4
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Rashid M, Rashid R, Gadewal N, Carethers JM, Koi M, Brim H, Ashktorab H. High-throughput sequencing and in-silico analysis confirm pathogenicity of novel MSH3 variants in African American colorectal cancer. Neoplasia 2024; 49:100970. [PMID: 38281411 PMCID: PMC10840101 DOI: 10.1016/j.neo.2024.100970] [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: 11/05/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
The maintenance of DNA sequence integrity is critical to avoid accumulation of cancer-causing mutations. Inactivation of DNA Mismatch Repair (MMR) genes (e.g., MLH1 and MSH2) is common among many cancers, including colorectal cancer (CRC) and is the driver of classic microsatellite instability (MSI) in tumors. Somatic MSH3 alterations have been linked to a specific form of MSI called elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) that is associated with patient poor prognosis and elevated among African American (AA) rectal cancer patients. Genetic variants of MSH3 and their pathogenicity vary among different populations, such as among AA, which are not well-represented in publicly available databases. Targeted exome sequencing of MSH3 among AA CRC samples followed by computational bioinformatic pipeline and molecular dynamic simulation analysis approach confirmed six identified MSH3 variants (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, c.G3241A) that corresponded to MSH3 amino-acid changes (p.E413K; p.S466N; p.S920F; p.E976K; p.H1010Y; p.E1081K). All identified MSH3 variants were non-synonymous, novel, pathogenic, and show loss or gain of hydrogen bonding, ionic bonding, hydrophobic bonding, and disulfide bonding and have a deleterious effect on the structure of MSH3 protein. Some variants were located within the ATPase site of MSH3, affecting ATP hydrolysis that is critical for MSH3's function. Other variants were in the MSH3-MSH2 interacting domain, important for MSH3's binding to MSH2. Overall, our data suggest that these variants among AA CRC patients affect the function of MSH3 making them pathogenic and likely contributing to the development or advancement of CRC among AA. Further clarifying functional studies will be necessary to fully understand the impact of these variants on MSH3 function and CRC development in AA patients.
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Affiliation(s)
- Mudasir Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Rumaisa Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Nikhil Gadewal
- Bioinformatics and Computational Biology Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210, India
| | - John M Carethers
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA; Moores Cancer Center, and Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Minoru Koi
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Hassan Brim
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA.
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5
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Nguyen HL, Geukens T, Maetens M, Aparicio S, Bassez A, Borg A, Brock J, Broeks A, Caldas C, Cardoso F, De Schepper M, Delorenzi M, Drukker CA, Glas AM, Green AR, Isnaldi E, Eyfjörð J, Khout H, Knappskog S, Krishnamurthy S, Lakhani SR, Langerod A, Martens JWM, McCart Reed AE, Murphy L, Naulaerts S, Nik-Zainal S, Nevelsteen I, Neven P, Piccart M, Poncet C, Punie K, Purdie C, Rakha EA, Richardson A, Rutgers E, Vincent-Salomon A, Simpson PT, Schmidt MK, Sotiriou C, Span PN, Tan KTB, Thompson A, Tommasi S, Van Baelen K, Van de Vijver M, Van Laere S, Van't Veer L, Viale G, Viari A, Vos H, Witteveen AT, Wildiers H, Floris G, Garg AD, Smeets A, Lambrechts D, Biganzoli E, Richard F, Desmedt C. Obesity-associated changes in molecular biology of primary breast cancer. Nat Commun 2023; 14:4418. [PMID: 37479706 PMCID: PMC10361985 DOI: 10.1038/s41467-023-39996-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Obesity is associated with an increased risk of developing breast cancer (BC) and worse prognosis in BC patients, yet its impact on BC biology remains understudied in humans. This study investigates how the biology of untreated primary BC differs according to patients' body mass index (BMI) using data from >2,000 patients. We identify several genomic alterations that are differentially prevalent in overweight or obese patients compared to lean patients. We report evidence supporting an ageing accelerating effect of obesity at the genetic level. We show that BMI-associated differences in bulk transcriptomic profile are subtle, while single cell profiling allows detection of more pronounced changes in different cell compartments. These analyses further reveal an elevated and unresolved inflammation of the BC tumor microenvironment associated with obesity, with distinct characteristics contingent on the estrogen receptor status. Collectively, our analyses imply that obesity is associated with an inflammaging-like phenotype. We conclude that patient adiposity may play a significant role in the heterogeneity of BC and should be considered for BC treatment tailoring.
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Affiliation(s)
- Ha-Linh Nguyen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Tatjana Geukens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Marion Maetens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ayse Bassez
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Ake Borg
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
- Lund University Cancer Center Lund, Lund, Sweden
- CREATE Health Strategic Centre for Translational Cancer Research, Lund University, Lund, Sweden
- Department of Clinical Sciences, SCIBLU Genomics, Lund University, Lund, Sweden
| | - Jane Brock
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Annegien Broeks
- Departments of Core Facility, Molecular Pathology and Biobanking, Antoni van Leeuwenhoek, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Fatima Cardoso
- Breast Unit, Champalimaud Clinical Center/Champalimaud Foundation, Lisbon, Portugal
| | - Maxim De Schepper
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
- SIB Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland
| | - Caroline A Drukker
- Department of Surgical Oncology, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Andrew R Green
- Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Edoardo Isnaldi
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jórunn Eyfjörð
- BioMedical Center, School of Health Sciences, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Hazem Khout
- Department of Breast Surgery, Glenfield Hospital, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Stian Knappskog
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Savitri Krishnamurthy
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- Pathology Queensland, The Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Anita Langerod
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen, Oslo, Norway
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Amy E McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Leigh Murphy
- University of Manitoba and Cancer Care Manitoba Research Institute, Winnipeg, MB, Canada
| | - Stefan Naulaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Serena Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Ines Nevelsteen
- Department of Surgical Oncology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Gynecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Martine Piccart
- Institut Jules Bordet and Université Libre de Bruxelles, Brussels, Belgium
| | - Coralie Poncet
- European Organisation for Research and Treatment of Cancer (EORTC) Headquarters, Brussels, Belgium
| | - Kevin Punie
- Department of General Medical Oncology and Multidisciplinary Breast Unit, Leuven Cancer Institute and University Hospitals Leuven, Leuven, Belgium
| | - Colin Purdie
- Department of Pathology, University of Dundee, NHS Tayside, Dundee, UK
| | - Emad A Rakha
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Histopathology, Nottingham University Hospital NHS Trust, City Hospital Campus, Nottingham, UK
| | | | - Emiel Rutgers
- Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anne Vincent-Salomon
- Diagnostic and Theranostic Medicine Division, Institut Curie, PSL Research University, Paris, France
| | - Peter T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Christos Sotiriou
- Institut Jules Bordet, Universite Libre de Bruxelles, Brussels, Belgium
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kiat Tee Benita Tan
- Department of General Surgery, Sengkang General Hospital, Singapore, Singapore
- Department of Breast Surgery, Singapore General Hospital, Singapore, Singapore
- Department of Breast Surgery, National Cancer Centre, Singapore, Singapore
| | - Alastair Thompson
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumouri "Giovanni Paolo II", Bari, Italy
| | - Karen Van Baelen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Marc Van de Vijver
- Department of Pathology, Amsterdam University Medical Centers, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium
| | - Laura Van't Veer
- Department of Laboratory Medicine, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Giuseppe Viale
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de Bio-informatique 'Gilles Thomas', Lyon, France
| | - Hanne Vos
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | | | - Hans Wildiers
- Department of General Medical Oncology and Multidisciplinary Breast Unit, Leuven Cancer Institute and University Hospitals Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Abhishek D Garg
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Ann Smeets
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Elia Biganzoli
- Unit of Medical Statistics, Biometry and Epidemiology, Department of Biomedical and Clinical Sciences (DIBIC) "L. Sacco" & DSRC, LITA Vialba campus, Università degli Studi di Milano, Milan, Italy
| | - François Richard
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium.
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8
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Wan JCM, Stephens D, Luo L, White JR, Stewart CM, Rousseau B, Tsui DWY, Diaz LA. Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA. Nat Commun 2022; 13:4953. [PMID: 35999207 PMCID: PMC9399180 DOI: 10.1038/s41467-022-32598-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Abstract
Mutational signatures accumulate in somatic cells as an admixture of endogenous and exogenous processes that occur during an individual’s lifetime. Since dividing cells release cell-free DNA (cfDNA) fragments into the circulation, we hypothesize that plasma cfDNA might reflect mutational signatures. Point mutations in plasma whole genome sequencing (WGS) are challenging to identify through conventional mutation calling due to low sequencing coverage and low mutant allele fractions. In this proof of concept study of plasma WGS at 0.3–1.5x coverage from 215 patients and 227 healthy individuals, we show that both pathological and physiological mutational signatures may be identified in plasma. By applying machine learning to mutation profiles, patients with stage I-IV cancer can be distinguished from healthy individuals with an Area Under the Curve of 0.96. Interrogating mutational processes in plasma may enable earlier cancer detection, and might enable the assessment of cancer risk and etiology. Detection of mutational signatures in cell-free DNA (cfDNA) is challenging due to low sequence coverage and low mutant allele fractions. Here, the authors identify mutational signatures in plasma whole genome sequencing of cancer patients and use machine learning to distinguish them from healthy individuals.
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Affiliation(s)
- Jonathan C M Wan
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Dennis Stephens
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lingqi Luo
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - James R White
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Resphera Biosciences, Baltimore, MD, 21231, USA
| | - Caitlin M Stewart
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10065, USA.,New York Genome Center, New York, NY, 10013, USA
| | - Benoît Rousseau
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Dana W Y Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,PetDx Inc., San Diego, CA, USA
| | - Luis A Diaz
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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