Salem
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - D Rotem
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - C Freymond
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - A Yosef
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - A Perilla-Glen
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - L Garderet
- Department of Hematology, St-Antoine University Hospital, Paris, 75000, France
| | - E M Van Allen
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - S Kumar
- Department of Hematology, Mayo Clinic, Rochester, MN, 55902, USA
| | - J C Love
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - V A Adalsteinsson
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - I M Ghobrial
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA. .,Brigham and Women's Hospital, Boston, MA, 02115, USA. .,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| |
Collapse
|
31
|
Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol 2018; 36:543-553. [PMID: 29298117 PMCID: PMC5815405 DOI: 10.1200/jco.2017.76.0033] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [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] [Indexed: 12/19/2022] Open
Abstract
Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.
Collapse
Affiliation(s)
- Daniel G. Stover
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Heather A. Parsons
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gavin Ha
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Samuel S. Freeman
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - William T. Barry
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Hao Guo
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Atish D. Choudhury
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gregory Gydush
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah C. Reed
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Justin Rhoades
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Denisse Rotem
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Melissa E. Hughes
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Deborah A. Dillon
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ann H. Partridge
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nikhil Wagle
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ian E. Krop
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gad Getz
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Todd R. Golub
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Christopher Love
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Eric P. Winer
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sara M. Tolaney
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nancy U. Lin
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Viktor A. Adalsteinsson
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| |
Collapse
|
32
|
Pectasides E, Stachler MD, Derks S, Liu Y, Maron S, Islam M, Alpert L, Kwak H, Kindler H, Polite B, Sharma MR, Allen K, O'Day E, Lomnicki S, Maranto M, Kanteti R, Fitzpatrick C, Weber C, Setia N, Xiao SY, Hart J, Nagy RJ, Kim KM, Choi MG, Min BH, Nason KS, O'Keefe L, Watanabe M, Baba H, Lanman R, Agoston AT, Oh DJ, Dunford A, Thorner AR, Ducar MD, Wollison BM, Coleman HA, Ji Y, Posner MC, Roggin K, Turaga K, Chang P, Hogarth K, Siddiqui U, Gelrud A, Ha G, Freeman SS, Rhoades J, Reed S, Gydush G, Rotem D, Davison J, Imamura Y, Adalsteinsson V, Lee J, Bass AJ, Catenacci DV. Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma. Cancer Discov 2017; 8:37-48. [PMID: 28978556 DOI: 10.1158/2159-8290.cd-17-0395] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/21/2017] [Accepted: 09/29/2017] [Indexed: 02/07/2023]
Abstract
Gastroesophageal adenocarcinoma (GEA) is a lethal disease where targeted therapies, even when guided by genomic biomarkers, have had limited efficacy. A potential reason for the failure of such therapies is that genomic profiling results could commonly differ between the primary and metastatic tumors. To evaluate genomic heterogeneity, we sequenced paired primary GEA and synchronous metastatic lesions across multiple cohorts, finding extensive differences in genomic alterations, including discrepancies in potentially clinically relevant alterations. Multiregion sequencing showed significant discrepancy within the primary tumor (PT) and between the PT and disseminated disease, with oncogene amplification profiles commonly discordant. In addition, a pilot analysis of cell-free DNA (cfDNA) sequencing demonstrated the feasibility of detecting genomic amplifications not detected in PT sampling. Lastly, we profiled paired primary tumors, metastatic tumors, and cfDNA from patients enrolled in the personalized antibodies for GEA (PANGEA) trial of targeted therapies in GEA and found that genomic biomarkers were recurrently discrepant between the PT and untreated metastases. Divergent primary and metastatic tissue profiling led to treatment reassignment in 32% (9/28) of patients. In discordant primary and metastatic lesions, we found 87.5% concordance for targetable alterations in metastatic tissue and cfDNA, suggesting the potential for cfDNA profiling to enhance selection of therapy.Significance: We demonstrate frequent baseline heterogeneity in targetable genomic alterations in GEA, indicating that current tissue sampling practices for biomarker testing do not effectively guide precision medicine in this disease and that routine profiling of metastatic lesions and/or cfDNA should be systematically evaluated. Cancer Discov; 8(1); 37-48. ©2017 AACR.See related commentary by Sundar and Tan, p. 14See related article by Janjigian et al., p. 49This article is highlighted in the In This Issue feature, p. 1.
Collapse
Affiliation(s)
- Eirini Pectasides
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Matthew D Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sarah Derks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Yang Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Steven Maron
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Mirazul Islam
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Lindsay Alpert
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Heewon Kwak
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Hedy Kindler
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Blase Polite
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Manish R Sharma
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Kenisha Allen
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Emily O'Day
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Samantha Lomnicki
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Melissa Maranto
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Rajani Kanteti
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Carrie Fitzpatrick
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Christopher Weber
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Namrata Setia
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Shu-Yuan Xiao
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - John Hart
- Department of Pathology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | | | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min-Gew Choi
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung-Hoon Min
- Department of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Katie S Nason
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lea O'Keefe
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Masayuki Watanabe
- Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Rick Lanman
- Guardant Health, Inc., Redwood City, California
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David J Oh
- University of New England College of Osteopathic Medicine, Biddeford, Maine
| | - Andrew Dunford
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew D Ducar
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bruce M Wollison
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Haley A Coleman
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Mitchell C Posner
- Department of Surgery, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Kevin Roggin
- Department of Surgery, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Kiran Turaga
- Department of Surgery, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Paul Chang
- Department of Radiology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Kyle Hogarth
- Department of Medicine, Section of Pulmonary and Critical Care, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Uzma Siddiqui
- Department of Medicine, Section of Gastroenterology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Andres Gelrud
- Department of Medicine, Section of Gastroenterology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Gavin Ha
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | | | - Justin Rhoades
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Sarah Reed
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Greg Gydush
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Denisse Rotem
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Jon Davison
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yu Imamura
- Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Daniel V Catenacci
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois.
| |
Collapse
|
33
|
Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 2016; 30:750-763. [PMID: 27818134 PMCID: PMC5127278 DOI: 10.1016/j.ccell.2016.10.005] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [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: 11/12/2015] [Revised: 09/01/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2022]
Abstract
Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to CLL progression remains poorly understood. We undertook a transcriptomic characterization of primary human CLL cells to identify transcripts and pathways affected by SF3B1 mutation. Splicing alterations, identified in the analysis of bulk cells, were confirmed in single SF3B1-mutated CLL cells and also found in cell lines ectopically expressing mutant SF3B1. SF3B1 mutation was found to dysregulate multiple cellular functions including DNA damage response, telomere maintenance, and Notch signaling (mediated through KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively). SF3B1 mutation leads to diverse changes in CLL-related pathways.
Collapse
Affiliation(s)
- Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Angela N Brooks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; University of California, Santa Cruz, CA 95064, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Youzhong Wan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; National Engineering Laboratory of AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin, PRC
| | - Rutendo Gambe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Shuqiang Li
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Sarah Hergert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Joshua Z Levin
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Lin Fan
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | | | | | | | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emanuela M Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stacey Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Donald B Bloch
- Center for Immunology and Inflammatory Disease, Massachusetts General Hospital, Boston, MA 02115, USA
| | | | - Dan A Landau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David S DeLuca
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Matthew M Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
34
|
Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V. Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease. Cell Mol Gastroenterol Hepatol 2016; 2:563-566.e5. [PMID: 28174737 PMCID: PMC5042890 DOI: 10.1016/j.jcmgh.2016.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/15/2016] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer. Diseased and healthy-appearing ileum was identified using microscopy, and paraffin blocks were macrodissected using a core needle to specifically isolate DNA. Illumina Whole Genome Sequencing was used for microbial sequence identification and subsequent taxonomic classification using the PathSeq tool. RESULTS We observed significant differences between the microbiome of CD samples vs inflammatory bowel disease-free controls, including depletion of Bacteroidetes and Clostridia. Notably, microbial composition at the phyla level did not differ markedly between healthy and diseased areas of CD patients. However, we observed enrichment of potentially pathogenic organisms at the species level. CONCLUSIONS Our study showed dysbiosis within deeper layers of the ileum of CD patients, specifically enrichment of enterotoxigenic Staphylococcus aureus and an environmental Mycobacterium species not described previously. Future studies with larger cohort sizes are warranted to confirm these findings. Studies would benefit from effective microbial DNA extraction methods from paraffin sections and host nucleic acid depletion approaches to increase microbial read coverage.
Collapse
Affiliation(s)
- Chandra Sekhar Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Ami S. Bhatt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sharyle Fowler
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Jacqueline Durand
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Joonil Jung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Fujiko Duke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Veronica Manzo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Diana Cai
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Akinyemi I. Ojesina
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aruna Ramachandran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ramnik J. Xavier
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Atul K. Bhan
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts,Matthew Meyerson, MD, PhD, Dana-Farber Cancer Institute, Boston, Massachusetts 02215. fax: 617-582-7880.Dana-Farber Cancer InstituteBostonMassachusetts 02215
| | - Vijay Yajnik
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts,Correspondence Address correspondence to: Vijay Yajnik, MD, PhD, Crohn's and Colitis Center, Massachusetts General Hospital, Massachusetts 02114.Crohn's and Colitis CenterMassachusetts General HospitalMassachusetts 02114
| |
Collapse
|
35
|
Brooks AN, Ge Y, Chau K, Freeman SS, Saksena G, Pedamallu CS, Meyerson M. Abstract B2-21: Identification of somatic RNA splicing alterations in human cancers. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-21] [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
Recent whole-exome sequencing studies have found that somatic mutations frequently occur in splicing factors across multiple cancer types, supporting the need to systematically and globally characterize splicing alterations across human cancers. Somatic alterations that affect RNA processing of cancer genes may be caused by multiple mechanisms, including mutations in splicing factors, mutations in cis-acting splice sites and other regulatory sequences, alterations in methylation, or alterations in chromatin structure. For a global look at somatic RNA splicing alterations, we are applying the Cancer Outlier Profile Analysis (COPA) approach on ~7,000 cancer transcriptomes from 12 tumor types in The Cancer Genome Atlas (TCGA) and investigating the underlying somatic mutations that cause these splicing alterations using matched whole-exome, whole-genome, and methylation data from these samples.
To identify and quantify alternative splicing in RNA-Seq data, including unannotated splicing events, we have further developed a computational pipeline called JuncBASE. To distinguish between cancer-specific splicing alterations and normal transcriptome variation, we are utilizing ~700 RNA-Seq libraries from healthy individuals from the Genotype-Tissue Expression (GTEx) project.
COPA analysis of outlier splicing events in lung adenocarcinomas and glioblastomas successfully identified known altered splicing events in MET and EGFR, respectively, that are caused by DNA level somatic mutations. The genomic mechanisms for novel somatic splicing events in known cancer genes such as FGFR3, as well as genes previously uncharacterized in cancer genomes, are currently being investigated.
To identify splicing events that may be novel somatic driver alterations, these events have been profiled using RNA-Seq data from the Cancer Cell Line Encyclopedia and are being used as biomarkers to identify genetic vulnerabilities in high-throughput shRNA screens. This work will have a significant impact on the identification of somatic splicing events that contribute to cancer pathogenesis.
Citation Format: Angela N. Brooks, Yawei Ge, Kevin Chau, Samuel S. Freeman, Gordon Saksena, Chandra Sekhar Pedamallu, Matthew Meyerson. Identification of somatic RNA splicing alterations in human cancers. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-21.
Collapse
Affiliation(s)
| | - Yawei Ge
- 2Harvard Medical School, Boston, MA,
| | | | | | | | | | | |
Collapse
|
36
|
Chung TKH, Van Hummelen P, Chan PKS, Cheung TH, Yim SF, Yu MY, Ducar MD, Thorner AR, MacConaill LE, Doran G, Pedamallu CS, Ojesina AI, Wong RRY, Wang VW, Freeman SS, Lau TS, Kwong J, Chan LKY, Fromer M, May T, Worley MJ, Esselen KM, Elias KM, Lawrence M, Getz G, Smith DI, Crum CP, Meyerson M, Berkowitz RS, Wong YF. Genomic aberrations in cervical adenocarcinomas in Hong Kong Chinese women. Int J Cancer 2015; 137:776-83. [PMID: 25626421 DOI: 10.1002/ijc.29456] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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: 08/12/2014] [Accepted: 01/12/2015] [Indexed: 01/14/2023]
Abstract
Although the rates of cervical squamous cell carcinoma have been declining, the rates of cervical adenocarcinoma are increasing in some countries. Outcomes for advanced cervical adenocarcinoma remain poor. Precision mapping of genetic alterations in cervical adenocarcinoma may enable better selection of therapies and deliver improved outcomes when combined with new sequencing diagnostics. We present whole-exome sequencing results from 15 cervical adenocarcinomas and paired normal samples from Hong Kong Chinese women. These data revealed a heterogeneous mutation spectrum and identified several frequently altered genes including FAT1, ARID1A, ERBB2 and PIK3CA. Exome sequencing identified human papillomavirus (HPV) sequences in 13 tumors in which the HPV genome might have integrated into and hence disrupted the functions of certain exons, raising the possibility that HPV integration can alter pathways other than p53 and pRb. Together, these provisionary data suggest the potential for individualized therapies for cervical adenocarcinoma based on genomic information.
Collapse
Affiliation(s)
- Tony K H Chung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Paul Van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Paul K S Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Tak Hong Cheung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - So Fan Yim
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Mei Y Yu
- Department of Anatomical & Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Matthew D Ducar
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Laura E MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Graeme Doran
- Department of Pathology, Harvard Medical School, Boston, MA
| | - Chandra Sekhar Pedamallu
- Cancer Program, The Broad Institute of MIT and Harvard University, Cambridge, MA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Akinyemi I Ojesina
- Cancer Program, The Broad Institute of MIT and Harvard University, Cambridge, MA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Raymond R Y Wong
- Harvard Medical School, Pediatric Surgical Laboratories, Massachusetts General Hospital, Boston, MA
| | - Vivian W Wang
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN
| | - Samuel S Freeman
- Cancer Program, The Broad Institute of MIT and Harvard University, Cambridge, MA
| | - Tat San Lau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Joseph Kwong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Loucia K Y Chan
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Menachem Fromer
- Division of Psychiatric Genomics, Mount Sinai School of Medicine, New York, NY
| | - Taymaa May
- Division of Gynecologic Oncology, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Michael J Worley
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Katharine M Esselen
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Kevin M Elias
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Michael Lawrence
- Cancer Genomics Informatics and Computational Biology, The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Gad Getz
- Cancer Genomics Informatics and Computational Biology, The Broad Institute of Harvard and MIT, Cambridge, MA
| | - David I Smith
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN
| | - Christopher P Crum
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew Meyerson
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Cancer Program, The Broad Institute of MIT and Harvard University, Cambridge, MA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ross S Berkowitz
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Yick Fu Wong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
37
|
Bhatt AS, Pedamallu CS, Duke F, Jung J, Freeman SS, Cherniak A, Park R, Kim J, Kwiatkowski D, Rosenberg J, Meyerson M. Abstract 4149: Transcriptomic and pathogen analysis in bladder cancer primary tumor and metastasis pairs. Mol Cell Biol 2014. [DOI: 10.1158/1538-7445.am2013-4149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
38
|
Ojesina AI, Murray B, Bjorge L, Woie K, Krakstad C, Lichtenstein L, Pedamallu CS, Taylor-Weiner A, Freeman SS, Cherniack AD, Lawrence MS, Cibulskis K, Carter SL, Walline H, Carey TE, Vintermyr OK, Bertelsen B, Crum CP, Getz G, Meyerson M, Salvesen HB. Abstract 4692: Relationships between somatic genomic alterations, tumor stage and progression-free survival in cervical cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-4692] [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:
Cervical cancer is a major public health problem worldwide. We have recently identified novel significantly recurrent somatic mutations in HLA-B, ERBB2 and MAPK1 in cervical squamous cell carcinomas. However, the significance of somatic mutations and copy number alterations for clinical phenotype in cervical cancer is not well understood. This study seeks to identify relationships between somatic genomic alterations, epidemiological exposures, tumor stage (FIGO) and progression-free survival in cervical carcinomas.
Methods:
Cervical tumors were surgically resected or biopsied from 100 Norwegian women with tumor stages I - IV. Patients were subsequently followed for 0-109 months (mean=25 months). Whole exome sequencing (WES) was performed on DNA extracted from tumors and corresponding normal blood. Somatic single nucleotide variants and small insertion/deletions were identified by the MuTect and Indelocator algorithms respectively. The ABSOLUTE algorithm was used to classify mutations as clonal or subclonal. Somatic copy number (CN) data were derived from WES data using the CapSeg algorithm, and significantly recurrent CN alterations were identified by GISTIC2.0 analysis (q<0.25). HPV typing was done by the multiplex fluorescent f-HPV DNA and MassARRAY assays. The log-rank test was used to compare survival curves.
Results:
Non-localized tumors (FIGO stages ≥ II) were associated with focal amplification of the FGFR2 gene on chromosomal cytoband 10q26 (GISTIC q = 0.18531). Indeed, 6 of 8 (75%) tumors with FGFR2 amplification were non-localized, in contrast to 16 of 92 (17%) tumors without FGFR2 amplification (p = 0.001). In addition, patients with somatic ERBB2 mutations and/or amplifications (p = 0.04), somatic TP53 mutations and/or deletions (p = 0.04), or infection with multiple HPV types (p = 0.02) had poorer prognosis (progression-free survival). We also observed a trend for higher frequency of subclonal driver events in patients with poorer survival (p = 0.07).
Conclusion:
We have identified novel relationships between somatic genomic alterations, tumor stage and patient prognosis in cervical cancer. Our data suggest a potential for exploring FGFR2 inhibition in non-localized cervical carcinomas with FGFR2 alterations in a clinical trial context.
Citation Format: Akinyemi I. Ojesina, Bradley Murray, Line Bjorge, Kathrine Woie, Camilla Krakstad, Lee Lichtenstein, Chandra Sekhar Pedamallu, Amaro Taylor-Weiner, Samuel S. Freeman, Andrew D. Cherniack, Michael S. Lawrence, Kristian Cibulskis, Scott L. Carter, Heather Walline, Thomas E. Carey, Olav K. Vintermyr, Bjorn Bertelsen, Christopher P. Crum, Gad Getz, Matthew Meyerson, Helga B. Salvesen. Relationships between somatic genomic alterations, tumor stage and progression-free survival in cervical cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4692. doi:10.1158/1538-7445.AM2014-4692
Collapse
Affiliation(s)
| | | | - Line Bjorge
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | - Kathrine Woie
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | - Camilla Krakstad
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | | | | | | | | | | | | | | | | | | | | | | | - Bjorn Bertelsen
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | | | - Gad Getz
- 6Broad Institute/Massachusetts General Hospital, Cambridge, MA
| | | | | |
Collapse
|
39
|
Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, Imaz-Rosshandler I, Pugh TJ, Cherniack AD, Ambrogio L, Cibulskis K, Bertelsen B, Romero-Cordoba S, Treviño V, Vazquez-Santillan K, Guadarrama AS, Wright AA, Rosenberg MW, Duke F, Kaplan B, Wang R, Nickerson E, Walline HM, Lawrence MS, Stewart C, Carter SL, McKenna A, Rodriguez-Sanchez IP, Espinosa-Castilla M, Woie K, Bjorge L, Wik E, Halle MK, Hoivik EA, Krakstad C, Gabiño NB, Gómez-Macías GS, Valdez-Chapa LD, Garza-Rodríguez ML, Maytorena G, Vazquez J, Rodea C, Cravioto A, Cortes ML, Greulich H, Crum CP, Neuberg DS, Hidalgo-Miranda A, Escareno CR, Akslen LA, Carey TE, Vintermyr OK, Gabriel SB, Barrera-Saldaña HA, Melendez-Zajgla J, Getz G, Salvesen HB, Meyerson M. Landscape of genomic alterations in cervical carcinomas. Nature 2013; 506:371-5. [PMID: 24390348 DOI: 10.1038/nature12881] [Citation(s) in RCA: 599] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 11/13/2013] [Indexed: 12/14/2022]
Abstract
Cervical cancer is responsible for 10-15% of cancer-related deaths in women worldwide. The aetiological role of infection with high-risk human papilloma viruses (HPVs) in cervical carcinomas is well established. Previous studies have also implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as several copy-number alterations in the pathogenesis of cervical carcinomas. Here we report whole-exome sequencing analysis of 115 cervical carcinoma-normal paired samples, transcriptome sequencing of 79 cases and whole-genome sequencing of 14 tumour-normal pairs. Previously unknown somatic mutations in 79 primary squamous cell carcinomas include recurrent E322K substitutions in the MAPK1 gene (8%), inactivating mutations in the HLA-B gene (9%), and mutations in EP300 (16%), FBXW7 (15%), NFE2L2 (4%), TP53 (5%) and ERBB2 (6%). We also observe somatic ELF3 (13%) and CBFB (8%) mutations in 24 adenocarcinomas. Squamous cell carcinomas have higher frequencies of somatic nucleotide substitutions occurring at cytosines preceded by thymines (Tp*C sites) than adenocarcinomas. Gene expression levels at HPV integration sites were statistically significantly higher in tumours with HPV integration compared with expression of the same genes in tumours without viral integration at the same site. These data demonstrate several recurrent genomic alterations in cervical carcinomas that suggest new strategies to combat this disease.
Collapse
Affiliation(s)
- Akinyemi I Ojesina
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3]
| | - Lee Lichtenstein
- 1] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [2]
| | - Samuel S Freeman
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Chandra Sekhar Pedamallu
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | | | - Trevor J Pugh
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Lauren Ambrogio
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Kristian Cibulskis
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Bjørn Bertelsen
- Department of Pathology, Haukeland University Hospital, N5021 Bergen, Norway
| | | | | | | | | | - Alexi A Wright
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Mara W Rosenberg
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Fujiko Duke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Bethany Kaplan
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Rui Wang
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Elizabeth Nickerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Heather M Walline
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael S Lawrence
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Chip Stewart
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Scott L Carter
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Aaron McKenna
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Iram P Rodriguez-Sanchez
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | | | - Kathrine Woie
- Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway
| | - Line Bjorge
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Elisabeth Wik
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Mari K Halle
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Erling A Hoivik
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Camilla Krakstad
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | | | - Gabriela Sofia Gómez-Macías
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Lezmes D Valdez-Chapa
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - María Lourdes Garza-Rodríguez
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | | | - Jorge Vazquez
- Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Carlos Rodea
- Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Adrian Cravioto
- Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Maria L Cortes
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Heidi Greulich
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher P Crum
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | | | - Claudia Rangel Escareno
- 1] Instituto Nacional de Medicina Genomica, Mexico City 14610, Mexico [2] Claremont Graduate University, Claremont, California 91711, USA
| | - Lars A Akslen
- 1] Department of Pathology, Haukeland University Hospital, N5021 Bergen, Norway [2] Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, N5020 Bergen, Norway
| | - Thomas E Carey
- Head and Neck Oncology Program and Department of Otolaryngology, University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan 38109, USA
| | - Olav K Vintermyr
- 1] Department of Pathology, Haukeland University Hospital, N5021 Bergen, Norway [2] Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, N5020 Bergen, Norway
| | - Stacey B Gabriel
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Hugo A Barrera-Saldaña
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | | | - Gad Getz
- 1] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Helga B Salvesen
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway [3]
| | - Matthew Meyerson
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [4]
| |
Collapse
|
40
|
Bhatt AS, Freeman SS, Herrera AF, Pedamallu CS, Gevers D, Duke F, Jung J, Michaud M, Walker BJ, Young S, Earl AM, Kostic AD, Ojesina AI, Hasserjian R, Ballen KK, Chen YB, Hobbs G, Antin JH, Soiffer RJ, Baden LR, Garrett WS, Hornick JL, Marty FM, Meyerson M. Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med 2013; 369:517-28. [PMID: 23924002 PMCID: PMC3889161 DOI: 10.1056/nejmoa1211115] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Immunosuppression is associated with a variety of idiopathic clinical syndromes that may have infectious causes. It has been hypothesized that the cord colitis syndrome, a complication of umbilical-cord hematopoietic stem-cell transplantation, is infectious in origin. METHODS We performed shotgun DNA sequencing on four archived, paraffin-embedded endoscopic colon-biopsy specimens obtained from two patients with cord colitis. Computational subtraction of human and known microbial sequences and assembly of residual sequences into a bacterial draft genome were performed. We used polymerase-chain-reaction (PCR) assays and fluorescence in situ hybridization to determine whether the corresponding bacterium was present in additional patients and controls. RESULTS DNA sequencing of the biopsy specimens revealed more than 2.5 million sequencing reads that did not match known organisms. These sequences were computationally assembled into a 7.65-Mb draft genome showing a high degree of homology with genomes of bacteria in the bradyrhizobium genus. The corresponding newly discovered bacterium was provisionally named Bradyrhizobium enterica. PCR identified B. enterica nucleotide sequences in biopsy specimens from all three additional patients with cord colitis whose samples were tested, whereas B. enterica sequences were absent in samples obtained from healthy controls and patients with colon cancer or graft-versus-host disease. CONCLUSIONS We assembled a novel bacterial draft genome from the direct sequencing of tissue specimens from patients with cord colitis. Association of these sequences with cord colitis suggests that B. enterica may be an opportunistic human pathogen. (Funded by the National Cancer Institute and others.)
Collapse
Affiliation(s)
- Ami S Bhatt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Abstract
Using organized nervous system tissue cultures of embryonic mouse spinal cord, time-lapse motion pictures of intra-axonal particle movements were made using Nomarski optics. The paths of 272 particles were followed and analyzed using digital computer methods. Particles had a bidirectional saltatory motility with net anterograde and retrograde velocities which were shown to be the same (about 1 micron per second). When anterograde moving and retrograde moving particles were analyzed separately for anterograde and retrograde saltations, the velocities of saltation in the direction of net movement were found to be 1.5 times greater than saltations against the direction of net movement. These differences were statistically significant. In addition, it was shown that there were regions within the axon where variations in particle motion were similar from particle to particle as they passed, and that more disturbed motion was found to occur near intra-axonal objects which were judged to be mitochondria. No decrease of particle velocity was noted in regions away from mitochondria nor was in increase in velocity noted near them. Computer-drawn particle plots illustrate the various facets of particle motion.
Collapse
|
42
|
Freeman SS, Engel AG, Drachman DB. Experimental acetylcholine blockade of the neuromuscular junction. Effects on end plate and muscle fiber ultrastructure. Ann N Y Acad Sci 1976; 274:46-59. [PMID: 1066994 DOI: 10.1111/j.1749-6632.1976.tb47675.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To investigate the effect of acetylcholine on the formation and maintenance of the end plate, presynaptic (hemicholinium-3 and botulinum toxin) and postsynaptic (curare and alpha-bungarotoxin) blocking agents were injected into the amniotic sac or chorioallantoic circulation of chick embryos during different stages of their development (days 3 to 11, 3 to 18, and 12 to 18). Tntercostal or anterior and posterior latissimus dorsi muscles were examined by electron microscopy. Regardless of the duration of treatment, the type of agent, or the type of muscle, nerve ingrowth into muscle and end-plate formation were not arrested and the ultrastructure of nerve terminals and postsynaptic regions was normal. By contrast, muscle fiber ultrastructure was affected by acetylcholine blockade if continued beyond day 11. By day 11 both treated and control muscles were composed primarily of myotubes. Muscles treated beyond day 11 showed impaired fiber differentiation and persistence of many myotubes. In addition, many fiber regions contained unassembled fine filaments intermingled with other organelles. In hemicholinium-3 treated muscles ther were also mitochondrial abnormalities and an increased number of lipid droplets. The findings suggest that the altered structure of the neuromusclar junction in myasthenia gravis is not due to the lack of a trophic effect of acetylcholine. The impaired fiber maturation in the chick embryos may be related to the lack of acetylcholine mediated fiber activity.
Collapse
|