1
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Lenis AT, Ravichandran V, Brown S, Alam SM, Katims A, Truong H, Reisz PA, Vasselman S, Nweji B, Autio KA, Morris MJ, Slovin SF, Rathkopf D, Danila D, Woo S, Vargas HA, Laudone VP, Ehdaie B, Reuter V, Arcila M, Berger MF, Viale A, Scher HI, Schultz N, Gopalan A, Donoghue MTA, Ostrovnaya I, Stopsack KH, Solit DB, Abida W. Microsatellite Instability, Tumor Mutational Burden, and Response to Immune Checkpoint Blockade in Patients with Prostate Cancer. Clin Cancer Res 2024; 30:3894-3903. [PMID: 38949888 DOI: 10.1158/1078-0432.ccr-23-3403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/20/2024] [Accepted: 06/27/2024] [Indexed: 07/03/2024]
Abstract
PURPOSE Patients with microsatellite instability-high/mismatch repair-deficient (MSI-H/dMMR) and high tumor mutational burden (TMB-H) prostate cancers are candidates for pembrolizumab. We define the genomic features, clinical course, and response to immune checkpoint blockade (ICB) in patients with MSI-H/dMMR and TMB-H prostate cancers without MSI [TMB-H/microsatellite stable (MSS)]. EXPERIMENTAL DESIGN We sequenced 3,244 tumors from 2,257 patients with prostate cancer. MSI-H/dMMR prostate cancer was defined as an MSIsensor score ≥10 or MSIsensor score ≥3 and <10 with a deleterious MMR alteration. TMB-H was defined as ≥10 mutations/megabase. PSA50 and RECIST responses were assigned. Overall survival and radiographic progression-free survival (rPFS) were compared using log-rank test. RESULTS Sixty-three (2.8%) men had MSI-H/dMMR, and 33 (1.5%) had TMB-H/MSS prostate cancers. Patients with MSI-H/dMMR and TMB-H/MSS tumors more commonly presented with grade group 5 and metastatic disease at diagnosis. MSI-H/dMMR tumors had higher TMB, indel, and neoantigen burden compared with TMB-H/MSS. Twenty-seven patients with MSI-H/dMMR and 8 patients with TMB-H/MSS tumors received ICB, none of whom harbored polymerase epsilon (polE) catalytic subunit mutations. About 45% of patients with MSI-H/dMMR had a RECIST response, and 65% had a PSA50 response. No patient with TMB-H/MSS had a RECIST response, and 50% had a PSA50 response. rPFS tended to be longer in patients with MSI-H/dMMR than in patients with TMB-H/MSS who received immunotherapy. Pronounced differences in genomics, TMB, or MSIsensor score were not detected between MSI-H/dMMR responders and nonresponders. CONCLUSIONS MSI-H/dMMR prostate cancers have greater TMB, indel, and neoantigen burden than TMB-H/MSS prostate cancers, and these differences may contribute to profound and durable responses to ICB.
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Affiliation(s)
- Andrew T Lenis
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vignesh Ravichandran
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samantha Brown
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Syed M Alam
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew Katims
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hong Truong
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter A Reisz
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samantha Vasselman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barbara Nweji
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen A Autio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael J Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan F Slovin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Danila
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sungmin Woo
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hebert A Vargas
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vincent P Laudone
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Behfar Ehdaie
- Urology Section, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor Reuter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark T A Donoghue
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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2
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Cornish AJ, Gruber AJ, Kinnersley B, Chubb D, Frangou A, Caravagna G, Noyvert B, Lakatos E, Wood HM, Thorn S, Culliford R, Arnedo-Pac C, Househam J, Cross W, Sud A, Law P, Leathlobhair MN, Hawari A, Woolley C, Sherwood K, Feeley N, Gül G, Fernandez-Tajes J, Zapata L, Alexandrov LB, Murugaesu N, Sosinsky A, Mitchell J, Lopez-Bigas N, Quirke P, Church DN, Tomlinson IPM, Sottoriva A, Graham TA, Wedge DC, Houlston RS. The genomic landscape of 2,023 colorectal cancers. Nature 2024:10.1038/s41586-024-07747-9. [PMID: 39112709 DOI: 10.1038/s41586-024-07747-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/24/2024] [Indexed: 08/17/2024]
Abstract
Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.
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Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- University College London Cancer Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Frangou
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Boris Noyvert
- Cancer Research UK Centre and Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steve Thorn
- Department of Oncology, University of Oxford, Oxford, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jacob Househam
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - William Cross
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | | | - Aliah Hawari
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Connor Woolley
- Department of Oncology, University of Oxford, Oxford, UK
| | - Kitty Sherwood
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nathalie Feeley
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Güler Gül
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Luis Zapata
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Nirupa Murugaesu
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alona Sosinsky
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Jonathan Mitchell
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Philip Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
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3
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Widman AJ, Shah M, Frydendahl A, Halmos D, Khamnei CC, Øgaard N, Rajagopalan S, Arora A, Deshpande A, Hooper WF, Quentin J, Bass J, Zhang M, Langanay T, Andersen L, Steinsnyder Z, Liao W, Rasmussen MH, Henriksen TV, Jensen SØ, Nors J, Therkildsen C, Sotelo J, Brand R, Schiffman JS, Shah RH, Cheng AP, Maher C, Spain L, Krause K, Frederick DT, den Brok W, Lohrisch C, Shenkier T, Simmons C, Villa D, Mungall AJ, Moore R, Zaikova E, Cerda V, Kong E, Lai D, Malbari MS, Marton M, Manaa D, Winterkorn L, Gelmon K, Callahan MK, Boland G, Potenski C, Wolchok JD, Saxena A, Turajlic S, Imielinski M, Berger MF, Aparicio S, Altorki NK, Postow MA, Robine N, Andersen CL, Landau DA. Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment. Nat Med 2024; 30:1655-1666. [PMID: 38877116 PMCID: PMC7616143 DOI: 10.1038/s41591-024-03040-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/30/2024] [Indexed: 06/16/2024]
Abstract
In solid tumor oncology, circulating tumor DNA (ctDNA) is poised to transform care through accurate assessment of minimal residual disease (MRD) and therapeutic response monitoring. To overcome the sparsity of ctDNA fragments in low tumor fraction (TF) settings and increase MRD sensitivity, we previously leveraged genome-wide mutational integration through plasma whole-genome sequencing (WGS). Here we now introduce MRD-EDGE, a machine-learning-guided WGS ctDNA single-nucleotide variant (SNV) and copy-number variant (CNV) detection platform designed to increase signal enrichment. MRD-EDGESNV uses deep learning and a ctDNA-specific feature space to increase SNV signal-to-noise enrichment in WGS by ~300× compared to previous WGS error suppression. MRD-EDGECNV also reduces the degree of aneuploidy needed for ultrasensitive CNV detection through WGS from 1 Gb to 200 Mb, vastly expanding its applicability within solid tumors. We harness the improved performance to identify MRD following surgery in multiple cancer types, track changes in TF in response to neoadjuvant immunotherapy in lung cancer and demonstrate ctDNA shedding in precancerous colorectal adenomas. Finally, the radical signal-to-noise enrichment in MRD-EDGESNV enables plasma-only (non-tumor-informed) disease monitoring in advanced melanoma and lung cancer, yielding clinically informative TF monitoring for patients on immune-checkpoint inhibition.
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Affiliation(s)
- Adam J Widman
- New York Genome Center, New York, NY, USA.
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | | | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Daniel Halmos
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Cole C Khamnei
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Srinivas Rajagopalan
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Anushri Arora
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Aditya Deshpande
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | | | - Jean Quentin
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jake Bass
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Mingxuan Zhang
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Theophile Langanay
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Laura Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Will Liao
- New York Genome Center, New York, NY, USA
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jesper Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christina Therkildsen
- Gastro Unit, Copenhagen University Hospital, Amager - Hvidovre Hospital, Hvidovre, Denmark
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Ryan Brand
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Joshua S Schiffman
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Ronak H Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Colleen Maher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kate Krause
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Dennie T Frederick
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Wendie den Brok
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tamara Shenkier
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christine Simmons
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Diego Villa
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Elena Zaikova
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Viviana Cerda
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Esther Kong
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Dina Manaa
- New York Genome Center, New York, NY, USA
| | | | - Karen Gelmon
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Genevieve Boland
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine Potenski
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jedd D Wolchok
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Sam Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Michael A Postow
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | | | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Weill Cornell Medicine, New York, NY, USA.
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4
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Lin AL, Rudneva VA, Richards AL, Zhang Y, Woo HJ, Cohen M, Tisnado J, Majd N, Wardlaw SL, Page-Wilson G, Sengupta S, Chow F, Goichot B, Ozer BH, Dietrich J, Nachtigall L, Desai A, Alano T, Ogilive S, Solit DB, Bale TA, Rosenblum M, Donoghue MTA, Geer EB, Tabar V. Genome-wide loss of heterozygosity predicts aggressive, treatment-refractory behavior in pituitary neuroendocrine tumors. Acta Neuropathol 2024; 147:85. [PMID: 38758238 PMCID: PMC11101347 DOI: 10.1007/s00401-024-02736-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Pituitary neuroendocrine tumors (PitNETs) exhibiting aggressive, treatment-refractory behavior are the rare subset that progress after surgery, conventional medical therapies, and an initial course of radiation and are characterized by unrelenting growth and/or metastatic dissemination. Two groups of patients with PitNETs were sequenced: a prospective group of patients (n = 66) who consented to sequencing prior to surgery and a retrospective group (n = 26) comprised of aggressive/higher risk PitNETs. A higher mutational burden and fraction of loss of heterozygosity (LOH) was found in the aggressive, treatment-refractory PitNETs compared to the benign tumors (p = 1.3 × 10-10 and p = 8.5 × 10-9, respectively). Within the corticotroph lineage, a characteristic pattern of recurrent chromosomal LOH in 12 specific chromosomes was associated with treatment-refractoriness (occurring in 11 of 14 treatment-refractory versus 1 of 14 benign corticotroph PitNETs, p = 1.7 × 10-4). Across the cohort, a higher fraction of LOH was identified in tumors with TP53 mutations (p = 3.3 × 10-8). A machine learning approach identified loss of heterozygosity as the most predictive variable for aggressive, treatment-refractory behavior, outperforming the most common gene-level alteration, TP53, with an accuracy of 0.88 (95% CI: 0.70-0.96). Aggressive, treatment-refractory PitNETs are characterized by significant aneuploidy due to widespread chromosomal LOH, most prominently in the corticotroph tumors. This LOH predicts treatment-refractoriness with high accuracy and represents a novel biomarker for this poorly defined PitNET category.
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Affiliation(s)
- Andrew L Lin
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vasilisa A Rudneva
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyung Jun Woo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Cohen
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie Tisnado
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nazanin Majd
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon L Wardlaw
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gabrielle Page-Wilson
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Soma Sengupta
- Department of Neurology and Neurosurgery, University of North Carolina, Chapel Hill, NC, USA
| | - Frances Chow
- Department of Neurology, Keck School of Medicine at University of Southern California Medical Center, Los Angeles, CA, USA
| | - Bernard Goichot
- Department of Endocrinology, Les Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Byram H Ozer
- Department of Oncology, Sibley Memorial Hospital/Johns Hopkins, Washington, DC, USA
| | - Jorg Dietrich
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa Nachtigall
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Arati Desai
- Department of Medicine, University of Pennsylvania Medical Center, Philadelphia, PA, USA
| | - Tina Alano
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shahiba Ogilive
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus A Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliza B Geer
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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5
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Senkin S, Moody S, Díaz-Gay M, Abedi-Ardekani B, Cattiaux T, Ferreiro-Iglesias A, Wang J, Fitzgerald S, Kazachkova M, Vangara R, Le AP, Bergstrom EN, Khandekar A, Otlu B, Cheema S, Latimer C, Thomas E, Atkins JR, Smith-Byrne K, Cortez Cardoso Penha R, Carreira C, Chopard P, Gaborieau V, Keski-Rahkonen P, Jones D, Teague JW, Ferlicot S, Asgari M, Sangkhathat S, Attawettayanon W, Świątkowska B, Jarmalaite S, Sabaliauskaite R, Shibata T, Fukagawa A, Mates D, Jinga V, Rascu S, Mijuskovic M, Savic S, Milosavljevic S, Bartlett JMS, Albert M, Phouthavongsy L, Ashton-Prolla P, Botton MR, Silva Neto B, Bezerra SM, Curado MP, Zequi SDC, Reis RM, Faria EF, de Menezes NS, Ferrari RS, Banks RE, Vasudev NS, Zaridze D, Mukeriya A, Shangina O, Matveev V, Foretova L, Navratilova M, Holcatova I, Hornakova A, Janout V, Purdue MP, Rothman N, Chanock SJ, Ueland PM, Johansson M, McKay J, Scelo G, Chanudet E, Humphreys L, de Carvalho AC, Perdomo S, Alexandrov LB, Stratton MR, Brennan P. Geographic variation of mutagenic exposures in kidney cancer genomes. Nature 2024; 629:910-918. [PMID: 38693263 PMCID: PMC11111402 DOI: 10.1038/s41586-024-07368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases, but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics.
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Affiliation(s)
- Sergey Senkin
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thomas Cattiaux
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aida Ferreiro-Iglesias
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Stephen Fitzgerald
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Anh Phuong Le
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Saamin Cheema
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Emily Thomas
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Joshua Ronald Atkins
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Christine Carreira
- Evidence Synthesis and Classification Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Priscilia Chopard
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Ferlicot
- Service d'Anatomie Pathologique, Assistance Publique-Hôpitaux de Paris, Univeristé Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Mojgan Asgari
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Surasak Sangkhathat
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Worapat Attawettayanon
- Division of Urology, Department of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Łódź, Poland
| | - Sonata Jarmalaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
- Department of Botany and Genetics, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Rasa Sabaliauskaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
| | - Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Dana Mates
- Occupational Health and Toxicology Department, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Stefan Rascu
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Mirjana Mijuskovic
- Clinic of Nephrology, Faculty of Medicine, Military Medical Academy, Belgrade, Serbia
| | - Slavisa Savic
- Department of Urology, University Hospital Dr D. Misovic Clinical Center, Belgrade, Serbia
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - John M S Bartlett
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Monique Albert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Larry Phouthavongsy
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patricia Ashton-Prolla
- Experimental Research Center, Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mariana R Botton
- Transplant Immunology and Personalized Medicine Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Brasil Silva Neto
- Service of Urology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Medicine: Surgical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Paula Curado
- Department of Epidemiology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Stênio de Cássio Zequi
- Department of Urology, A. C. Camargo Cancer Center, São Paulo, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, A.C. Camargo Cancer Center, São Paulo, Brazil
- Latin American Renal Cancer Group (LARCG), São Paulo, Brazil
- Department of Surgery, Division of Urology, Sao Paulo Federal University (UNIFESP), São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Minho University, Braga, Portugal
| | - Eliney Ferreira Faria
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
- Department of Urology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Rosamonde E Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naveen S Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David Zaridze
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Anush Mukeriya
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Oxana Shangina
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Vsevolod Matveev
- Department of Urology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Anna Hornakova
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ghislaine Scelo
- Observational and Pragmatic Research Institute Pte Ltd, Singapore, Singapore
| | - Estelle Chanudet
- Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Ana Carolina de Carvalho
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France.
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6
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Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Rep 2024; 43:113988. [PMID: 38517886 PMCID: PMC11063629 DOI: 10.1016/j.celrep.2024.113988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/02/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024] Open
Abstract
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.
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Affiliation(s)
- Elena Kuzmin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.
| | | | | | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Kento T Abe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael Schwartz
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Joseph Del Corpo
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Dongmei Zou
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Genevieve Morin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Alain Pacis
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Yang Yang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Constanza Martinez
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
| | - Jarrett Barber
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Anne-Marie Fortier
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Peter G Davison
- Department of Surgery, McGill University, Montreal, QC H3G 1A4, Canada; McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Atilla Omeroglu
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada
| | - Sidong Huang
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Peter Van Loo
- The Francis Crick Institute, NW1 1AT London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada.
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7
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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8
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Sud A, Parry EM, Wu CJ. The molecular map of CLL and Richter's syndrome. Semin Hematol 2024; 61:73-82. [PMID: 38368146 DOI: 10.1053/j.seminhematol.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/19/2024]
Abstract
Clonal expansion of B-cells, from the early stages of monoclonal B-cell lymphocytosis through to chronic lymphocytic leukemia (CLL), and then in some cases to Richter's syndrome (RS) provides a comprehensive model of cancer evolution, notable for the marked morphological transformation and distinct clinical phenotypes. High-throughput sequencing of large cohorts of patients and single-cell studies have generated a molecular map of CLL and more recently, of RS, yielding fundamental insights into these diseases and of clonal evolution. A selection of CLL driver genes have been functionally interrogated to yield novel insights into the biology of CLL. Such findings have the potential to impact patient care through risk stratification, treatment selection and drug discovery. However, this molecular map remains incomplete, with extant questions concerning the origin of the B-cell clone, the role of the TME, inter- and intra-compartmental heterogeneity and of therapeutic resistance mechanisms. Through the application of multi-modal single-cell technologies across tissues, disease states and clinical contexts, these questions can now be addressed with the answers holding great promise of generating translatable knowledge to improve patient care.
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Affiliation(s)
- Amit Sud
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Erin M Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Medicine, Brigham and Women's Hospital, Boston, MA
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9
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Antonello A, Bergamin R, Calonaci N, Househam J, Milite S, Williams MJ, Anselmi F, d'Onofrio A, Sundaram V, Sosinsky A, Cross WCH, Caravagna G. Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome Biol 2024; 25:38. [PMID: 38297376 PMCID: PMC10832148 DOI: 10.1186/s13059-024-03170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
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Affiliation(s)
- Alice Antonello
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Riccardo Bergamin
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Nicola Calonaci
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Jacob Househam
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Salvatore Milite
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
- Centre for Computational Biology, Human Technopole, Milan, Italy
| | - Marc J Williams
- Department of Computational Oncology, Memorial Sloan Kettering, New York, USA
| | - Fabio Anselmi
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Alberto d'Onofrio
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | | | | | - William C H Cross
- Department of Research Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy.
- Evolutionary Genomics and Modelling Team, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
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10
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Mitchell J, Milite S, Bartram J, Walker S, Volkova N, Yavorska O, Zarowiecki M, Chalker J, Thomas R, Vago L, Sosinsky A, Caravagna G. Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nat Commun 2024; 15:323. [PMID: 38238294 PMCID: PMC10796348 DOI: 10.1038/s41467-023-44158-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
The unexpected contamination of normal samples with tumour cells reduces variant detection sensitivity, compromising downstream analyses in canonical tumour-normal analyses. Leveraging whole-genome sequencing data available at Genomics England, we develop a tool for normal sample contamination assessment, which we validate in silico and against minimal residual disease testing. From a systematic review of [Formula: see text] patients with haematological malignancies and sarcomas, we find contamination across a range of cancer clinical indications and DNA sources, with highest prevalence in saliva samples from acute myeloid leukaemia patients, and sorted CD3+ T-cells from myeloproliferative neoplasms. Further exploration reveals 108 hotspot mutations in genes associated with haematological cancers at risk of being subtracted by standard variant calling pipelines. Our work highlights the importance of contamination assessment for accurate somatic variants detection in research and clinical settings, especially with large-scale sequencing projects being utilised to deliver accurate data from which to make clinical decisions for patient care.
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Affiliation(s)
| | - Salvatore Milite
- Computational Biology Research Centre, Human Technopole, Milan, Italy
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | | | | | | | | | - Jane Chalker
- Specialist Integrated Haematological Malignancy Diagnostic Service - Acquired Genomics, Great Ormond Street Hospital for Children, London, UK
| | - Rebecca Thomas
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Luca Vago
- Research Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS Hospital San Raffaele, Milan, Italy
| | | | - Giulio Caravagna
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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11
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Qu S, Gong M, Deng Y, Xiang Y, Ye D. Research progress and application of single-cell sequencing in head and neck malignant tumors. Cancer Gene Ther 2024; 31:18-27. [PMID: 37968342 PMCID: PMC10794142 DOI: 10.1038/s41417-023-00691-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023]
Abstract
Single-cell sequencing (SCS) is a technology that separates thousands of cells from the organism and accurately analyzes the genetic material expressed in each cell using high-throughput sequencing technology. Unlike the traditional bulk sequencing approach, which can only provide the average value of a cell population and cannot obtain specific single-cell data, single-cell sequencing can identify the gene sequence and expression changes of a single cell, and reflects the differences between genetic material and protein between cells, and ultimately the role played by the tumor microenvironment. single-cell sequencing can further explore the pathogenesis of head and neck malignancies from the single-cell biological level and provides a theoretical basis for the clinical diagnosis and treatment of head and neck malignancies. This article will systematically introduce the latest progress and application of single-cell sequencing in malignant head and neck tumors.
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Affiliation(s)
- Siyuan Qu
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Mengdan Gong
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yongqin Deng
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yizhen Xiang
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Dong Ye
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China.
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12
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Grigoriadis K, Huebner A, Bunkum A, Colliver E, Frankell AM, Hill MS, Thol K, Birkbak NJ, Swanton C, Zaccaria S, McGranahan N. CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction. Nat Protoc 2024; 19:159-183. [PMID: 38017136 DOI: 10.1038/s41596-023-00913-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
Abstract
Intratumor heterogeneity provides the fuel for the evolution and selection of subclonal tumor cell populations. However, accurate inference of tumor subclonal architecture and reconstruction of tumor evolutionary histories from bulk DNA sequencing data remains challenging. Frequently, sequencing and alignment artifacts are not fully filtered out from cancer somatic mutations, and errors in the identification of copy number alterations or complex evolutionary events (e.g., mutation losses) affect the estimated cellular prevalence of mutations. Together, such errors propagate into the analysis of mutation clustering and phylogenetic reconstruction. In this Protocol, we present a new computational framework, CONIPHER (COrrecting Noise In PHylogenetic Evaluation and Reconstruction), that accurately infers subclonal structure and phylogenetic relationships from multisample tumor sequencing, accounting for both copy number alterations and mutation errors. CONIPHER has been used to reconstruct subclonal architecture and tumor phylogeny from multisample tumors with high-depth whole-exome sequencing from the TRACERx421 dataset, as well as matched primary-metastatic cases. CONIPHER outperforms similar methods on simulated datasets, and in particular scales to a large number of tumor samples and clones, while completing in under 1.5 h on average. CONIPHER enables automated phylogenetic analysis that can be effectively applied to large sequencing datasets generated with different technologies. CONIPHER can be run with a basic knowledge of bioinformatics and R and bash scripting languages.
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Affiliation(s)
- Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Lab, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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13
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Hasan AMM, Cremaschi P, Wetterskog D, Jayaram A, Wong SQ, Williams S, Pasam A, Trigos A, Trujillo B, Grist E, Friedrich S, Vainauskas O, Parry M, Ismail M, Devlies W, Wingate A, Linch M, Naceur-Lombardelli C, Swanton C, Jamal-Hanjani M, Lise S, Sandhu S, Attard G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nat Commun 2023; 14:4823. [PMID: 37563129 PMCID: PMC10415299 DOI: 10.1038/s41467-023-40315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories.
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Affiliation(s)
| | | | | | - Anuradha Jayaram
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Scott Williams
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Blanca Trujillo
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Emily Grist
- University College London Cancer Institute, London, UK
| | | | | | - Marina Parry
- University College London Cancer Institute, London, UK
| | | | - Wout Devlies
- University College London Cancer Institute, London, UK
| | - Anna Wingate
- University College London Cancer Institute, London, UK
| | - Mark Linch
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Stefano Lise
- University College London Cancer Institute, London, UK
| | | | - Gerhardt Attard
- University College London Cancer Institute, London, UK.
- University College London Hospitals, London, UK.
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14
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Coorens THH, Collord G, Treger TD, Adams S, Mitchell E, Newman B, Getz G, Godfrey AL, Bartram J, Behjati S. Clonal origin of KMT2A wild-type lineage-switch leukemia following CAR-T cell and blinatumomab therapy. NATURE CANCER 2023; 4:1095-1101. [PMID: 37474833 PMCID: PMC10447231 DOI: 10.1038/s43018-023-00604-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/22/2023] [Indexed: 07/22/2023]
Abstract
Children with acute lymphoblastic leukemia (ALL) undergoing anti-CD19 therapy occasionally develop acute myeloid leukemia (AML). The clonal origin of such lineage-switch leukemias1-4 remains unresolved. Here, we reconstructed the phylogeny of multiple leukemias in a girl who, following multiply relapsed ALL, received anti-CD19 cellular and antibody treatment and subsequently developed AML. Whole genome sequencing unambiguously revealed the AML derived from the initial ALL, with distinct driver mutations that were detectable before emergence. Extensive prior diversification and subsequent clonal selection underpins this fatal lineage switch. Genomic monitoring of primary leukemias and recurrences may predict therapy resistance, especially regarding anti-CD19 treatment.
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Affiliation(s)
| | - Grace Collord
- Great Ormond Street Hospital for Children, London, UK
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Stuart Adams
- Great Ormond Street Hospital for Children, London, UK
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Barbara Newman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gad Getz
- 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
| | - Anna L Godfrey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack Bartram
- Great Ormond Street Hospital for Children, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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15
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Revkov E, Kulshrestha T, Sung KWK, Skanderup AJ. PUREE: accurate pan-cancer tumor purity estimation from gene expression data. Commun Biol 2023; 6:394. [PMID: 37041233 PMCID: PMC10090153 DOI: 10.1038/s42003-023-04764-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion of cancer cells in a sample) can both confound integrative analysis and enable studies of tumor heterogeneity. Here we developed PUREE, which uses a weakly supervised learning approach to infer tumor purity from a tumor gene expression profile. PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. PUREE predicted purity with high accuracy across distinct solid tumor types and generalized to tumor samples from unseen tumor types and cohorts. Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. In a comprehensive benchmark, PUREE outperformed existing transcriptome-based purity estimation approaches. Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data, which can complement genomics-based approaches or be used in settings where genomic data is unavailable.
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Affiliation(s)
- Egor Revkov
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore
| | - Tanmay Kulshrestha
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - Ken Wing-Kin Sung
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore.
- National Cancer Centre Singapore, Division of Medical Oncology, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore.
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16
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Jun SH, Toosi H, Mold J, Engblom C, Chen X, O'Flanagan C, Hagemann-Jensen M, Sandberg R, Aparicio S, Hartman J, Roth A, Lagergren J. Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics. Nat Commun 2023; 14:982. [PMID: 36813776 PMCID: PMC9946941 DOI: 10.1038/s41467-023-36202-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 01/20/2023] [Indexed: 02/24/2023] Open
Abstract
Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.
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Affiliation(s)
- Seong-Hwan Jun
- SciLifeLab, School of EECS, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, USA
| | - Hosein Toosi
- SciLifeLab, School of EECS, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jeff Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Xinsong Chen
- Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Ciara O'Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden.,Department of Clinical Pathology and Cytology, Karolinska University Laboratory, Stockholm, Sweden
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada. .,Department of Computer Science, University of British Columbia, Vancouver, Canada.
| | - Jens Lagergren
- SciLifeLab, School of EECS, KTH Royal Institute of Technology, Stockholm, Sweden.
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17
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Seillier L, Peifer M. Reconstructing Phylogenetic Relationship in Bladder Cancer: A Methodological Overview. Methods Mol Biol 2023; 2684:113-132. [PMID: 37410230 DOI: 10.1007/978-1-0716-3291-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Bladder cancer (BC) expresses itself as a highly heterogeneous disease both at the histological and molecular level, often occurring as synchronous or metachronous multifocal disease with high risk of recurrence and potential to metastasize. Multiple sequencing studies focusing on both non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC) gave insights into the extent of both inter- and intrapatient heterogeneity, but many questions on clonal evolution in BC remain unanswered. In this review article, we provide an overview over the technical and theoretical concepts linked to reconstructing evolutionary trajectories in BC and propose a set of tools and established software for phylogenetic analysis.
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Affiliation(s)
| | - Martin Peifer
- Department of Translational Genomics, University of Cologne, Cologne, Germany
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18
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Somatic XIST activation and features of X chromosome inactivation in male human cancers. Cell Syst 2022; 13:932-944.e5. [PMID: 36356577 DOI: 10.1016/j.cels.2022.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/09/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022]
Abstract
Expression of the non-coding RNA XIST is essential for initiating X chromosome inactivation (XCI) during early development in female mammals. As the main function of XCI is to enable dosage compensation of chromosome X genes between the sexes, XCI and XIST expression are generally absent in male normal tissues, except in germ cells and in individuals with supernumerary X chromosomes. Via a systematic analysis of public sequencing data of both cancerous and normal tissues, we report that XIST is somatically activated in a subset of male human cancers across diverse lineages. Some of these cancers display hallmarks of XCI, including silencing of gene expression, reduced chromatin accessibility, and increased DNA methylation across chromosome X, suggesting that the developmentally restricted, female-specific program of XCI can be somatically accessed in male cancers.
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19
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Yoo A, Tang C, Zucker M, Fitzgerald K, DiNatale RG, Rappold PM, Weiss K, Freeman B, Lee CH, Schultz N, Motzer R, Russo P, Coleman J, Reuter VE, Chen YB, Carlo MI, Gill AJ, Kotecha RR, Hakimi AA, Reznik E. Genomic and Metabolic Hallmarks of SDH- and FH-deficient Renal Cell Carcinomas. Eur Urol Focus 2022; 8:1278-1288. [PMID: 35288096 PMCID: PMC9464266 DOI: 10.1016/j.euf.2021.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 12/01/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Succinate dehydrogenase-deficient and fumarate hydratase-deficient renal cell carcinomas (SDHRCC and FHRCC) are rare kidney cancers driven by loss of TCA cycle enzymes. OBJECTIVE To define and compare the genomic and metabolomic hallmarks of SDHRCC and FHRCC. DESIGN, SETTING, AND PARTICIPANTS We analyzed SDHRCC and FHRCC tumors with either immunohistochemical evidence of loss of protein expression or genomically confirmed biallelic inactivation of SDHA/B/C/D/AF2 or FH. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Somatic alterations were identified using clinical pipelines, with allele-specific copy number alterations (CNAs) identified using FACETS. Mass spectrometry-based metabolomic profiling was performed on available SDHRCC and FHRCC tumors. RESULTS AND LIMITATIONS Tumors were analyzed for 42 patients (25 FHRCC, 17 SDHRCC). In the germline analysis, 16/17 SDHRCCs harbored a germline alteration in SDHB, whereas only 17/22 FHRCCs had pathogenic germline FH variants. SDHRCCs had a lower mutation burden (p = 0.02) and CNA burden (p = 0.0002) than FHRCCs. All SDHRCCs presented with deletion of chromosome 1p (overlapping SDHB), whereas FHRCCs demonstrated high but not ubiquitous loss of 1q (FH locus). Both SDHRCCs and FHRCCs exhibited significant idiopathic accumulation of the metabolite guanine. FHRCC tumors had elevated levels of urea cycle metabolites (argininosuccinate, citrulline, and fumarate), whereas SDHRCC tumors had elevation of numerous acylcarnitines. These characteristic metabolic changes allowed identification of a previously unrecognized SDH-deficient RCC. CONCLUSIONS Despite sharing similar genetic etiology, SDHRCC and FHRCC represent distinct molecular entities with unique genetic and metabolic abnormalities. PATIENT SUMMARY Kidney cancers driven by loss of the gene encoding either the succinate dehydrogenase or fumarate hydratase enzyme are rare. We sought to define and compare the genetic and metabolic features of these cancer entities.
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Affiliation(s)
- Angela Yoo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA,SUNY Downstate Health Sciences University, Brooklyn, NY, USA,Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cerise Tang
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Mark Zucker
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly Fitzgerald
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renzo G. DiNatale
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Phillip M. Rappold
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kate Weiss
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Freeman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chung-Han Lee
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victor E. Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria I. Carlo
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony J. Gill
- Sydney Medical School, University of Sydney, Sydney, Australia,Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St. Leonards, Australia,NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St. Leonards, Australia
| | - Ritesh R. Kotecha
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Corresponding authors. Memorial Sloan Kettering Cancer Center, New York, NY, USA. (R.R. Kotecha), (A. Ari Hakimi), (E. Reznik)
| | - A. Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Corresponding authors. Memorial Sloan Kettering Cancer Center, New York, NY, USA. (R.R. Kotecha), (A. Ari Hakimi), (E. Reznik)
| | - Ed Reznik
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Corresponding authors. Memorial Sloan Kettering Cancer Center, New York, NY, USA. (R.R. Kotecha), (A. Ari Hakimi), (E. Reznik)
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20
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Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nat Med 2022; 28:1662-1671. [PMID: 35953718 PMCID: PMC9388377 DOI: 10.1038/s41591-022-01927-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Abstract
Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT. Single-cell genomic and transcriptomic analyses of longitudinal samples of patients with Richter syndrome reveal the presence and dynamics of clones driving transformation from chronic lymphocytic leukemia years before clinical manifestation
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ramon Massoni-Badosa
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Neus Villamor
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Vicente Chapaprieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Sara Ruiz-Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Núria Verdaguer-Dot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica Romo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria Rozman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Alfredo Rivas-Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Tycho Baumann
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fina Climent
- Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellví
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Armando López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Pedro Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Pablo M Garcia-Roves
- Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Hospital Clínic of Barcelona, Barcelona, Spain. .,Universitat de Barcelona, Barcelona, Spain.
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21
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Baslan T, Morris JP, Zhao Z, Reyes J, Ho YJ, Tsanov KM, Bermeo J, Tian S, Zhang S, Askan G, Yavas A, Lecomte N, Erakky A, Varghese AM, Zhang A, Kendall J, Ghiban E, Chorbadjiev L, Wu J, Dimitrova N, Chadalavada K, Nanjangud GJ, Bandlamudi C, Gong Y, Donoghue MTA, Socci ND, Krasnitz A, Notta F, Leach SD, Iacobuzio-Donahue CA, Lowe SW. Ordered and deterministic cancer genome evolution after p53 loss. Nature 2022; 608:795-802. [PMID: 35978189 PMCID: PMC9402436 DOI: 10.1038/s41586-022-05082-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/06/2022] [Indexed: 11/08/2022]
Abstract
Although p53 inactivation promotes genomic instability1 and presents a route to malignancy for more than half of all human cancers2,3, the patterns through which heterogenous TP53 (encoding human p53) mutant genomes emerge and influence tumorigenesis remain poorly understood. Here, in a mouse model of pancreatic ductal adenocarcinoma that reports sporadic p53 loss of heterozygosity before cancer onset, we find that malignant properties enabled by p53 inactivation are acquired through a predictable pattern of genome evolution. Single-cell sequencing and in situ genotyping of cells from the point of p53 inactivation through progression to frank cancer reveal that this deterministic behaviour involves four sequential phases-Trp53 (encoding mouse p53) loss of heterozygosity, accumulation of deletions, genome doubling, and the emergence of gains and amplifications-each associated with specific histological stages across the premalignant and malignant spectrum. Despite rampant heterogeneity, the deletion events that follow p53 inactivation target functionally relevant pathways that can shape genomic evolution and remain fixed as homogenous events in diverse malignant populations. Thus, loss of p53-the 'guardian of the genome'-is not merely a gateway to genetic chaos but, rather, can enable deterministic patterns of genome evolution that may point to new strategies for the treatment of TP53-mutant tumours.
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Affiliation(s)
- Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John P Morris
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhen Zhao
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose Reyes
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Bermeo
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sha Tian
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gokce Askan
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aslihan Yavas
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicolas Lecomte
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda Erakky
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M Varghese
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lubomir Chorbadjiev
- Technical School of Electronic Systems, Technical University of Sofia, Sofia, Bulgaria
| | - Jie Wu
- Phillips Research North America, Oncology Informatics and Genomics, Cambridge, MA, USA
| | - Nevenka Dimitrova
- Phillips Research North America, Oncology Informatics and Genomics, Cambridge, MA, USA
| | - Kalyani Chadalavada
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gouri J Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yixiao Gong
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steve D Leach
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Dartmouth Cancer Center, Hanover, NH, USA
| | | | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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22
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Farrokhian N, Maltas J, Dinh M, Durmaz A, Ellsworth P, Hitomi M, McClure E, Marusyk A, Kaznatcheev A, Scott JG. Measuring competitive exclusion in non-small cell lung cancer. SCIENCE ADVANCES 2022; 8:eabm7212. [PMID: 35776787 PMCID: PMC10883359 DOI: 10.1126/sciadv.abm7212] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, we experimentally measure the frequency-dependent interactions between a gefitinib-resistant non-small cell lung cancer population and its sensitive ancestor via the evolutionary game assay. We show that cost of resistance is insufficient to accurately predict competitive exclusion and that frequency-dependent growth rate measurements are required. Using frequency-dependent growth rate data, we then show that gefitinib treatment results in competitive exclusion of the ancestor, while the absence of treatment results in a likely, but not guaranteed, exclusion of the resistant strain. Then, using simulations, we demonstrate that incorporating ecological growth effects can influence the predicted extinction time. In addition, we show that higher drug concentrations may not lead to the optimal reduction in tumor burden. Together, these results highlight the potential importance of frequency-dependent growth rate data for understanding competing populations, both in the laboratory and as we translate adaptive therapy regimens to the clinic.
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Affiliation(s)
| | - Jeff Maltas
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Mina Dinh
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Masahiro Hitomi
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Erin McClure
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Artem Kaznatcheev
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob G Scott
- CWRU School of Medicine, Cleveland, OH, USA
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH, USA
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23
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The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma. Nat Commun 2022; 13:3750. [PMID: 35768438 PMCID: PMC9243087 DOI: 10.1038/s41467-022-31430-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022] Open
Abstract
Multiple myeloma is the second most common hematological malignancy. Despite significant advances in treatment, relapse is common and carries a poor prognosis. Thus, it is critical to elucidate the genetic factors contributing to disease progression and drug resistance. Here, we carry out integrative clinical sequencing of 511 relapsed, refractory multiple myeloma (RRMM) patients to define the disease’s molecular alterations landscape. The NF-κB and RAS/MAPK pathways are more commonly altered than previously reported, with a prevalence of 45–65% each. In the RAS/MAPK pathway, there is a long tail of variants associated with the RASopathies. By comparing our RRMM cases with untreated patients, we identify a diverse set of alterations conferring resistance to three main classes of targeted therapy in 22% of our cohort. Activating mutations in IL6ST are also enriched in RRMM. Taken together, our study serves as a resource for future investigations of RRMM biology and potentially informs clinical management. The genetic factors involved in disease progression and drug resistance in multiple myeloma (MM) are varied and complex. Here, genomic and transcriptomic profiling of 511 relapsed and refractory MM patients reveals genetic alterations in several oncogenic pathways contributing to progression and resistance to MM therapies.
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24
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Wintersinger JA, Dobson SM, Kulman E, Stein LD, Dick JE, Morris Q. Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree. Blood Cancer Discov 2022; 3:208-219. [PMID: 35247876 PMCID: PMC9780082 DOI: 10.1158/2643-3230.bcd-21-0092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/23/2021] [Accepted: 02/28/2022] [Indexed: 01/25/2023] Open
Abstract
Cancers are composed of genetically distinct subpopulations of malignant cells. DNA-sequencing data can be used to determine the somatic point mutations specific to each population and build clone trees describing the evolutionary relationships between them. These clone trees can reveal critical points in disease development and inform treatment. Pairtree is a new method that constructs more accurate and detailed clone trees than previously possible using variant allele frequency data from one or more bulk cancer samples. It does so by first building a Pairs Tensor that captures the evolutionary relationships between pairs of subpopulations, and then it uses these relations to constrain clone trees and infer violations of the infinite sites assumption. Pairtree can accurately build clone trees using up to 100 samples per cancer that contain 30 or more subclonal populations. On 14 B-progenitor acute lymphoblastic leukemias, Pairtree replicates or improves upon expert-derived clone tree reconstructions. SIGNIFICANCE Clone trees illustrate the evolutionary history of a cancer and can provide insights into how the disease changed through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples of the same cancer to build more detailed and accurate clone trees than previously possible. See related commentary by Miller, p. 176. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Jeff A. Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Stephanie M. Dobson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ethan Kulman
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John E. Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Quaid Morris
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Memorial Sloan Kettering Cancer Center, New York, New York.,Corresponding Author: Quaid Morris, Sloan Kettering Institute, 417 East 68th Street, New York, NY 10021. Phone: 646-888-2201; E-mail:
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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26
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Lahoz S, Archilla I, Asensio E, Hernández‐Illán E, Ferrer Q, López‐Prades S, Nadeu F, Del Rey J, Sanz‐Pamplona R, Lozano JJ, Castells A, Cuatrecasas M, Camps J. Copy-number intratumor heterogeneity increases the risk of relapse in chemotherapy-naive stage II colon cancer. J Pathol 2022; 257:68-81. [PMID: 35066875 PMCID: PMC9790656 DOI: 10.1002/path.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Optimal selection of high-risk patients with stage II colon cancer is crucial to ensure clinical benefit of adjuvant chemotherapy. Here, we investigated the prognostic value of genomic intratumor heterogeneity and aneuploidy for disease recurrence. We combined targeted sequencing, SNP arrays, fluorescence in situ hybridization, and immunohistochemistry on a retrospective cohort of 84 untreated stage II colon cancer patients. We assessed the clonality of copy-number alterations (CNAs) and mutations, CD8+ lymphocyte infiltration, and their association with time to recurrence. Prognostic factors were included in machine learning analysis to evaluate their ability to predict individual relapse risk. Tumors from recurrent patients displayed a greater proportion of CNAs compared with non-recurrent (mean 31.3% versus 23%, respectively; p = 0.014). Furthermore, patients with elevated tumor CNA load exhibited a higher risk of recurrence compared with those with low levels [p = 0.038; hazard ratio (HR) 2.46], which was confirmed in an independent cohort (p = 0.004; HR 3.82). Candidate chromosome-specific aberrations frequently observed in recurrent cases included gain of the chromosome arm 13q (p = 0.02; HR 2.67) and loss of heterozygosity at 17q22-q24.3 (p = 0.05; HR 2.69). CNA load positively correlated with intratumor heterogeneity (R = 0.52; p < 0.0001). Consistently, incremental subclonal CNAs were associated with an elevated risk of relapse (p = 0.028; HR 2.20), which we did not observe for subclonal single-nucleotide variants and small insertions and deletions. The clinico-genomic model rated an area under the curve of 0.83, achieving a 10% incremental gain compared with clinicopathological markers (p = 0.047). In conclusion, tumor aneuploidy and copy-number intratumor heterogeneity were predictive of poor outcome and improved discriminative performance in early-stage colon cancer. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Ivan Archilla
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Elena Asensio
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Eva Hernández‐Illán
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Queralt Ferrer
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Sandra López‐Prades
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Ferran Nadeu
- Molecular Pathology of Lymphoid NeoplasmsInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)BarcelonaSpain
| | - Javier Del Rey
- Department of Cell Biology, Physiology and Immunology, Faculty of MedicineUniversity Autonomous of BarcelonaBellaterraSpain
| | - Rebeca Sanz‐Pamplona
- Unit of Biomarkers and SusceptibilityOncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESPl'Hospitalet de LlobregatSpain
| | - Juan José Lozano
- Bioinformatics PlatformCentro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD)MadridSpain
| | - Antoni Castells
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Miriam Cuatrecasas
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain,Department of Cell Biology, Physiology and Immunology, Faculty of MedicineUniversity Autonomous of BarcelonaBellaterraSpain
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27
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Laganà A. Computational Approaches for the Investigation of Intra-tumor Heterogeneity and Clonal Evolution from Bulk Sequencing Data in Precision Oncology Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:101-118. [DOI: 10.1007/978-3-030-91836-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Laganà A. The Architecture of a Precision Oncology Platform. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:1-22. [DOI: 10.1007/978-3-030-91836-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends Biotechnol 2021; 40:647-676. [PMID: 34972597 DOI: 10.1016/j.tibtech.2021.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations with variable molecular profiles, aggressiveness, and proliferation potential coexist and interact. Understanding how heterogeneity influences tumor progression has important clinical implications for improving diagnosis, prognosis, and treatment response prediction. Several recent innovations in data acquisition methods and computational metrics have enabled the quantification of spatiotemporal heterogeneity across different scales of tumor organization. Here, we summarize the most promising efforts from a common experimental and computational perspective, discussing their advantages, shortcomings, and challenges. With personalized medicine entering a new era of unprecedented opportunities, our vision is that of future workflows integrating across modalities, scales, and dimensions to capture intricate aspects of the tumor ecosystem and to open new avenues for improved patient care.
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Affiliation(s)
- Aditya Kashyap
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | | | - Vesna Barros
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Anna Fomitcheva-Khartchenko
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland; Eidgenössische Technische Hochschule (ETH-Zurich), Vladimir-Prelog-Weg 1-5/10, 8099 Zurich, Switzerland
| | | | | | - Maria Gabrani
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | - Michal Rosen-Zvi
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Govind Kaigala
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland.
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Mai Z, Liu Q, Wang X, Xie J, Yuan J, Zhong J, Fang S, Xie X, Yang H, Wen J, Fu J. Integration of Tumor Heterogeneity for Recurrence Prediction in Patients with Esophageal Squamous Cell Cancer. Cancers (Basel) 2021; 13:cancers13236084. [PMID: 34885197 PMCID: PMC8656931 DOI: 10.3390/cancers13236084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary This manuscript reports a deep sequencing study comprehensively analyzing the clinical impact of mutations considering the abundance of mutations. We built an eight-gene mutation predictor considering intratumoral heterogeneity to predict post-surgery recurrence in ESCC patients. Unlike previous studies that simply treated mutations as binary variables (mutant and wild type), we quantified mutations by the fraction of cancer cells carrying the mutations, and our results showed that the cancer cell fraction of mutations was more informative than the mutation status of genes in recurrence prediction. The predictor was further validated as a powerful recurrence indicator in our validation set and the TCGA-ESCC cohort. With the popularization of targeted deep sequencing in clinical work, our study will help clinicians make accurate predictions of recurrence for patients and will provide a new perspective in the clinical transformation of genomic findings. Abstract Esophageal squamous cell carcinoma (ESCC) is one of the deadliest malignancies in China. The prognostic value of mutations, especially those in minor tumor clones, has not been systematically investigated. We conducted targeted deep sequencing to analyze the mutation status and the cancer cell fraction (CCF) of mutations in 201 ESCC patients. Our analysis showed that the prognostic effect of mutations was relevant to the CCF, and it should be considered in prognosis prediction. EP300 was a promising biomarker for overall survival, impairing prognosis in a CCF dose-dependent manner. We constructed a CCF-based predictor using a smooth clipped absolute deviation Cox model in the training set of 143 patients. The 3-year disease-free survival rates were 6.3% (95% CI: 1.6–23.9%), 29.8% (20.9–42.6%) and 70.5% (56.6–87.7%) in high-, intermediate- and low-risk patients, respectively, in the training set. The prognostic accuracy was verified in a validation set of 58 patients and the TCGA-ESCC cohort. The eight-gene model predicted prognosis independent of clinicopathological factors and the combination of our model and pathological staging markedly improved the prognostic accuracy of pathological staging alone. Our study describes a novel recurrence predictor for ESCC patients and provides a new perspective for the clinical translation of genomic findings.
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Affiliation(s)
- Zihang Mai
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Qianwen Liu
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Xinye Wang
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Jiaxin Xie
- School of Statistics, Renmin University of China, Beijing 100872, China;
| | - Jianye Yuan
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Jian Zhong
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Shuogui Fang
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Xiuying Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Hong Yang
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
| | - Jing Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
- Correspondence: (J.W.); (J.F.)
| | - Jianhua Fu
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China; (Z.M.); (Q.L.); (X.W.); (J.Y.); (J.Z.); (S.F.); (H.Y.)
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Institute, Guangzhou 510060, China
- Correspondence: (J.W.); (J.F.)
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Valind A, Gisselsson D. Immune checkpoint inhibitors in Wilms' tumor and Neuroblastoma: What now? Cancer Rep (Hoboken) 2021; 4:e1397. [PMID: 33932141 PMCID: PMC8714551 DOI: 10.1002/cnr2.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/13/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Therapeutic activation of tumor-infiltrating lymphocytes using monoclonal antibodies targeting PD1 or PD-L1 (immune checkpoint inhibitors-ICIs) has revolutionized treatment of specific solid tumors in adult cancer patients, and much hope has been placed on a similar effect in relapsed or refractory solid pediatric tumors. Recent clinical trials have disappointingly shown an almost nonexistent response rate, while case reports have demonstrated that some pediatric patients do achieve durable responses when treated with this type of drug. AIM To elucidate this paradox, we mapped the landscape of expressed neoantigens as well as the levels of immune cell infiltration in the two most common extracranial solid pediatric tumors: Wilms tumor and neuroblastoma using state-of-the-art in silico analysis of a large cohort of patients with these tumors. METHODS By integration of whole exome sequencing and RNA-sequencing, we mapped the landscape of neoantigens in the TARGET cohorts for these diagnoses and correlated these findings with known genetic prognostic markers. RESULTS Our analysis shows that these tumors typically have much lower levels of expressed neoantigens than commonly seen in adult cancers, but we also identify subgroups with significantly higher levels of neoantigens. For neuroblastomas, the cases with higher levels of neoantigens were confined to the group without MYCN-amplification and for Wilms tumor restricted to the TP53-mutated cases. Furthermore, we demonstrate that neuroblastomas have an unexpectedly high level of CD8+ tumor-infiltrating lymphocytes, even when compared to adult tumor types where ICI is an approved treatment. CONCLUSION These results could be important to consider when designing future clinical trials of ICI treatment in pediatric patients with relapsed or refractory solid tumors.
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Affiliation(s)
- Anders Valind
- Division of Clinical GeneticsLund UniversityLundSweden
- Department of PediatricsSkåne University HospitalLundSweden
| | - David Gisselsson
- Division of Clinical GeneticsLund UniversityLundSweden
- Department of PathologyLaboratory Medicine SkåneLundSweden
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32
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Chattopadhyay S, Karlsson J, Valind A, Andersson N, Gisselsson D. Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST. Brief Bioinform 2021; 22:bbab292. [PMID: 34343239 PMCID: PMC8981300 DOI: 10.1093/bib/bbab292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/16/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer. Two limiting factors for clonal deconvolution that have remained unresolved are variation in purity and chromosomal copy number across different samples of the same tumor. We developed a semi-supervised algorithm that tracks variant calls through multi-sample spatiotemporal tumor data. While normalizing allele frequencies based on purity, it also adjusts for copy number changes at clonal deconvolution. Absent à priori copy number data, it renders in silico copy number estimations from bulk sequences. Using published and simulated tumor sequences, we reliably segregated clonal/subclonal variants even at a low sequencing depth (~50×). Given at least one pure tumor sample (>70% purity), we could normalize and deconvolve paired samples down to a purity of 40%. This renders a reliable clonal reconstruction well adapted to multi-regionally sampled solid tumors, which are often aneuploid and contaminated by non-cancer cells.
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Affiliation(s)
- Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University
Hospital, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical
Sciences, Lund University, Lund, Sweden
- Clinical Genetics and Pathology, Laboratory Medicine,
Lund University Hospital, Lund, Sweden
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33
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Satas G, Zaccaria S, El-Kebir M, Raphael BJ. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Syst 2021; 12:1004-1018.e10. [PMID: 34416171 DOI: 10.1016/j.cels.2021.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/09/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022]
Abstract
The cancer cell fraction (CCF), or proportion of cancerous cells in a tumor containing a single-nucleotide variant (SNV), is a fundamental statistic used to quantify tumor heterogeneity and evolution. Existing CCF estimation methods from bulk DNA sequencing data assume that every cell with an SNV contains the same number of copies of the SNV. This assumption is unrealistic in tumors with copy-number aberrations that alter SNV multiplicities. Furthermore, the CCF does not account for SNV losses due to copy-number aberrations, confounding downstream phylogenetic analyses. We introduce DeCiFer, an algorithm that overcomes these limitations by clustering SNVs using a novel statistic, the descendant cell fraction (DCF). The DCF quantifies both the prevalence of an SNV at the present time and its past evolutionary history using an evolutionary model that allows mutation losses. We show that DeCiFer yields more parsimonious reconstructions of tumor evolution than previously reported for 49 prostate cancer samples.
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Affiliation(s)
- Gryte Satas
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
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Krasnov GS, Ghukasyan LG, Abramov IS, Nasedkina TV. Determination of the Subclonal Tumor Structure in Childhood Acute Myeloid Leukemia and Acral Melanoma by Next-Generation Sequencing. Mol Biol 2021. [DOI: 10.1134/s0026893321040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abécassis J, Reyal F, Vert JP. CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data. Nat Commun 2021; 12:5352. [PMID: 34504064 PMCID: PMC8429716 DOI: 10.1038/s41467-021-24992-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Systematic DNA sequencing of cancer samples has highlighted the importance of two aspects of cancer genomics: intra-tumor heterogeneity (ITH) and mutational processes. These two aspects may not always be independent, as different mutational processes could be involved in different stages or regions of the tumor, but existing computational approaches to study them largely ignore this potential dependency. Here, we present CloneSig, a computational method to jointly infer ITH and mutational processes in a tumor from bulk-sequencing data. Extensive simulations show that CloneSig outperforms current methods for ITH inference and detection of mutational processes when the distribution of mutational signatures changes between clones. Applied to a large cohort of 8,951 tumors with whole-exome sequencing data from The Cancer Genome Atlas, and on a pan-cancer dataset of 2,632 whole-genome sequencing tumor samples from the Pan-Cancer Analysis of Whole Genomes initiative, CloneSig obtains results overall coherent with previous studies.
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Affiliation(s)
- Judith Abécassis
- Institut Curie, PSL Research University, Translational Research Department, INSERM, U932 Immunity and Cancer, Residual Tumor & Response to Treatment Laboratory (RT2Lab), Paris, France
- MINES ParisTech, PSL University, CBIO - Centre for Computational Biology, Paris, France
- Institut Curie, PSL Research University, Paris, France
| | - Fabien Reyal
- Institut Curie, PSL Research University, Translational Research Department, INSERM, U932 Immunity and Cancer, Residual Tumor & Response to Treatment Laboratory (RT2Lab), Paris, France
- Department of Surgery, Institut Curie, Paris, France
| | - Jean-Philippe Vert
- MINES ParisTech, PSL University, CBIO - Centre for Computational Biology, Paris, France.
- Google Research, Brain team, Paris, France.
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36
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Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R, Macklin AM, Khan S, Singh O, Karimi S, Corona RI, Liu LY, Chen CY, Chakravarthy A, Wei Q, Mehani B, Suppiah S, Gao A, Workewych AM, Tabatabai G, Boutros PC, Bader GD, de Carvalho DD, Kislinger T, Aldape K, Zadeh G. A clinically applicable integrative molecular classification of meningiomas. Nature 2021; 597:119-125. [PMID: 34433969 DOI: 10.1038/s41586-021-03850-3] [Citation(s) in RCA: 186] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Meningiomas are the most common primary intracranial tumour in adults1. Patients with symptoms are generally treated with surgery as there are no effective medical therapies. The World Health Organization histopathological grade of the tumour and the extent of resection at surgery (Simpson grade) are associated with the recurrence of disease; however, they do not accurately reflect the clinical behaviour of all meningiomas2. Molecular classifications of meningioma that reliably reflect tumour behaviour and inform on therapies are required. Here we introduce four consensus molecular groups of meningioma by combining DNA somatic copy-number aberrations, DNA somatic point mutations, DNA methylation and messenger RNA abundance in a unified analysis. These molecular groups more accurately predicted clinical outcomes compared with existing classification schemes. Each molecular group showed distinctive and prototypical biology (immunogenic, benign NF2 wild-type, hypermetabolic and proliferative) that informed therapeutic options. Proteogenomic characterization reinforced the robustness of the newly defined molecular groups and uncovered highly abundant and group-specific protein targets that we validated using immunohistochemistry. Single-cell RNA sequencing revealed inter-individual variations in meningioma as well as variations in intrinsic expression programs in neoplastic cells that mirrored the biology of the molecular groups identified.
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Affiliation(s)
- Farshad Nassiri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
| | - Jeff Liu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
| | - Justin Z Wang
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
| | - Rupert Hugh-White
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrew M Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olivia Singh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Shirin Karimi
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Rosario I Corona
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lydia Y Liu
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Caroline Y Chen
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Qingxia Wei
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Bharati Mehani
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Suganth Suppiah
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
| | - Andrew Gao
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Adriana M Workewych
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ghazaleh Tabatabai
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Tubingen, Germany
| | - Paul C Boutros
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gary D Bader
- The Donnelly Center, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Daniel D de Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Thomas Kislinger
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth Aldape
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- The International Consortium on Meningiomas, Toronto, Ontario, Canada
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- The International Consortium on Meningiomas, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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Zhang T, Joubert P, Ansari-Pour N, Zhao W, Hoang PH, Lokanga R, Moye AL, Rosenbaum J, Gonzalez-Perez A, Martínez-Jiménez F, Castro A, Muscarella LA, Hofman P, Consonni D, Pesatori AC, Kebede M, Li M, Gould Rothberg BE, Peneva I, Schabath MB, Poeta ML, Costantini M, Hirsch D, Heselmeyer-Haddad K, Hutchinson A, Olanich M, Lawrence SM, Lenz P, Duggan M, Bhawsar PMS, Sang J, Kim J, Mendoza L, Saini N, Klimczak LJ, Islam SMA, Otlu B, Khandekar A, Cole N, Stewart DR, Choi J, Brown KM, Caporaso NE, Wilson SH, Pommier Y, Lan Q, Rothman N, Almeida JS, Carter H, Ried T, Kim CF, Lopez-Bigas N, Garcia-Closas M, Shi J, Bossé Y, Zhu B, Gordenin DA, Alexandrov LB, Chanock SJ, Wedge DC, Landi MT. Genomic and evolutionary classification of lung cancer in never smokers. Nat Genet 2021; 53:1348-1359. [PMID: 34493867 PMCID: PMC8432745 DOI: 10.1038/s41588-021-00920-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022]
Abstract
Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined by copy number aberrations. The dominant subtype (piano), which is rare in lung cancer in smokers, features somatic UBA1 mutations, germline AR variants and stem cell-like properties, including low mutational burden, high intratumor heterogeneity, long telomeres, frequent KRAS mutations and slow growth, as suggested by the occurrence of cancer drivers' progenitor cells many years before tumor diagnosis. The other subtypes are characterized by specific amplifications and EGFR mutations (mezzo-forte) and whole-genome doubling (forte). No strong tobacco smoking signatures were detected, even in cases with exposure to secondhand tobacco smoke. Genes within the receptor tyrosine kinase-Ras pathway had distinct impacts on survival; five genomic alterations independently doubled mortality. These findings create avenues for personalized treatment in LCINS.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rachel Lokanga
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Aaron L Moye
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Federation OncoAge, Nice Hospital, University Côte d'Azur, Nice, France
| | - Dario Consonni
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela C Pesatori
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Michael Kebede
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bonnie E Gould Rothberg
- Smilow Cancer Hospital, Yale-New Haven Health, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Maria Luana Poeta
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Manuela Costantini
- Department of Urology, Istituto di Ricovero e Cura a Carattere Scientifico Regina Elena National Cancer Institute, Rome, Italy
| | - Daniela Hirsch
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Olanich
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Petra Lenz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maire Duggan
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Praphulla M S Bhawsar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura Mendoza
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Thomas Ried
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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38
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Giunta S. Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020. Cancer Metastasis Rev 2021; 40:909-924. [PMID: 34097189 PMCID: PMC8180541 DOI: 10.1007/s10555-021-09969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022]
Abstract
Cancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as well as the corresponding healthy tissue, with the aim of identifying genome-wide mutations exclusively found in cancer and uncovering new genetic changes that drive tumor formation. What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer's non-coding genome. WGS of the entire cohort allowed to tease apart driving mutations that initiate and support carcinogenesis from passenger mutations that do not play an overt role in the disease. At least one causative mutation was found in 95% of all cancers, with many tumors showing an average of 5 driver mutations. The PCAWG Project also assessed the transcriptional output altered in cancer and rebuilt the evolutionary history of each tumor showing that initial driver mutations can occur years if not decades prior to a diagnosis. Here, I provide a concise review of the Pan-Cancer Project papers published on February 2020, along with key computational tools and the digital framework generated as part of the project. This represents an historic effort by hundreds of international collaborators, which provides a comprehensive understanding of cancer genetics, with publicly available data and resources representing a treasure trove of information to advance cancer research for years to come.
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Affiliation(s)
- Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology "Charles Darwin", University of Rome Sapienza, Rome, Italy.
- The Rockefeller University, 1230 York Avenue, New York, NY, USA.
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39
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Nowicki-Osuch K, Zhuang L, Jammula S, Bleaney CW, Mahbubani KT, Devonshire G, Katz-Summercorn A, Eling N, Wilbrey-Clark A, Madissoon E, Gamble J, Di Pietro M, O'Donovan M, Meyer KB, Saeb-Parsy K, Sharrocks AD, Teichmann SA, Marioni JC, Fitzgerald RC. Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition. Science 2021; 373:760-767. [PMID: 34385390 DOI: 10.1126/science.abd1449] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 01/26/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022]
Abstract
The origin of human metaplastic states and their propensity for cancer is poorly understood. Barrett's esophagus is a common metaplastic condition that increases the risk for esophageal adenocarcinoma, and its cellular origin is enigmatic. To address this, we harvested tissues spanning the gastroesophageal junction from healthy and diseased donors, including isolation of esophageal submucosal glands. A combination of single-cell transcriptomic profiling, in silico lineage tracing from methylation, open chromatin and somatic mutation analyses, and functional studies in organoid models showed that Barrett's esophagus originates from gastric cardia through c-MYC and HNF4A-driven transcriptional programs. Furthermore, our data indicate that esophageal adenocarcinoma likely arises from undifferentiated Barrett's esophagus cell types even in the absence of a pathologically identifiable metaplastic precursor, illuminating early detection strategies.
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Affiliation(s)
- Karol Nowicki-Osuch
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Lizhe Zhuang
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Christopher W Bleaney
- Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, University of Manchester, Manchester, UK
| | - Krishnaa T Mahbubani
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Annalise Katz-Summercorn
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Nils Eling
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Elo Madissoon
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John Gamble
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Massimiliano Di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Maria O'Donovan
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kourosh Saeb-Parsy
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, University of Manchester, Manchester, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK.
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40
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Marin-Bejar O, Rogiers A, Dewaele M, Femel J, Karras P, Pozniak J, Bervoets G, Van Raemdonck N, Pedri D, Swings T, Demeulemeester J, Borght SV, Lehnert S, Bosisio F, van den Oord JJ, Bempt IV, Lambrechts D, Voet T, Bechter O, Rizos H, Levesque MP, Leucci E, Lund AW, Rambow F, Marine JC. Evolutionary predictability of genetic versus nongenetic resistance to anticancer drugs in melanoma. Cancer Cell 2021; 39:1135-1149.e8. [PMID: 34143978 DOI: 10.1016/j.ccell.2021.05.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Therapy resistance arises from heterogeneous drug-tolerant persister cells or minimal residual disease (MRD) through genetic and nongenetic mechanisms. A key question is whether specific molecular features of the MRD ecosystem determine which of these two distinct trajectories will eventually prevail. We show that, in melanoma exposed to mitogen-activated protein kinase therapeutics, emergence of a transient neural crest stem cell (NCSC) population in MRD concurs with the development of nongenetic resistance. This increase relies on a glial cell line-derived neurotrophic factor-dependent signaling cascade, which activates the AKT survival pathway in a focal adhesion kinase (FAK)-dependent manner. Ablation of the NCSC population through FAK inhibition delays relapse in patient-derived tumor xenografts. Strikingly, all tumors that ultimately escape this treatment exhibit resistance-conferring genetic alterations and increased sensitivity to extracellular signal-regulated kinase inhibition. These findings identify an approach that abrogates the nongenetic resistance trajectory in melanoma and demonstrate that the cellular composition of MRD deterministically imposes distinct drug resistance evolutionary paths.
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Affiliation(s)
- Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Aljosja Rogiers
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Michael Dewaele
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Julia Femel
- Ronald O. Perelman Department of Dermatology and Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Nina Van Raemdonck
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Dennis Pedri
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Toon Swings
- VIB Technology Watch, Technology Innovation Lab, VIB, Leuven, Belgium
| | - Jonas Demeulemeester
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Cancer Genomic Laboratory, The Francis Crick Institute, London, UK
| | | | | | - Francesca Bosisio
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Joost J van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | | | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Translational Genetics, Center for Human Genetics, KU Leuven, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics, LISCO, KU Leuven, Leuven, Belgium
| | - Oliver Bechter
- Department of General Medical Oncology UZ Leuven, Belgium
| | - Helen Rizos
- Macquarie University, Sydney, NSW, Australia; Melanoma Institute Australia, Sydney, NSW, Australia
| | - Mitchell P Levesque
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zürich, Switzerland
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, Leuven, Belgium; Trace PDX Platform, Department of Oncology, LKI, KU Leuven, Leuven, Belgium
| | - Amanda W Lund
- Ronald O. Perelman Department of Dermatology and Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium.
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium.
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41
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Anderson ND, Babichev Y, Fuligni F, Comitani F, Layeghifard M, Venier RE, Dentro SC, Maheshwari A, Guram S, Wunker C, Thompson JD, Yuki KE, Hou H, Zatzman M, Light N, Bernardini MQ, Wunder JS, Andrulis IL, Ferguson P, Razak ARA, Swallow CJ, Dowling JJ, Al-Awar RS, Marcellus R, Rouzbahman M, Gerstung M, Durocher D, Alexandrov LB, Dickson BC, Gladdy RA, Shlien A. Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival. Nat Commun 2021; 12:4496. [PMID: 34301934 PMCID: PMC8302638 DOI: 10.1038/s41467-021-24677-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Leiomyosarcomas (LMS) are genetically heterogeneous tumors differentiating along smooth muscle lines. Currently, LMS treatment is not informed by molecular subtyping and is associated with highly variable survival. While disease site continues to dictate clinical management, the contribution of genetic factors to LMS subtype, origins, and timing are unknown. Here we analyze 70 genomes and 130 transcriptomes of LMS, including multiple tumor regions and paired metastases. Molecular profiling highlight the very early origins of LMS. We uncover three specific subtypes of LMS that likely develop from distinct lineages of smooth muscle cells. Of these, dedifferentiated LMS with high immune infiltration and tumors primarily of gynecological origin harbor genomic dystrophin deletions and/or loss of dystrophin expression, acquire the highest burden of genomic mutation, and are associated with worse survival. Homologous recombination defects lead to genome-wide mutational signatures, and a corresponding sensitivity to PARP trappers and other DNA damage response inhibitors, suggesting a promising therapeutic strategy for LMS. Finally, by phylogenetic reconstruction, we present evidence that clones seeding lethal metastases arise decades prior to LMS diagnosis.
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Affiliation(s)
- Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Yael Babichev
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Fabio Fuligni
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, ON, Ontario, Canada
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Layeghifard
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rosemarie E Venier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Stefan C Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Anant Maheshwari
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sheena Guram
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Claire Wunker
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - J Drew Thompson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kyoko E Yuki
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Huayun Hou
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew Zatzman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Nicholas Light
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Marcus Q Bernardini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - Jay S Wunder
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, ON, Canada
| | - Irene L Andrulis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Ferguson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Carol J Swallow
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of General Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - James J Dowling
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Rima S Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Marjan Rouzbahman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rebecca A Gladdy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Surgery, University of Toronto, Toronto, ON, Canada.
- Division of General Surgery, Mount Sinai Hospital, Toronto, ON, Canada.
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, ON, Ontario, Canada.
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Transient expansion of TP53 mutated clones in polycythemia vera patients treated with idasanutlin. Blood Adv 2021; 4:5735-5744. [PMID: 33216890 DOI: 10.1182/bloodadvances.2020002379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
Activation of the P53 pathway through inhibition of MDM2 using nutlins has shown clinical promise in the treatment of solid tumors and hematologic malignancies. There is concern, however, that nutlin therapy might stimulate the emergence or expansion of TP53-mutated subclones. We recently published the results of a phase 1 trial of idasanutlin in patients with polycythemia vera (PV) that revealed tolerability and clinical activity. Here, we present data indicating that idasanutlin therapy is associated with expansion of TP53 mutant subclones. End-of-study sequencing of patients found that 5 patients in this trial harbored 12 TP53 mutations; however, only 1 patient had been previously identified as having a TP53 mutation at baseline. To identify the origin of these mutations, further analysis of raw sequencing data of baseline samples was performed and revealed that a subset of these mutations was present at baseline and expanded during treatment with idasanutlin. Follow-up samples were obtained from 4 of 5 patients in this cohort, and we observed that after cessation of idasanutlin, the variant allele frequency (VAF) of 8 of 9 TP53 mutations decreased. Furthermore, disease progression to myelofibrosis or myeloproliferative neoplasm blast phase was not observed in any of these patients after 19- to 32-month observation. These data suggest that idasanutlin treatment may promote transient TP53 mutant clonal expansion. A larger study geared toward high-resolution detection of low VAF mutations is required to explore whether patients acquire de novo TP53 mutations after idasanutlin therapy.
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43
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Morotti M, Albukhari A, Alsaadi A, Artibani M, Brenton JD, Curbishley SM, Dong T, Dustin ML, Hu Z, McGranahan N, Miller ML, Santana-Gonzalez L, Seymour LW, Shi T, Van Loo P, Yau C, White H, Wietek N, Church DN, Wedge DC, Ahmed AA. Promises and challenges of adoptive T-cell therapies for solid tumours. Br J Cancer 2021; 124:1759-1776. [PMID: 33782566 PMCID: PMC8144577 DOI: 10.1038/s41416-021-01353-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, many patients with advanced-stage- or high-risk cancers still die, owing to metastatic disease. Adoptive T-cell therapy, involving the autologous or allogeneic transplant of tumour-infiltrating lymphocytes or genetically modified T cells expressing novel T-cell receptors or chimeric antigen receptors, has shown promise in the treatment of cancer patients, leading to durable responses and, in some cases, cure. Technological advances in genomics, computational biology, immunology and cell manufacturing have brought the aspiration of individualised therapies for cancer patients closer to reality. This new era of cell-based individualised therapeutics challenges the traditional standards of therapeutic interventions and provides opportunities for a paradigm shift in our approach to cancer therapy. Invited speakers at a 2020 symposium discussed three areas-cancer genomics, cancer immunology and cell-therapy manufacturing-that are essential to the effective translation of T-cell therapies in the treatment of solid malignancies. Key advances have been made in understanding genetic intratumour heterogeneity, and strategies to accurately identify neoantigens, overcome T-cell exhaustion and circumvent tumour immunosuppression after cell-therapy infusion are being developed. Advances are being made in cell-manufacturing approaches that have the potential to establish cell-therapies as credible therapeutic options. T-cell therapies face many challenges but hold great promise for improving clinical outcomes for patients with solid tumours.
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Affiliation(s)
- Matteo Morotti
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ashwag Albukhari
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulkhaliq Alsaadi
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James D Brenton
- Functional Genomics of Ovarian Cancer Laboratory, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Stuart M Curbishley
- Advanced Therapies Facility and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Tao Dong
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Martin L Miller
- Cancer System Biology Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Laura Santana-Gonzalez
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Leonard W Seymour
- Gene Therapy Group, Department of Oncology, University of Oxford, Oxford, UK
| | - Tingyan Shi
- Department of Gynecological Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Christopher Yau
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
- The Alan Turing Institute, London, UK
| | - Helen White
- Patient Representative, Endometrial Cancer Genomics England Clinical Interpretation Partnership (GeCIP) Domain, London, UK
| | - Nina Wietek
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - David C Wedge
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK.
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44
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Vavoulis DV, Cutts A, Taylor JC, Schuh A. A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data. Bioinformatics 2021; 37:147-154. [PMID: 32722772 PMCID: PMC8055230 DOI: 10.1093/bioinformatics/btaa672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION Tumours are composed of distinct cancer cell populations (clones), which continuously adapt to their local micro-environment. Standard methods for clonal deconvolution seek to identify groups of mutations and estimate the prevalence of each group in the tumour, while considering its purity and copy number profile. These methods have been applied on cross-sectional data and on longitudinal data after discarding information on the timing of sample collection. Two key questions are how can we incorporate such information in our analyses and is there any benefit in doing so? RESULTS We developed a clonal deconvolution method, which incorporates explicitly the temporal spacing of longitudinally sampled tumours. By merging a Dirichlet Process Mixture Model with Gaussian Process priors and using as input a sequence of several sparsely collected samples, our method can reconstruct the temporal profile of the abundance of any mutation cluster supported by the data as a continuous function of time. We benchmarked our method on whole genome, whole exome and targeted sequencing data from patients with chronic lymphocytic leukaemia, on liquid biopsy data from a patient with melanoma and on synthetic data and we found that incorporating information on the timing of tissue collection improves model performance, as long as data of sufficient volume and complexity are available for estimating free model parameters. Thus, our approach is particularly useful when collecting a relatively long sequence of tumour samples is feasible, as in liquid cancers (e.g. leukaemia) and liquid biopsies. AVAILABILITY AND IMPLEMENTATION The statistical methodology presented in this paper is freely available at github.com/dvav/clonosGP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dimitrios V Vavoulis
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Molecular Diagnostic Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Anthony Cutts
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Oncology, Molecular Diagnostic Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Jenny C Taylor
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Molecular Diagnostic Centre, University of Oxford, Oxford OX3 9DU, UK
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford OX3 9DU, UK
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45
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Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 2021; 184:2239-2254.e39. [PMID: 33831375 PMCID: PMC8054914 DOI: 10.1016/j.cell.2021.03.009] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
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Affiliation(s)
- Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | | | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Jeff Wintersinger
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Amit G Deshwar
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Kaixian Yu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulia Rubanova
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Ignacio Vázquez-García
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; University of Cambridge, Cambridge CB2 0QQ, UK; Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Kortine Kleinheinz
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany
| | | | - Salem Malikic
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nilgun Donmez
- Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | | | - Pavana Anur
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97231, USA
| | - Clemency Jolly
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Marek Cmero
- University of Melbourne, Melbourne, VIC 3010, Australia; Walter + Eliza Hall Institute, Melbourne, VIC 3000, Australia
| | | | | | - Yu Fan
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Fittall
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruben M Drews
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Xiaotong Yao
- Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY 10013, USA
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Juhee Lee
- University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Hongtu Zhu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, London WC1E 6DD, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Massachusetts General Hospital, Department of Pathology, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Paul C Boutros
- University of Toronto, Toronto, ON M5S 3E1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marcin Imielinski
- Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY 10013, USA
| | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - S Cenk Sahinalp
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yuan Ji
- NorthShore University HealthSystem, Evanston, IL 60201, USA; The University of Chicago, Chicago, IL 60637, USA
| | - Martin Peifer
- Department of Translational Genomics, Center for Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | | | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ke Yuan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Paul T Spellman
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97231, USA
| | - Wenyi Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Quaid D Morris
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK; Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, UK; Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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Nath A, Bild AH. Leveraging Single-Cell Approaches in Cancer Precision Medicine. Trends Cancer 2021; 7:359-372. [PMID: 33563578 PMCID: PMC7969443 DOI: 10.1016/j.trecan.2021.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/24/2022]
Abstract
Cancer precision medicine aims to improve patient outcomes by tailoring treatment to the unique genomic background of a tumor. However, efforts to develop prognostic and drug response biomarkers largely rely on bulk 'omic' data, which fails to capture intratumor heterogeneity (ITH) and deconvolve signals from normal versus tumor cells. These shortcomings in measuring clinically relevant features are being addressed with single-cell technologies, which provide a fine-resolution map of the genetic and phenotypic heterogeneity in tumors and their microenvironment, as well as an improved understanding of the patterns of subclonal tumor populations. Here we present recent advances in the application of single-cell technologies, towards gaining a deeper understanding of ITH and evolution, and potential applications in developing personalized therapeutic strategies.
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Affiliation(s)
- Aritro Nath
- Department of Medical Oncology and Therapeutics Research, City of Hope, Monrovia, CA 91016, USA.
| | - Andrea H Bild
- Department of Medical Oncology and Therapeutics Research, City of Hope, Monrovia, CA 91016, USA
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47
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Cornish AJ, Chubb D, Frangou A, Hoang PH, Kaiser M, Wedge DC, Houlston RS. Reference bias in the Illumina Isaac aligner. Bioinformatics 2021; 36:4671-4672. [PMID: 32437525 PMCID: PMC7653636 DOI: 10.1093/bioinformatics/btaa514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/23/2020] [Accepted: 05/17/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
| | - Anna Frangou
- Nuffield Department of Medicine, Big Data Institute University of Oxford, OX3 7LF 3, UK.,Molecular Diagnostics Theme, Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LF 3, UK
| | - Phuc H Hoang
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG 5, UK
| | - David C Wedge
- Nuffield Department of Medicine, Big Data Institute University of Oxford, OX3 7LF 3, UK.,Molecular Diagnostics Theme, Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LF 3, UK.,Manchester Cancer Research Centre, University of Manchester, M20 4GJ, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
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48
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Taylor J, Donoghue MT, Ho C, Petrova-Drus K, Al-Ahmadie HA, Funt SA, Zhang Y, Aypar U, Rao P, Chavan SS, Haddadin M, Tamari R, Giralt S, Tallman MS, Rampal RK, Baez P, Kappagantula R, Kosuri S, Dogan A, Tickoo SK, Reuter VE, Bosl GJ, Iacobuzio-Donahue CA, Solit DB, Taylor BS, Feldman DR, Abdel-Wahab O. Germ cell tumors and associated hematologic malignancies evolve from a common shared precursor. J Clin Invest 2021; 130:6668-6676. [PMID: 32897884 DOI: 10.1172/jci139682] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Germ cell tumors (GCTs) are the most common cancer in men between the ages of 15 and 40. Although most patients are cured, those with disease arising in the mediastinum have distinctly poor outcomes. One in every 17 patients with primary mediastinal nonseminomatous GCTs develop an incurable hematologic malignancy and prior data intriguingly suggest a clonal relationship exists between hematologic malignancies and GCTs in these cases. To date, however, the precise clonal relationship between GCTs and the diverse additional somatic malignancies arising in such individuals have not been determined. Here, we traced the clonal evolution and characterized the genetic features of each neoplasm from a cohort of 15 patients with GCTs and associated hematologic malignancies. We discovered that GCTs and hematologic malignancies developing in such individuals evolved from a common shared precursor, nearly all of which harbored allelically imbalanced p53 and/or RAS pathway mutations. Hematologic malignancies arising in this setting genetically resembled mediastinal GCTs rather than de novo myeloid neoplasms. Our findings argue that this scenario represents a unique clinical syndrome, distinct from de novo GCTs or hematologic malignancies, initiated by an ancestral precursor that gives rise to the parallel evolution of GCTs and blood cancers in these patients.
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Affiliation(s)
- Justin Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | | | | | | | - Samuel A Funt
- Genitourinary Oncology Service, Department of Medicine
| | | | | | - Pavitra Rao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology
| | - Michael Haddadin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Roni Tamari
- Bone Marrow Transplant Service, Department of Medicine
| | - Sergio Giralt
- Bone Marrow Transplant Service, Department of Medicine
| | | | | | - Priscilla Baez
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rajya Kappagantula
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | | | | | - George J Bosl
- Genitourinary Oncology Service, Department of Medicine
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pathology
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology.,Genitourinary Oncology Service, Department of Medicine
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology.,Deparment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Leukemia Service, Department of Medicine
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49
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Zaccaria S, Raphael BJ. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nat Biotechnol 2021; 39:207-214. [PMID: 32879467 PMCID: PMC9876616 DOI: 10.1038/s41587-020-0661-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 08/04/2020] [Indexed: 01/28/2023]
Abstract
Single-cell barcoding technologies enable genome sequencing of thousands of individual cells in parallel, but with extremely low sequencing coverage (<0.05×) per cell. While the total copy number of large multi-megabase segments can be derived from such data, important allele-specific mutations-such as copy-neutral loss of heterozygosity (LOH) in cancer-are missed. We introduce copy-number haplotype inference in single cells using evolutionary links (CHISEL), a method to infer allele- and haplotype-specific copy numbers in single cells and subpopulations of cells by aggregating sparse signal across hundreds or thousands of individual cells. We applied CHISEL to ten single-cell sequencing datasets of ~2,000 cells from two patients with breast cancer. We identified extensive allele-specific copy-number aberrations (CNAs) in these samples, including copy-neutral LOHs, whole-genome duplications (WGDs) and mirrored-subclonal CNAs. These allele-specific CNAs affect genomic regions containing well-known breast-cancer genes. We also refined the reconstruction of tumor evolution, timing allele-specific CNAs before and after WGDs, identifying low-frequency subpopulations distinguished by unique CNAs and uncovering evidence of convergent evolution.
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Affiliation(s)
- Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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50
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Tarabichi M, Salcedo A, Deshwar AG, Leathlobhair MN, Wintersinger J, Wedge DC, Loo PV, Morris QD, Boutros PC. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods 2021; 18:144-155. [PMID: 33398189 PMCID: PMC7867630 DOI: 10.1038/s41592-020-01013-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/09/2020] [Indexed: 01/28/2023]
Abstract
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.
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Affiliation(s)
- Maxime Tarabichi
- The Francis Crick Institute, London, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adriana Salcedo
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles
- Institute for Precision Health, University of California, Los Angeles
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Amit G. Deshwar
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Canada
| | - Máire Ni Leathlobhair
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Jeff Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - David C. Wedge
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
- Manchester Cancer Research Centre, University of Manchester, Manchester, United Kingdom
| | | | - Quaid D. Morris
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Paul C. Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles
- Institute for Precision Health, University of California, Los Angeles
- Vector Institute, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles
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