1
|
Walker R, Joo JE, Mahmood K, Clendenning M, Como J, Preston SG, Joseland S, Pope BJ, Medeiros ABD, Murillo BV, Pachter N, Sweet K, Spigelman AD, Groves A, Gleeson M, Bernatowicz K, Poplawski N, Andrews L, Healey E, Gallinger S, Grant RC, Win AK, Hopper JL, Jenkins MA, Torrezan GT, Rosty C, Macrae FA, Winship IM, Buchanan DD, Georgeson P. Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.08.24311713. [PMID: 39148833 PMCID: PMC11326331 DOI: 10.1101/2024.08.08.24311713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Background Colorectal cancers (CRCs) from people with biallelic germline likely pathogenic/pathogenic variants in MUTYH or NTHL1 exhibit specific single base substitution (SBS) mutational signatures, namely combined SBS18 and SBS36 (SBS18+SBS36), and SBS30, respectively. The aim was to determine if adenomas from biallelic cases demonstrated these mutational signatures at diagnostic levels. Methods Whole-exome sequencing of FFPE tissue and matched blood-derived DNA was performed on 9 adenomas and 15 CRCs from 13 biallelic MUTYH cases, on 7 adenomas and 2 CRCs from 5 biallelic NTHL1 cases and on 27 adenomas and 26 CRCs from 46 non-hereditary (sporadic) participants. All samples were assessed for COSMIC v3.2 SBS mutational signatures. Results In biallelic MUTYH cases, SBS18+SBS36 signature proportions in adenomas (mean±standard deviation, 65.6%±29.6%) were not significantly different to those observed in CRCs (76.2%±20.5%, p-value =0.37), but were significantly higher compared with non-hereditary adenomas (7.6%±7.0%, p-value =3.4x10 -4 ). Similarly, in biallelic NTHL1 cases, SBS30 signature proportions in adenomas (74.5%±9.4%) were similar to those in CRCs (78.8%±2.4%) but significantly higher compared with non-hereditary adenomas (2.8%±3.6%, p-value =5.1x10 -7 ). Additionally, a compound heterozygote with the c.1187G>A p.(Gly396Asp) pathogenic variant and the c.533G>C p.(Gly178Ala) variant of unknown significance (VUS) in MUTYH demonstrated high levels of SBS18+SBS36 in four adenomas and one CRC, providing evidence for reclassification of the VUS to pathogenic. Conclusions SBS18+SBS36 and SBS30 were enriched in adenomas at comparable proportions observed in CRCs from biallelic MUTYH and biallelic NTHL1 cases, respectively. Therefore, testing adenomas may improve the identification of biallelic cases and facilitate variant classification, ultimately enabling opportunities for CRC prevention.
Collapse
|
2
|
Georgeson P, Harrison TA, Pope BJ, Zaidi SH, Qu C, Steinfelder RS, Lin Y, Joo JE, Mahmood K, Clendenning M, Walker R, Amitay EL, Berndt SI, Brenner H, Campbell PT, Cao Y, Chan AT, Chang-Claude J, Doheny KF, Drew DA, Figueiredo JC, French AJ, Gallinger S, Giannakis M, Giles GG, Gsur A, Gunter MJ, Hoffmeister M, Hsu L, Huang WY, Limburg P, Manson JE, Moreno V, Nassir R, Nowak JA, Obón-Santacana M, Ogino S, Phipps AI, Potter JD, Schoen RE, Sun W, Toland AE, Trinh QM, Ugai T, Macrae FA, Rosty C, Hudson TJ, Jenkins MA, Thibodeau SN, Winship IM, Peters U, Buchanan DD. Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures. Nat Commun 2022; 13:3254. [PMID: 35668106 PMCID: PMC9170691 DOI: 10.1038/s41467-022-30916-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023] Open
Abstract
Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.
Collapse
Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert S Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
| | - Efrat L Amitay
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center(DKFZ), Heidelberg, Germany
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Amy J French
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Limburg
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rami Nassir
- Department of Pathology, College of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Finlay A Macrae
- Parkville Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, Australia
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | | | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, 3010, Australia.
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia.
| |
Collapse
|
3
|
Cannataro VL, Mandell JD, Townsend JP. Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. Mol Biol Evol 2022; 39:msac084. [PMID: 35580068 PMCID: PMC9113445 DOI: 10.1093/molbev/msac084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mutational processes in tumors create distinctive patterns of mutations, composed of neutral "passenger" mutations and oncogenic drivers that have quantifiable effects on the proliferation and survival of cancer cell lineages. Increases in proliferation and survival are mediated by natural selection, which can be quantified by comparing the frequency at which we detect substitutions to the frequency at which we expect to detect substitutions assuming neutrality. Most of the variants detectable with whole-exome sequencing in tumors are neutral or nearly neutral in effect, and thus the processes generating the majority of mutations may not be the primary sources of the tumorigenic mutations. Across 24 cancer types, we identify the contributions of mutational processes to each oncogenic variant and quantify the degree to which each process contributes to tumorigenesis. We demonstrate that the origination of variants driving melanomas and lung cancers is predominantly attributable to the preventable, exogenous mutational processes associated with ultraviolet light and tobacco exposure, respectively, whereas the origination of selected variants in gliomas and prostate adenocarcinomas is largely attributable to endogenous processes associated with aging. Preventable mutations associated with pathogen exposure and apolipoprotein B mRNA-editing enzyme activity account for a large proportion of the cancer effect within head-and-neck, bladder, cervical, and breast cancers. These attributions complement epidemiological approaches-revealing the burden of cancer driven by single-nucleotide variants caused by either endogenous or exogenous, nonpreventable, or preventable processes, and crucially inform public health strategies.
Collapse
Affiliation(s)
| | - Jeffrey D. Mandell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Jeffrey P. Townsend
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| |
Collapse
|
4
|
Lee D, Wang D, Yang XR, Shi J, Landi MT, Zhu B. SUITOR: Selecting the number of mutational signatures through cross-validation. PLoS Comput Biol 2022; 18:e1009309. [PMID: 35377867 PMCID: PMC9009674 DOI: 10.1371/journal.pcbi.1009309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/14/2022] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance. Mutational signatures are the footprints of exogenous exposures and endogenous mutational processes on the cancer genomes. To estimate de novo mutational signatures, the first step is to decide how many signatures should be extracted in a cancer genomics study, which determines downstream analytical steps and has been insufficiently studied. We developed SUITOR, an unsupervised cross-validation method to select the optimal number of signatures without overfitting the data. We demonstrated SUITOR’s superior performance using in vitro experimental studies, in silico simulations and in vivo pan-cancer applications of 2,540 whole-genome sequenced tumors across 22 cancer types, and validated signatures of breast cancer in additional 440 breast tumors. SUITOR advances the methodological frontier of identifying de novo mutational signatures and would help discover the causes of cancer and the means of cancer prevention and treatment.
Collapse
Affiliation(s)
- Donghyuk Lee
- Department of Statistics, Pusan National University, Busan, Korea
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
5
|
Guo J, Zhou Y, Xu C, Chen Q, Sztupinszki Z, Börcsök J, Xu C, Ye F, Tang W, Kang J, Yang L, Zhong J, Zhong T, Hu T, Yu R, Szallasi Z, Deng X, Li Q. Genetic Determinants of Somatic Selection of Mutational Processes in 3,566 Human Cancers. Cancer Res 2021; 81:4205-4217. [PMID: 34215622 PMCID: PMC9662923 DOI: 10.1158/0008-5472.can-21-0086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/21/2021] [Accepted: 06/29/2021] [Indexed: 01/07/2023]
Abstract
The somatic landscape of the cancer genome results from different mutational processes represented by distinct "mutational signatures." Although several mutagenic mechanisms are known to cause specific mutational signatures in cell lines, the variation of somatic mutational activities in patients, which is mostly attributed to somatic selection, is still poorly explained. Here, we introduce a quantitative trait, mutational propensity (MP), and describe an integrated method to infer genetic determinants of variations in the mutational processes in 3,566 cancers with specific underlying mechanisms. As a result, we report 2,314 candidate determinants with both significant germline and somatic effects on somatic selection of mutational processes, of which, 485 act via cancer gene expression and 1,427 act through the tumor-immune microenvironment. These data demonstrate that the genetic determinants of MPs provide complementary information to known cancer driver genes, clonal evolution, and clinical biomarkers. SIGNIFICANCE: The genetic determinants of the somatic mutational processes in cancer elucidate the biology underlying somatic selection and evolution of cancers and demonstrate complementary predictive power across cancer types.
Collapse
Affiliation(s)
- Jintao Guo
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Chaoqun Xu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Qinwei Chen
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | | | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Canqiang Xu
- XMU-Aginome Joint Lab, School of Informatics, Xiamen University, Xiamen, China
| | - Feng Ye
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Weiwei Tang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jiapeng Kang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Lu Yang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jiaxin Zhong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Taoling Zhong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Tianhui Hu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rongshan Yu
- XMU-Aginome Joint Lab, School of Informatics, Xiamen University, Xiamen, China
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Science, Xiamen University, Xiamen, China
| | - Qiyuan Li
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Corresponding Author: Qiyuan Li, School of Medicine, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China. Phone: 8659-2218-5175; E-mail:
| |
Collapse
|
6
|
Discovering the Mutational Profile of Early Colorectal Lesions: A Translational Impact. Cancers (Basel) 2021; 13:cancers13092081. [PMID: 33923068 PMCID: PMC8123354 DOI: 10.3390/cancers13092081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is one of the most common malignancies worldwide. Next-generation sequencing technologies have identified new candidate genes and deepened the knowledge of the molecular mechanisms underlying the progression of colonic adenomas towards CRC. The main genetic, epigenetic, and molecular alterations driving the onset and progression of CRC in both hereditary and sporadic settings have also been investigated. The evaluation of the CRC risk based on the molecular characterization of early pre-cancerous lesions may contribute to the development of targeted preventive strategies development, help define specific risk profiles, and identify patients who will benefit from targeted endoscopic surveillance. Abstract Colorectal cancer (CRC) develops through a multi-step process characterized by the acquisition of multiple somatic mutations in oncogenes and tumor-suppressor genes, epigenetic alterations and genomic instability. These events lead to the progression from precancerous lesions to advanced carcinomas. This process requires several years in a sporadic setting, while occurring at an early age and or faster in patients affected by hereditary CRC-predisposing syndromes. Since advanced CRC is largely untreatable or unresponsive to standard or targeted therapies, the endoscopic treatment of colonic lesions remains the most efficient CRC-preventive strategy. In this review, we discuss recent studies that have assessed the genetic alterations in early colorectal lesions in both hereditary and sporadic settings. Establishing the genetic profile of early colorectal lesions is a critical goal in the development of risk-based preventive strategies.
Collapse
|
7
|
Díaz-Gay M, Alexandrov LB. Unraveling the genomic landscape of colorectal cancer through mutational signatures. Adv Cancer Res 2021; 151:385-424. [PMID: 34148618 DOI: 10.1016/bs.acr.2021.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colorectal cancer, along with most other cancer types, is driven by somatic mutations. Characteristic patterns of somatic mutations, known as mutational signatures, arise as a result of the activities of different mutational processes. Mutational signatures have diverse origins, including exogenous and endogenous sources. In the case of colorectal cancer, the analysis of mutational signatures has elucidated specific signatures for classically associated DNA repair deficiencies, namely mismatch repair (leading to microsatellite instability), base excision repair (due to MUTYH or NTHL1 mutations), and polymerase proofreading (due to POLE and POLD1 exonuclease domain mutations). Additional signatures also play a role in colorectal cancer, including those related to normal aging and those associated with gut microbiota, as well as a number of signatures with unknown etiologies. This chapter provides an overview of the current knowledge of mutational signatures, with a focus on colorectal cancer and on the recently reported signatures in physiologically normal and inflammatory bowel disease-affected somatic colon tissues.
Collapse
Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, United States; Department of Bioengineering, UC San Diego, La Jolla, CA, United States; Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, United States; Department of Bioengineering, UC San Diego, La Jolla, CA, United States; Moores Cancer Center, UC San Diego, La Jolla, CA, United States.
| |
Collapse
|
8
|
Bai M, Li ZG, Ba Y. Influence of KDR Genetic Variation on the Efficacy and Safety of Patients with Chemotherapy Refractory Metastatic CRC Who Received Apatinib Treatment. Int J Gen Med 2021; 14:1041-1055. [PMID: 33790633 PMCID: PMC8006973 DOI: 10.2147/ijgm.s300968] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background The aim of the present study was to investigate the influence of kinase insert domain containing receptor (KDR) genetic variation on the efficacy of treatment and safety of patients with chemotherapy-refractory metastatic colorectal cancer (CRC) receiving apatinib. Methods A total of 108 patients with chemotherapy refractory metastatic CRC who were treated with apatinib participated in this study retrospectively. Efficacy of the patients' treatment was evaluated. Prognosis was carried out and safety profile was documented, respectively. Blood specimens and peripheral blood mononuclear cells (PBMC) of the patients were obtained for the analysis of genetic variation and KDR gene mRNA expression, respectively. The association between genotype status and clinical outcomes was presented. Results Objective response rate (ORR) and disease control rate (DCR) of the 108 patients with metastatic CRC receiving apatinib treatment were 5.6% and 69.4%, respectively. Survival analysis results exhibited that the median progression-free survival (PFS) and overall survival (OS) of the 108 patients with metastatic CRC was 3.6 months (95% confidence interval (CI): 3.03-4.17 months) and 8.9 months (95% CI: 7.57-10.23 months), respectively. Subsequently, the analysis of KDR genetic variation indicated that rs2071559 was of clinical significance. The minor allele frequency of rs2071559 was 0.22 and the genotype status corresponded with Hardy-Weinberg equilibrium (P=0.949). Prognosis analysis in a dominant inheritance manner through the combination of patients with TC and CC genotype showed that the median PFS of patients with TT genotype and TC/CC genotype was 4.1 and 3.0 months, respectively (P=0.012). Furthermore, the median OS of patients with the two genotypes was 10.5 and 6.1 months, respectively (P=0.007). Additionally, multivariate Cox regression analysis of OS showed that TC/CC genotype was an independent factor for OS (Hazard ratio (HR)=0.65, P=0.021). Interestingly, mRNA expression analysis suggested that the mRNA expression of KDR in PBMC differed significantly according to rs2071559 genotype status (P<0.001). Conclusion Apatinib demonstrated a potentially superior clinical outcome for patients with chemotherapy-refractory metastatic CRC. KDR polymorphism rs2071559 could be used as a potential biomarker for the prognosis evaluation of patients with CRC receiving apatinib therapy.
Collapse
Affiliation(s)
- Ming Bai
- Department of Gastrointestinal Oncology, Affiliated Tumor Hospital of Tianjin Medical University, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
| | - Zhi-Guo Li
- Department of Minimally Invasive Digestive Surgery, Shanxi Cancer Hospital, Taiyuan, People's Republic of China
| | - Yi Ba
- Department of Gastrointestinal Oncology, Affiliated Tumor Hospital of Tianjin Medical University, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China
| |
Collapse
|
9
|
Soares de Lima Y, Arnau-Collell C, Díaz-Gay M, Bonjoch L, Franch-Expósito S, Muñoz J, Moreira L, Ocaña T, Cuatrecasas M, Herrera-Pariente C, Carballal S, Moreno L, Díaz de Bustamante A, Castells A, Bujanda L, Cubiella J, Rodríguez-Alcalde D, Balaguer F, Castellví-Bel S. Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome. Cancers (Basel) 2021; 13:929. [PMID: 33672345 PMCID: PMC7927050 DOI: 10.3390/cancers13040929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
The serrated polyposis syndrome (SPS) is the most common and yet underdiagnosed colorectal polyposis syndrome. It is characterized by multiple and/or large colonic serrated polyps and a higher associated risk for colorectal cancer (CRC). The main objective of this study was to identify new candidate genes involved in the germline predisposition to SPS/CRC. Thirty-nine SPS patients from 16 families (≥2 patients per family) were recruited without alterations in well-known hereditary CRC genes, and germline and somatic whole-exome sequencing were performed. Germline rare variants with plausible pathogenicity, located in genes involved in cancer development, senescence and epigenetic regulation were selected. Somatic mutational profiling and signature analysis was pursued in one sample per family, when possible. After data filtering, ANXA10, ASXL1, CFTR, DOT1L, HIC1, INO80, KLF3, MCM3AP, MCM8, PDLIM2, POLD1, TP53BP1, WNK2 and WRN were highlighted as the more promising candidate genes for SPS germline predisposition with potentially pathogenic variants shared within families. Somatic analysis characterized mutational profiles in advanced serrated polyps/tumors, revealing a high proportion of hypermutated samples, with a prevalence of clock-like mutational signatures in most samples and the presence of DNA mismatch repair-defective signatures in some cases. In conclusion, we identified new candidate genes to be involved in familial SPS. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.
Collapse
Affiliation(s)
- Yasmin Soares de Lima
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Coral Arnau-Collell
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Marcos Díaz-Gay
- Moores Cancer Center, Department of Cellular and Molecular Medicine, Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA;
| | - Laia Bonjoch
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sebastià Franch-Expósito
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Jenifer Muñoz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Leticia Moreira
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Teresa Ocaña
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Miriam Cuatrecasas
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Tumor Bank-Biobank, Hospital Clínic, 08036 Barcelona, Spain;
| | - Cristina Herrera-Pariente
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sabela Carballal
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Lorena Moreno
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | | | - Antoni Castells
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), 20014 San Sebastián, Spain;
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 32005 Ourense, Spain;
| | | | - Francesc Balaguer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sergi Castellví-Bel
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| |
Collapse
|
10
|
Mäki-Nevala S, Ukwattage S, Olkinuora A, Almusa H, Ahtiainen M, Ristimäki A, Seppälä T, Lepistö A, Mecklin JP, Peltomäki P. Somatic mutation profiles as molecular classifiers of ulcerative colitis-associated colorectal cancer. Int J Cancer 2021; 148:2997-3007. [PMID: 33521965 DOI: 10.1002/ijc.33492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/22/2022]
Abstract
Ulcerative colitis increases colorectal cancer risk by mechanisms that remain incompletely understood. We approached this question by determining the genetic and epigenetic profiles of colitis-associated colorectal carcinomas (CA-CRC). The findings were compared to Lynch syndrome (LS), a different form of cancer predisposition that shares the importance of immunological factors in tumorigenesis. CA-CRCs (n = 27) were investigated for microsatellite instability, CpG island methylator phenotype and somatic mutations of 999 cancer-relevant genes ("Pan-cancer" panel). A subpanel of "Pan-cancer" design (578 genes) was used for LS colorectal tumors (n = 28). Mutational loads and signatures stratified CA-CRCs into three subgroups: hypermutated microsatellite-unstable (Group 1, n = 1), hypermutated microsatellite-stable (Group 2, n = 9) and nonhypermutated microsatellite-stable (Group 3, n = 17). The Group 1 tumor was the only one with MLH1 promoter hypermethylation and exhibited the mismatch repair deficiency-associated Signatures 21 and 15. Signatures 30 and 32 characterized Group 2, whereas no prominent single signature existed in Group 3. TP53, the most common mutational target in CA-CRC (16/27, 59%), was similarly affected in Groups 2 and 3, but DNA repair genes and Wnt signaling genes were mutated significantly more often in Group 2. In LS tumors, the degree of hypermutability exceeded that of the hypermutated CA-CRC Groups 1 and 2, and somatic mutational profiles and signatures were different. In conclusion, Groups 1 (4%) and 3 (63%) comply with published studies, whereas Group 2 (33%) is novel. The existence of molecularly distinct subgroups within CA-CRC may guide clinical management, such as therapy options.
Collapse
Affiliation(s)
- Satu Mäki-Nevala
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Sanjeevi Ukwattage
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Maarit Ahtiainen
- Department of Education and Research, Central Finland Central Hospital, Jyväskylä, Finland
| | - Ari Ristimäki
- Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Toni Seppälä
- Department of Gastrointestinal Surgery, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Anna Lepistö
- Department of Gastrointestinal Surgery, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Sport and Health Sciences, University of Jyväskylä and Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| |
Collapse
|
11
|
Zhou J, Zhou XA, Zhang N, Wang J. Evolving insights: how DNA repair pathways impact cancer evolution. Cancer Biol Med 2020; 17:805-827. [PMID: 33299637 PMCID: PMC7721097 DOI: 10.20892/j.issn.2095-3941.2020.0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
Viewing cancer as a large, evolving population of heterogeneous cells is a common perspective. Because genomic instability is one of the fundamental features of cancer, this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation, development, metastasis, and relapse. With the increased mutation rate and abundant diversity of the gene pool, this heterogeneity leads to cancer evolution, which is the major obstacle in the clinical treatment of cancer. Cells rely on the integrity of DNA repair machineries to maintain genomic stability, but these machineries often do not function properly in cancer cells. The deficiency of DNA repair could contribute to the generation of cancer genomic instability, and ultimately promote cancer evolution. With the rapid advance of new technologies, such as single-cell sequencing in recent years, we have the opportunity to better understand the specific processes and mechanisms of cancer evolution, and its relationship with DNA repair. Here, we review recent findings on how DNA repair affects cancer evolution, and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.
Collapse
Affiliation(s)
- Jiadong Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ning Zhang
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Biomedical Pioneering Innovation Center (BIOPIC) and Translational Cancer Research Center, School of Life Sciences, First Hospital, Peking University, Beijing 100871, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| |
Collapse
|
12
|
te Paske IBAW, Ligtenberg MJL, Hoogerbrugge N, de Voer RM. Candidate Gene Discovery in Hereditary Colorectal Cancer and Polyposis Syndromes-Considerations for Future Studies. Int J Mol Sci 2020; 21:E8757. [PMID: 33228212 PMCID: PMC7699508 DOI: 10.3390/ijms21228757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
To discover novel high-penetrant risk loci for hereditary colorectal cancer (hCRC) and polyposis syndromes many whole-exome and whole-genome sequencing (WES/WGS) studies have been performed. Remarkably, these studies resulted in only a few novel high-penetrant risk genes. Given this observation, the possibility and strategy to identify high-penetrant risk genes for hCRC and polyposis needs reconsideration. Therefore, we reviewed the study design of WES/WGS-based hCRC and polyposis gene discovery studies (n = 37) and provide recommendations to optimize discovery and validation strategies. The group of genetically unresolved patients is phenotypically heterogeneous, and likely composed of distinct molecular subtypes. This knowledge advocates for the screening of a homogeneous, stringently preselected discovery cohort and obtaining multi-level evidence for variant pathogenicity. This evidence can be collected by characterizing the molecular landscape of tumors from individuals with the same affected gene or by functional validation in cell-based models. Together, the combined approach of a phenotype-driven, tumor-based candidate gene search might elucidate the potential contribution of novel genetic predispositions in genetically unresolved hCRC and polyposis.
Collapse
Affiliation(s)
- Iris B. A. W. te Paske
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Richarda M. de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| |
Collapse
|