1
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Maron SB, Chatila W, Walch H, Chou JF, Ceglia N, Ptashkin R, Do RKG, Paroder V, Pandit-Taskar N, Lewis JS, Biachi De Castria T, Sabwa S, Socolow F, Feder L, Thomas J, Schulze I, Kim K, Elzein A, Bojilova V, Zatzman M, Bhanot U, Nagy RJ, Lee J, Simmons M, Segal M, Ku GY, Ilson DH, Capanu M, Hechtman JF, Merghoub T, Shah S, Schultz N, Solit DB, Janjigian YY. Determinants of Survival with Combined HER2 and PD-1 Blockade in Metastatic Esophagogastric Cancer. Clin Cancer Res 2023; 29:3633-3640. [PMID: 37406106 PMCID: PMC10502449 DOI: 10.1158/1078-0432.ccr-22-3769] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE We report updated clinical outcomes from a phase II study of pembrolizumab, trastuzumab, and chemotherapy (PTC) in metastatic esophagogastric cancer in conjunction with outcomes from an independent Memorial Sloan Kettering (MSK) cohort. PATIENTS AND METHODS The significance of pretreatment 89Zr-trastuzumab PET, plasma circulating tumor DNA (ctDNA) dynamics, and tumor HER2 expression and whole exome sequencing was evaluated to identify prognostic biomarkers and mechanisms of resistance in patients treated on-protocol with PTC. Additional prognostic features were evaluated using a multivariable Cox regression model of trastuzumab-treated MSK patients (n = 226). Single-cell RNA sequencing (scRNA-seq) data from MSK and Samsung were evaluated for mechanisms of therapy resistance. RESULTS 89Zr-trastuzumab PET, scRNA-seq, and serial ctDNA with CT imaging identified how pre-treatment intrapatient genomic heterogeneity contributes to inferior progression-free survival (PFS). We demonstrated that the presence of intensely avid lesions by 89Zr-trastuzumab PET declines in tumor-matched ctDNA by 3 weeks, and clearance of tumor-matched ctDNA by 9 weeks were minimally invasive biomarkers of durable PFS. Paired pre- and on-treatment scRNA-seq identified rapid clearance of HER2-expressing tumor clones with expansion of clones expressing a transcriptional resistance program, which was associated with MT1H, MT1E, MT2A, and MSMB expression. Among trastuzumab-treated patients at MSK, ERBB2 amplification was associated with improved PFS, while alterations in MYC and CDKN2A/B were associated with inferior PFS. CONCLUSIONS These findings highlight the clinical relevance of identifying baseline intrapatient heterogeneity and serial ctDNA monitoring of HER2-positive esophagogastric cancer patients to identify early evidence of treatment resistance, which could guide proactive therapy escalation or deescalation.
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Affiliation(s)
- Steven B. Maron
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Walid Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Henry Walch
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F. Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard Kinh Gian Do
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Viktoriya Paroder
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neeta Pandit-Taskar
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason S. Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tiago Biachi De Castria
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shalom Sabwa
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fiona Socolow
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lara Feder
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasmine Thomas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabell Schulze
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kwanghee Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arijh Elzein
- Department of Pharmacology, Weill Cornell Medicine Graduate School of Medical Sciences, New York, New York
| | - Viktoria Bojilova
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Zatzman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh Bhanot
- Precision Pathology Center, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Marc Simmons
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michal Segal
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Yuyat Ku
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - David H. Ilson
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Taha Merghoub
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sohrab Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y. Janjigian
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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2
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Shahid S, Ceglia N, Le Luduec JB, McPherson A, Spitzer B, Kontopoulos T, Bojilova V, Panjwani MK, Roshal M, Shah SP, Abdel-Wahab O, Greenbaum B, Hsu KC. Immune profiling after allogeneic hematopoietic cell transplantation in pediatric acute myeloid leukemia. Blood Adv 2023; 7:5069-5081. [PMID: 37327118 PMCID: PMC10471937 DOI: 10.1182/bloodadvances.2022009468] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/08/2023] [Accepted: 05/24/2023] [Indexed: 06/18/2023] Open
Abstract
Although allogeneic hematopoietic cell transplant (allo-HCT) is curative for high-risk pediatric acute myeloid leukemia (AML), disease relapse remains the primary cause of posttransplant mortality. To identify pressures imposed by allo-HCT on AML cells that escape the graft-versus-leukemia effect, we evaluated immune signatures at diagnosis and posttransplant relapse in bone marrow samples from 4 pediatric patients using a multimodal single-cell proteogenomic approach. Downregulation of major histocompatibility complex class II expression was most profound in progenitor-like blasts and accompanied by correlative changes in transcriptional regulation. Dysfunction of activated natural killer cells and CD8+ T-cell subsets at relapse was evidenced by the loss of response to interferon gamma, tumor necrosis factor α signaling via NF-κB, and interleukin-2/STAT5 signaling. Clonotype analysis of posttransplant relapse samples revealed an expansion of dysfunctional T cells and enrichment of T-regulatory and T-helper cells. Using novel computational methods, our results illustrate a diverse immune-related transcriptional signature in posttransplant relapses not previously reported in pediatric AML.
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Affiliation(s)
- Sanam Shahid
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas Ceglia
- Memorial Hospital Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jean-Benoît Le Luduec
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew McPherson
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Theodota Kontopoulos
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Viktoria Bojilova
- Memorial Hospital Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - M. Kazim Panjwani
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sohrab P. Shah
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Omar Abdel-Wahab
- Department of Medicine, New York Presbyterian Hospital Weill Cornell Medical Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Greenbaum
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katharine C. Hsu
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, New York Presbyterian Hospital Weill Cornell Medical Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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3
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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.
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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
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4
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Shahid S, Ceglia N, Luduec JBL, McPherson A, Spitzer B, Bojilova V, Kazim Panjwani M, Roshal M, Shah SP, Abdel-Wahab O, Greenbaum B, Hsu KC. Signatures of Immune Evasion in Pediatric Acute Myeloid Leukemia after Allogeneic Hematopoietic Cell Transplantation. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00622-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Vázquez-García I, Uhlitz F, Ceglia N, Lim JLP, Wu M, Mohibullah N, Niyazov J, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Da Cruz Paula A, Gardner GJ, Kim SH, Lennon M, Long Roche K, Sonoda Y, Zivanovic O, Kundra R, Viale A, Derakhshan FN, Geneslaw L, Issa Bhaloo S, Maroldi A, Nunez R, Pareja F, Stylianou A, Vahdatinia M, Bykov Y, Grisham RN, Liu YL, Lakhman Y, Nikolovski I, Kelly D, Gao J, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum NR, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Ovarian cancer mutational processes drive site-specific immune evasion. Nature 2022; 612:778-786. [PMID: 36517593 PMCID: PMC9771812 DOI: 10.1038/s41586-022-05496-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/28/2022] [Indexed: 12/15/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1-4 patterned by distinct mutational processes5,6, tumour heterogeneity7-9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11-13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFβ signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.
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Affiliation(s)
- Ignacio Vázquez-García
- 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
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie L P Lim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neeman Mohibullah
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliana Niyazov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arvin Eric B Ruiz
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin M Boehm
- 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
| | - Christopher J Fong
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Funnell
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eliyahu Havasov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samantha Leung
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arfath Pasha
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Druv M Patel
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maryam Pourmaleki
- 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
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rami Vanguri
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allen W Zhang
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vance Broach
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis S Chi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ginger J Gardner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah H Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Lennon
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kara Long Roche
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yukio Sonoda
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oliver Zivanovic
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh N Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luke Geneslaw
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana Maroldi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rahelly Nunez
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthe Stylianou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahsa Vahdatinia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yonina Bykov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel N Grisham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Ying L Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Yulia Lakhman
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ines Nikolovski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Kelly
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jianjiong Gao
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Schietinger
- Weill Cornell Medical Center, New York, NY, USA
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollmann
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Bristol Myers Squibb, Princeton, NJ, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claire F Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical Center, New York, NY, USA.
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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6
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Vázquez-García I, Uhlitz F, Ceglia N, Lim JL, Wu M, Mohibullah N, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Paula ADC, Gardner GJ, Kim SH, Lennon M, Roche KL, Sonoda Y, Zivanovic O, Kundra R, Viale A, Bykov Y, Derakhshan FN, Geneslaw L, Maroldi A, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum N, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Abstract 2553: Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2553] [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
High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, a high degree of tumor heterogeneity and intraperitoneal spread. As immunotherapies have thus far proven ineffective in this disease, we sought to establish the determinants of immune recognition, avoidance and evasion in disease natural history to gain insight into the co-evolutionary processes underlying malignant progression and host immunity. Accordingly we linked mutational processes and anatomic sites of tumor foci as determinants of tumor microenvironment (TME) cellular phenotypes within and between patients using genome-based stratification of homologous recombination proficient (HRP) and deficient (HRD) disease subtypes, and profiling single cell phenotypes from ~1 million cells including cancer cells, T cells, myeloid cells and fibroblasts derived from single cell RNA sequencing, and in situ spatial profiling of histopathology, cancer cell, T cell and macrophage states of 160 tumor sites obtained from 42 treatment-naive patients. Mutational processes in HRD-Dup (BRCA1 mutant-like) tumors were associated with cancer cell-intrinsic JAK/STAT signaling and predominance of highly-differentiated dysfunctional CD8+ T cells in the TME; HRD-Del (BRCA2 mutant-like) tumors were associated with cancer cell-intrinsic NF-κB and TNFα signaling and expansion of M2-type macrophages; and foldback inversion (FBI, HRP) tumors were associated with cancer cell-intrinsic TGFβ signaling and overall immune exclusion, with a predominance of naive/central memory-like T cells. Increased neoantigen burden and HLA loss of heterozygosity (LOH) were defining genomic features of the HRD, but not FBI tumors. These mechanisms of escape from immune predation, with distinct signalling activity and losses of HLA allelic diversity in HRD tumors, connect evolutionary selection with immunological phenotypic states. Multi-region sampling revealed substantial spatial variation, highlighting site-specific properties of the ovary and fallopian tube as putative “immune-privileged” sites. These results establish that in patients with widespread intraperitoneal disease, the local properties of organ sites may determine malignant cell selection and immune pruning. Furthermore, we observed that spatial cellular topology is a major determinant of tumor-immune interactions by in situ protein measurements, revealing ubiquitous PD1-PDL1 interactions in HRD tumors. Together, our findings yield mechanistic insights for how distinct mutational processes in HGSOC lead to diverse patterns of within- and between- patient variation in immune resistance, which can be exploited to optimize future immuno-therapeutic treatment strategies.
Citation Format: Ignacio Vázquez-García, Florian Uhlitz, Nicholas Ceglia, Jamie L. Lim, Michelle Wu, Neeman Mohibullah, Arvin Eric B. Ruiz, Kevin M. Boehm, Viktoria Bojilova, Christopher J. Fong, Tyler Funnell, Diljot Grewal, Eliyahu Havasov, Samantha Leung, Arfath Pasha, Druv M. Patel, Maryam Pourmaleki, Nicole Rusk, Hongyu Shi, Rami Vanguri, Marc J. Williams, Allen W. Zhang, Vance Broach, Dennis S. Chi, Arnaud Da Cruz Paula, Ginger J. Gardner, Sarah H. Kim, Matthew Lennon, Kara Long Roche, Yukio Sonoda, Oliver Zivanovic, Ritika Kundra, Agnes Viale, Yonina Bykov, Fatemeh N. Derakhshan, Luke Geneslaw, Ana Maroldi, Andrea Schietinger, Travis J. Hollmann, Samuel F. Bakhoum, Robert A. Soslow, Lora H. Ellenson, Nadeem Abu-Rustum, Carol Aghajanian, Claire F. Friedman, Andrew McPherson, Britta Weigelt, MSK SPECTRUM Consortium, Dmitriy Zamarin, Sohrab P. Shah. Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes [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 2553.
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Affiliation(s)
| | | | | | - Jamie L. Lim
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michelle Wu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Tyler Funnell
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diljot Grewal
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Arfath Pasha
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Druv M. Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Nicole Rusk
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongyu Shi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rami Vanguri
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Vance Broach
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dennis S. Chi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Sarah H. Kim
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Yukio Sonoda
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yonina Bykov
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Luke Geneslaw
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ana Maroldi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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7
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Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, Shah SP, Aparicio S, Cannell IG, Casbolt H, Jauset C, Kovačević T, Mulvey CM, Nugent F, Ribes MP, Pearson I, Qosaj F, Sawicka K, Wild SA, Williams E, Laks E, Smith A, Lai D, Roth A, Balasubramanian S, Lee M, Bodenmiller B, Burger M, Kuett L, Tietscher S, Windhager J, Boyden ES, Alon S, Cui Y, Emenari A, Goodwin DR, Karagiannis ED, Sinha A, Wassie AT, Caldas C, Bruna A, Callari M, Greenwood W, Lerda G, Eyal-Lubling Y, Rueda OM, Shea A, Harris O, Becker R, Grimaldo F, Harris S, Vogl SL, Joyce JA, Watson SS, Tavare S, Dinh KN, Fisher E, Kunes R, Walton NA, Al Sa’d M, Chornay N, Dariush A, González-Solares EA, González-Fernández C, Yoldaş AK, Miller N, Zhuang X, Fan J, Lee H, Sepúlveda LA, Xia C, Zheng P, Shah SP, Aparicio S. Single-cell genomic variation induced by mutational processes in cancer. Nature 2022; 612:106-115. [PMID: 36289342 PMCID: PMC9712114 DOI: 10.1038/s41586-022-05249-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.
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Affiliation(s)
- Tyler Funnell
- grid.5386.8000000041936877XTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY USA ,grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ciara H. O’Flanagan
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Marc J. Williams
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Andrew McPherson
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Steven McKinney
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Farhia Kabeer
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Hakwoo Lee
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Sohrab Salehi
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ignacio Vázquez-García
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Hongyu Shi
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Emily Leventhal
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Tehmina Masud
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Peter Eirew
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Damian Yap
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Allen W. Zhang
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jamie L. P. Lim
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Beixi Wang
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jazmine Brimhall
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Justina Biele
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jerome Ting
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Vinci Au
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Michael Van Vliet
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Yi Fei Liu
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Sean Beatty
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Daniel Lai
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Jenifer Pham
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Diljot Grewal
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Douglas Abrams
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eliyahu Havasov
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Samantha Leung
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Viktoria Bojilova
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Richard A. Moore
- grid.434706.20000 0004 0410 5424Michael Smith Genome Sciences Centre, Vancouver, British Columbia Canada
| | - Nicole Rusk
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Florian Uhlitz
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Nicholas Ceglia
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Adam C. Weiner
- grid.5386.8000000041936877XTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY USA ,grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Elena Zaikova
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - J. Maxwell Douglas
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Dmitriy Zamarin
- grid.51462.340000 0001 2171 9952GYN Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Britta Weigelt
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sarah H. Kim
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Arnaud Da Cruz Paula
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Jorge S. Reis-Filho
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Spencer D. Martin
- grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Yangguang Li
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Hong Xu
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Teresa Ruiz de Algara
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - So Ra Lee
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Viviana Cerda Llanos
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - David G. Huntsman
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Jessica N. McAlpine
- grid.17091.3e0000 0001 2288 9830Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia Canada
| | | | - Sohrab P. Shah
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - 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.
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8
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Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T, Ting J, Grewal D, Nielsen C, Leung S, Bojilova V, Smith M, Golovko O, Poon S, Eirew P, Kabeer F, Ruiz de Algara T, Lee SR, Taghiyar MJ, Huebner C, Ngo J, Chan T, Vatrt-Watts S, Walters P, Abrar N, Chan S, Wiens M, Martin L, Scott RW, Underhill TM, Chavez E, Steidl C, Da Costa D, Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Mar C, Cafferty F, Gelmon K, Chia S, Marra MA, Hansen C, Shah SP, Aparicio S. Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing. Cell 2019; 179:1207-1221.e22. [PMID: 31730858 PMCID: PMC6912164 DOI: 10.1016/j.cell.2019.10.026] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 06/14/2019] [Accepted: 10/22/2019] [Indexed: 01/21/2023]
Abstract
Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.
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Affiliation(s)
- Emma Laks
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Andrew McPherson
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Hans Zahn
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada; Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Adi Steif
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Beixi Wang
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Tehmina Masud
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Jerome Ting
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Diljot Grewal
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Cydney Nielsen
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Samantha Leung
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Viktoria Bojilova
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Maia Smith
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Oleg Golovko
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Steven Poon
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Teresa Ruiz de Algara
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - So Ra Lee
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - M Jafar Taghiyar
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Curtis Huebner
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Jessica Ngo
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Tim Chan
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Spencer Vatrt-Watts
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Pascale Walters
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Nafis Abrar
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Sophia Chan
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Matt Wiens
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Lauren Martin
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - R Wilder Scott
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - T Michael Underhill
- Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Elizabeth Chavez
- Centre for Lymphoid Cancer, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Daniel Da Costa
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Robin J N Coope
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Richard Corbett
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Stephen Pleasance
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Colin Mar
- Department of Radiology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Fergus Cafferty
- Department of Radiology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Karen Gelmon
- Department of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Stephen Chia
- Department of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Carl Hansen
- Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA.
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada.
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