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Wills C, Houseman A, Watts K, Maughan TS, Fisher D, Houlston RS, West HD, Escott-Price V, Cheadle JP. Relationship between 233 colorectal cancer risk loci and survival in 1926 patients with advanced disease. BJC REPORTS 2023; 1:2. [PMID: 38665548 PMCID: PMC11041780 DOI: 10.1038/s44276-023-00003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 04/28/2024]
Abstract
Background Genome, transcriptome and methylome-wide association studies have identified single-nucleotide polymorphisms (SNPs) or genes at 258 loci associated with colorectal cancer (CRC) risk. We studied the relationship between these and patient outcome. Methods We studied 1926 unrelated patients with advanced CRC from COIN and COIN-B. Of 205 CRC-risk SNPs, 19 were directly genotyped and 162 were imputed, and of 53 risk genes, 52 were tested. An additive Cox model for overall survival was adjusted for known prognostic factors. For nominally significant SNPs or genes, we considered a recessive model with a Bonferroni corrected threshold of P = 2.1 × 10-4. We examined SNPs as expression quantitative trait loci (eQTL) and the relationship between gene expression in colorectal tumours and survival in 597 unrelated patients. Results Eleven SNPs or genes were nominally associated with survival under an additive model. Only rs117079142 mapping to UTP23 and EIF3H (Hazard Ratio [HR] = 2.79, 95% Confidence Intervals [CI] = 1.70-4.58, P = 4.7 × 10-5) and rs9924886 mapping to CDH1 and CDH3 (HR = 1.24, 95% CI = 1.12-1.38, P = 5.2 × 10-5) passed the multiple testing threshold under a recessive model. rs117079142 was an eQTL for UTP23 and rs9924886 for CDH1, CDH3 and ZFP90. Decreased CDH1 expression in CRCs was associated with worse survival (HR = 2.18, 95% CI = 1.3-3.5, P = 1.8 × 10-3). Conclusion rs117079142 and rs9924886 may represent potential prognostic biomarkers for CRC.
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Affiliation(s)
- Christopher Wills
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Amy Houseman
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Katie Watts
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Timothy S. Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - David Fisher
- MRC Clinical Trials Unit, University College of London, 125 Kingsway, London, WC2B 6NH UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP UK
| | - Hannah D. West
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Jeremy P. Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
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2
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Campa D, Gentiluomo M, Stein A, Aoki MN, Oliverius M, Vodičková L, Jamroziak K, Theodoropoulos G, Pasquali C, Greenhalf W, Arcidiacono PG, Uzunoglu F, Pezzilli R, Luchini C, Puzzono M, Loos M, Giaccherini M, Katzke V, Mambrini A, Kiudeliene E, Federico KE, Johansen J, Hussein T, Mohelnikova-Duchonova B, van Eijck CHJ, Brenner H, Farinella R, Pérez JS, Lovecek M, Büchler MW, Hlavac V, Izbicki JR, Hackert T, Chammas R, Zerbi A, Lawlor R, Felici A, Götz M, Capurso G, Ginocchi L, Gazouli M, Kupcinskas J, Cavestro GM, Vodicka P, Moz S, Neoptolemos JP, Kunovsky L, Bojesen SE, Carrara S, Gioffreda D, Morkunas E, Abian O, Bunduc S, Basso D, Boggi U, Wlodarczyk B, Szentesi A, Vanella G, Chen I, Bijlsma MF, Kiudelis V, Landi S, Schöttker B, Corradi C, Giese N, Kaaks R, Peduzzi G, Hegyi P, Morelli L, Furbetta N, Soucek P, Latiano A, Talar-Wojnarowska R, Lindgaard SC, Dijk F, Milanetto AC, Tavano F, Cervena K, Erőss B, Testoni SG, Verhagen-Oldenampsen JHE, Małecka-Wojciesko E, Costello E, Salvia R, Maiello E, Ermini S, Sperti C, Holleczek B, Perri F, Skieceviciene J, Archibugi L, Lucchesi M, Rizzato C, Canzian F. The PANcreatic Disease ReseArch (PANDoRA) consortium: Ten years' experience of association studies to understand the genetic architecture of pancreatic cancer. Crit Rev Oncol Hematol 2023; 186:104020. [PMID: 37164172 DOI: 10.1016/j.critrevonc.2023.104020] [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: 03/06/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/12/2023] Open
Abstract
Pancreatic cancer has an incidence that almost matches its mortality. Only a small number of risk factors and 33 susceptibility loci have been identified. so Moreover, the relative rarity of pancreatic cancer poses significant hurdles for research aimed at increasing our knowledge of the genetic mechanisms contributing to the disease. Additionally, the inability to adequately power research questions prevents small monocentric studies from being successful. Several consortia have been established to pursue a better understanding of the genetic architecture of pancreatic cancers. The Pancreatic disease research (PANDoRA) consortium is the largest in Europe. PANDoRA is spread across 12 European countries, Brazil and Japan, bringing together 29 basic and clinical research groups. In the last ten years, PANDoRA has contributed to the discovery of 25 susceptibility loci, a feat that will be instrumental in stratifying the population by risk and optimizing preventive strategies.
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Affiliation(s)
- Daniele Campa
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy.
| | - Manuel Gentiluomo
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Angelika Stein
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | - Martin Oliverius
- Department of Surgery, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodičková
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen Charles University, Pilsen, Czech Republic
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - George Theodoropoulos
- First Department of Propaedeutic Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Claudio Pasquali
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 3, Padova, Italy
| | - William Greenhalf
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, United Kingdom
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientic Institute, Milan, Italy
| | - Faik Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Marta Puzzono
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Loos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Verena Katzke
- Division of Cancer Epidemiology C020, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Mambrini
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Edita Kiudeliene
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | | | - Julia Johansen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Tamás Hussein
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary
| | | | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - 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
| | | | - Juan Sainz Pérez
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Complejo Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain; Department of Immunology, University of Granada, Granada, Spain
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Departamento de Radiologia e Oncologia, Instituto Do Câncer Do Estado de São Paulo (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Rita Lawlor
- ARC-Net Research Center, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Alessio Felici
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Mara Götz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Laura Ginocchi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Juozas Kupcinskas
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen Charles University, Pilsen, Czech Republic
| | - Stefania Moz
- Azienda Ospedale-Università di Padova Medicina di Laboratorio, Padova, Italy
| | - John P Neoptolemos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Lumir Kunovsky
- Department of Surgery, University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Department of Gastroenterology and Digestive Endoscopy, Masaryk Memorial Cancer Institute, Brno, Czech Republic; 2nd Department of Internal Medicine - Gastroenterology and Geriatrics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Stig E Bojesen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Egidijus Morkunas
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Olga Abian
- Instituto BIFI-Universidad de Zaragoza, Zaragoza, Spain
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Carol Davila University of Medicine and Pharmacy, Bucharest, Romania; Center for Digestive Diseases and Liver Transplant, Fundeni Clinical Insitute, Bucharest, Romania
| | - Daniela Basso
- Dept. of Medicine, University of Padova Medicina di Laboratorio, Padova, Italy
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Barbara Wlodarczyk
- Dept of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Giuseppe Vanella
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Inna Chen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Maarten F Bijlsma
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Vytautas Kiudelis
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Stefano Landi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiara Corradi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology C020, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giulia Peduzzi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Péter Hegyi
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; Translational Pancreatology Research Group, Interdisciplinary Centre of Excellence for Research Development and Innovation University of Szeged, Szeged, Hungary
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Niccolò Furbetta
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Anna Latiano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | | | - Sidsel C Lindgaard
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Frederike Dijk
- Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands; Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Anna Caterina Milanetto
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 3, Padova, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bálint Erőss
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Sabrina G Testoni
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientic Institute, Milan, Italy
| | | | | | - Eithne Costello
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, United Kingdom
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Evaristo Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | | | - Cosimo Sperti
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 1, Padova, Italy
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Saarland Cancer Registry, Saarbrücken, Germany
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Jurgita Skieceviciene
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Maurizio Lucchesi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Cosmeri Rizzato
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Passi M, Gamble LA, Samaranayake SG, Schueler SA, Curtin BF, Fasaye GA, Bowden C, Gurram S, Quezado M, Miettinen M, Koh C, Heller T, Davis JL. Association of CDH1 Germline Variants and Colon Polyp Phenotypes in Patients with Hereditary Diffuse Gastric Cancer. GASTRO HEP ADVANCES 2023; 2:244-251. [PMID: 36776716 PMCID: PMC9913407 DOI: 10.1016/j.gastha.2022.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background and Aims Germline CDH1 variants resulting in E-cadherin loss of function result in an increased risk of diffuse type gastric cancer and lobular type breast cancer. However, the risk of developing other epithelial neoplasms, specifically colorectal cancer, is unknown. Methods Patients enrolled in a prospective natural history study of hereditary gastric cancer who underwent at least one colonoscopy were evaluated. Results Out of 300 patients with CDH1 pathogenic or likely pathogenic variants, 85 underwent colonoscopy. More than half of patients (56%, 48/85) had at least one colorectal polyp. Most of those patients (83%, 40/48) had at least one precancerous polyp (adenoma or sessile serrated lesion). More than half (56%) of patients younger than age 45 had a colorectal polyp. Of those with polyps, the most frequent CDH1 variant type was canonical splice site (27%, 13/48) followed by nonsense (21%, 10/48). There was no association between CDH1 variant type and increased likelihood of colorectal polyps. Conclusions In summary, a majority of CDH1 variant carriers who underwent colonoscopy had colorectal polyps detected, and most subjects were less than 45 years old. This study of colorectal cancer risk based on the prevalence of colorectal polyps in the CDH1 population requires further investigation to appropriately counsel patients on colorectal cancer screening. Clinical trial registry website: https://clinicaltrials.gov/. Clinical trial number: NCT03030404.
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Affiliation(s)
- Monica Passi
- Digestive Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Lauren A. Gamble
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Sarah G. Samaranayake
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Samuel A. Schueler
- Digestive Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Bryan F. Curtin
- Digestive Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Grace-Ann Fasaye
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Cassidy Bowden
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Sandeep Gurram
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health
| | - Christopher Koh
- Digestive Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Theo Heller
- Digestive Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Jeremy L. Davis
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health
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4
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Macauda A, Clay-Gilmour A, Hielscher T, Hildebrandt MAT, Kruszewski M, Orlowski RZ, Kumar SK, Ziv E, Orciuolo E, Brown EE, Försti A, Waller RG, Machiela MJ, Chanock SJ, Camp NJ, Rymko M, Raźny M, Cozen W, Várkonyi J, Piredda C, Pelosini M, Belachew AA, Subocz E, Hemminki K, Rybicka-Ramos M, Giles GG, Milne RL, Hofmann JN, Zaucha JM, Vangsted AJ, Goldschmidt H, Rajkumar SV, Tomczak W, Sainz J, Butrym A, Watek M, Iskierka-Jazdzewska E, Buda G, Robinson DP, Jurczyszyn A, Dudziński M, Martinez-Lopez J, Sinnwell JP, Slager SL, Jamroziak K, Reis RMV, Weinhold N, Bhatti P, Carvajal-Carmona LG, Zawirska D, Norman AD, Mazur G, Berndt SI, Campa D, Vachon CM, Canzian F. Does a Multiple Myeloma Polygenic Risk Score Predict Overall Survival of Patients with Myeloma? Cancer Epidemiol Biomarkers Prev 2022; 31:1863-1866. [PMID: 35700034 DOI: 10.1158/1055-9965.epi-22-0043] [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: 01/13/2022] [Revised: 03/18/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) of multiple myeloma in populations of European ancestry (EA) identified and confirmed 24 susceptibility loci. For other cancers (e.g., colorectum and melanoma), risk loci have also been associated with patient survival. METHODS We explored the possible association of all the known risk variants and their polygenic risk score (PRS) with multiple myeloma overall survival (OS) in multiple populations of EA [the International Multiple Myeloma rESEarch (IMMEnSE) consortium, the International Lymphoma Epidemiology consortium, CoMMpass, and the German GWAS] for a total of 3,748 multiple myeloma cases. Cox proportional hazards regression was used to assess the association between each risk SNP with OS under the allelic and codominant models of inheritance. All analyses were adjusted for age, sex, country of origin (for IMMEnSE) or principal components (for the others) and disease stage (ISS). SNP associations were meta-analyzed. RESULTS SNP associations were meta-analyzed. From the meta-analysis, two multiple myeloma risk SNPs were associated with OS (P < 0.05), specifically POT1-AS1-rs2170352 [HR = 1.37; 95% confidence interval (CI) = 1.09-1.73; P = 0.007] and TNFRSF13B-rs4273077 (HR = 1.19; 95% CI = 1.01-1.41; P = 0.04). The association between the combined 24 SNP MM-PRS and OS, however, was not significant. CONCLUSIONS Overall, our results did not support an association between the majority of multiple myeloma risk SNPs and OS. IMPACT This is the first study to investigate the association between multiple myeloma PRS and OS in multiple myeloma.
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Affiliation(s)
- Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Alyssa Clay-Gilmour
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Greenville, South Carolina
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michelle A T Hildebrandt
- Department of Lymphoma - Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcin Kruszewski
- Department of Hematology University Hospital Bydgoszcz, Bydgoszcz, Poland
| | - Robert Z Orlowski
- Department of Lymphoma - Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shaji K Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Elad Ziv
- Department of Medicine, University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Enrico Orciuolo
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Elizabeth E Brown
- Department of Pathology, School of Medicine, University of Alabama, Birmingham, Alabama
| | - Asta Försti
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Rosalie G Waller
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Nicola J Camp
- Division of Hematology and Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Marcin Rymko
- Department of Haematology and Bone Marrow Transplantation, SSM im. M. Kopernika, Torun, Poland
| | | | - Wendy Cozen
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, Department of Pathology, School of Medicine, Susan and Henry Samueli College of Health Sciences, Chao Family Comprehensive Cancer Center, University of California at Irvine, California
| | - Judit Várkonyi
- Department of Hematology and Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Chiara Piredda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matteo Pelosini
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Alem A Belachew
- Department of Lymphoma - Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edyta Subocz
- Department of Hematology, Military Institute of Medicine, Warsaw, Poland
| | - Kari Hemminki
- Biomedical Center, Faculty of Medicine, Charles University in Pilsen, Pilsen, Czech Republic
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Jan Maciej Zaucha
- Department of Hematology and Transplantology, Medical Univeristy of Gdańsk, Gdańsk, Poland
| | - Annette Juul Vangsted
- Department of Haematology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - S Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Waldemar Tomczak
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Poland
| | - Juan Sainz
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada/Andalusian Regional Government, Granada, Spain
- Hematology department, Virgen de las Nieves University Hospital, Granada, Spain
| | - Aleksandra Butrym
- Department of Internal and Occupational Diseases, Medical University Wroclaw, Wroclaw, Poland
| | - Marzena Watek
- Hematology Clinic, Holycross Cancer Center, Kielce, Poland
| | | | - Gabriele Buda
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Dennis P Robinson
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Artur Jurczyszyn
- Plasma Cell Dyscrasias Center, Department of Hematology, Faculty of Medicine, Jagiellonian University, Kraków, Poland
| | - Marek Dudziński
- Department of Hematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszów, Rzeszów, Poland
| | | | - Jason P Sinnwell
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Susan L Slager
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Disease, Medical University of Warsaw, Warsaw, Poland
| | - Rui Manuel Vieira Reis
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal and ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- CCU Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Parveen Bhatti
- Division of Population Oncology Cancer Control Research, BC Cancer, Vancouver, Bristish Columbia, Canada
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Luis G Carvajal-Carmona
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California
- Latinos United for Cancer Health Advancement Initiative, University of California Davis Comprehensive Cancer Center, Sacramento, California
- Community Engagement Program, Clinical and Translational Science Center, University of California Davis, Sacramento, California
| | - Daria Zawirska
- Department of Hematology, University Hospital of Cracow, Cracow, Poland
| | - Aaron D Norman
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Grzegorz Mazur
- Department of Internal and Occupational Diseases, Medical University Wroclaw, Wroclaw, Poland
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Celine M Vachon
- Division of Epidemiology, Department of Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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5
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Chao BN, Carrick DM, Filipski KK, Nelson SA. Overview of Research on Germline Genetic Variation in Immune Genes and Cancer Outcomes. Cancer Epidemiol Biomarkers Prev 2022; 31:495-506. [PMID: 35027433 DOI: 10.1158/1055-9965.epi-21-0583] [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: 05/13/2021] [Revised: 10/13/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Since the late 19th century, the immune system has been known to play a role in cancer risk, initiation, and progression. Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for autoimmune and inflammatory diseases, yet the connection between human genetic variation and immune-mediated response to cancer treatments remains less well-explored. Understanding inherited genetic variation, with respect to germline genetic polymorphisms that affect immune system pathways, could lead to greater insights about how these processes may best be harnessed to successfully treat cancer. Our goal in this manuscript was to understand progress and challenges in assessing the role of inherited genetic variation in response to cancer treatments. Overall, the 39 studies reviewed here suggest that germline genetic variation in immune system related genes may potentially affect responses to cancer treatments. Although further research is needed, considering information on germline immune genetic variation may help, in some cases, to optimize cancer treatment.
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Affiliation(s)
- Brittany N Chao
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Danielle M Carrick
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Kelly K Filipski
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Stefanie A Nelson
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
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6
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Salem Werdyani
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Megan Carey
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Patrick Parfrey
- Discipline of MedicineFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Yildiz E. Yilmaz
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Discipline of MedicineFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Department of Mathematics and StatisticsFaculty of ScienceMemorial UniversitySt. John’sNLCanada
| | - Sevtap Savas
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Discipline of OncologyFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
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7
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Qu X, Zhao L, Wang M, Zhang R, Cheng L, Qiu L, Tong X, Cai S, Wei Q, Li Q. Novel functional variants in the Notch pathway and survival of Chinese colorectal cancer. Int J Cancer 2021; 149:84-96. [PMID: 33728681 DOI: 10.1002/ijc.33561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 12/09/2022]
Abstract
Notch signaling pathway plays crucial roles in progression of colorectal cancer (CRC), likely affecting overall survival (OS). In a two-stage survival analysis of 1116 CRC patients in East China, we found that one locus at MINAR1 out of 133 genes in the Notch signaling pathway was significantly associated with OS (P < 1 × 10-6 , false discovery rate < 0.01). This locus containing seven single-nucleotide polymorphisms (SNPs) in high linkage disequilibrium (R2 = 1) is located on chromosome 15, of which the MINAR1 rs72430409 G allele was associated with a greater death risk (HR = 1.98, 95% CI = 1.55-2.54, P = 6.8 × 10-8 ). Further analysis of ChIP-sequencing data from the encyclopedia of DNA Elements showed that rs72430409 and rs72630408 were potential cis-regulatory elements for the MINAR1 promoter. Additional expression quantitative trait loci analysis revealed that rs72430409 G>A and rs72630408 A>G were correlated with increased MINAR1 expression levels in both blood cells and colon tissues. Dual luciferase assays revealed that the rs72430409 A allele increased MINAR1 promoter activity. The Cancer Genome Atlas data showed that expression levels of MINAR1 in CRC samples were significantly higher than that in normal colorectal tissue and that high expression of MINAR1 was associated with a shortened OS, likely via activating the epithelial mesenchymal transition (EMT) pathway as shown in the gene-set enrichment analysis. In vitro, RNAi-mediated silencing of MINAR1 led to decreased migration and proliferation in CRC cancer cells, and MINAR1 silencing could downregulate the expression of key effector genes in EMT and glycolysis. Larger cohort studies and further experiments are needed to validate our findings.
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Affiliation(s)
- Xiaofei Qu
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liqin Zhao
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengyun Wang
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruoxin Zhang
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lei Cheng
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lixin Qiu
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoxia Tong
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sanjun Cai
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qingyi Wei
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Qingguo Li
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
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8
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Chatrath A, Ratan A, Dutta A. Germline Variants That Affect Tumor Progression. Trends Genet 2020; 37:433-443. [PMID: 33203571 DOI: 10.1016/j.tig.2020.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 01/31/2023]
Abstract
Germline variants have a rich history of being studied in the context of cancer risk. Emerging studies now suggest that germline variants contribute not only to cancer risk but to tumor progression as well. In this opinion article, we discuss the initial discoveries associating germline variants with patient outcome and the mechanisms by which germline variants affect molecular pathways. Germline variants affect molecular pathways through amino acid changes, alteration of splicing patterns or expression of genes, influencing the selection for somatic mutations, and causing genome-wide mutational enrichment. These molecular alterations can lead to tumor phenotypes that become clinically apparent such as metastasis, alterations to the immune microenvironment, and modulation of therapeutic response. Overall, the growing body of evidence suggests that germline variants play a larger role in tumor progression than has been previously appreciated and that germline variation holds substantial potential for improving personalized medicine and patient outcomes.
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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9
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Deutelmoser H, Lorenzo Bermejo J, Benner A, Weigl K, Park HA, Haffa M, Herpel E, Schneider M, Ulrich CM, Hoffmeister M, Chang-Claude J, Brenner H, Scherer D. Genotype-Based Gene Expression in Colon Tissue-Prediction Accuracy and Relationship with the Prognosis of Colorectal Cancer Patients. Int J Mol Sci 2020; 21:E8150. [PMID: 33142733 PMCID: PMC7662650 DOI: 10.3390/ijms21218150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) survival has environmental and inherited components. The expression of specific genes can be inferred based on individual genotypes-so called expression quantitative trait loci. In this study, we used the PrediXcan method to predict gene expression in normal colon tissue using individual genotype data from 91 CRC patients and examined the correlation ρ between predicted and measured gene expression levels. Out of 5434 predicted genes, 58% showed a negative ρ value and only 16% presented a ρ higher than 0.10. We subsequently investigated the association between genotype-based gene expression in colon tissue for genes with ρ > 0.10 and survival of 4436 CRC patients. We identified an inverse association between the predicted expression of ARID3B and CRC-specific survival for patients with a body mass index greater than or equal to 30 kg/m2 (HR (hazard ratio) = 0.66 for an expression higher vs. lower than the median, p = 0.005). This association was validated using genotype and clinical data from the UK Biobank (HR = 0.74, p = 0.04). In addition to the identification of ARID3B expression in normal colon tissue as a candidate prognostic biomarker for obese CRC patients, our study illustrates the challenges of genotype-based prediction of gene expression, and the advantage of reassessing the prediction accuracy in a subset of the study population using measured gene expression data.
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Affiliation(s)
- Heike Deutelmoser
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Institute of Medical Biometry and Informatics, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany;
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany;
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany;
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (K.W.); (M.H.)
| | - Hanla A. Park
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (H.A.P.); (J.C.-C.)
| | - Mariam Haffa
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Division of Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Esther Herpel
- NCT Tissue Bank, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany;
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral, and Transplantation Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany;
| | - Cornelia M. Ulrich
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Huntsman Cancer Institute, 2000 Cir of Hope Dr 1950, Salt Lake City, UT 84112, USA
- Department of Population Health Sciences, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (K.W.); (M.H.)
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (H.A.P.); (J.C.-C.)
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf (UKE), Martinstraße 52, 20246 Hamburg, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (K.W.); (M.H.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dominique Scherer
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Institute of Medical Biometry and Informatics, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany;
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10
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Scherer D, Deutelmoser H, Balavarca Y, Toth R, Habermann N, Buck K, Kap EJ, Botma A, Seibold P, Jansen L, Lorenzo Bermejo J, Weigl K, Benner A, Hoffmeister M, Ulrich A, Brenner H, Burwinkel B, Chang-Claude J, Ulrich CM. Polymorphisms in the Angiogenesis-Related Genes EFNB2, MMP2 and JAG1 Are Associated with Survival of Colorectal Cancer Patients. Int J Mol Sci 2020; 21:E5395. [PMID: 32751332 PMCID: PMC7432124 DOI: 10.3390/ijms21155395] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
An individual's inherited genetic variation may contribute to the 'angiogenic switch', which is essential for blood supply and tumor growth of microscopic and macroscopic tumors. Polymorphisms in angiogenesis-related genes potentially predispose to colorectal cancer (CRC) or affect the survival of CRC patients. We investigated the association of 392 single nucleotide polymorphisms (SNPs) in 33 angiogenesis-related genes with CRC risk and survival of CRC patients in 1754 CRC cases and 1781 healthy controls within DACHS (Darmkrebs: Chancen der Verhütung durch Screening), a German population-based case-control study. Odds ratios and 95% confidence intervals (CI) were estimated from unconditional logistic regression to test for genetic associations with CRC risk. The Cox proportional hazard model was used to estimate hazard ratios (HR) and 95% CIs for survival. Multiple testing was adjusted for by a false discovery rate. No variant was associated with CRC risk. Variants in EFNB2, MMP2 and JAG1 were significantly associated with overall survival. The association of the EFNB2 tagging SNP rs9520090 (p < 0.0001) was confirmed in two validation datasets (p-values: 0.01 and 0.05). The associations of the tagging SNPs rs6040062 in JAG1 (p-value 0.0003) and rs2241145 in MMP2 (p-value 0.0005) showed the same direction of association with overall survival in the first and second validation sets, respectively, although they did not reach significance (p-values: 0.09 and 0.25, respectively). EFNB2, MMP2 and JAG1 are known for their functional role in angiogenesis and the present study points to novel evidence for the impact of angiogenesis-related genetic variants on the CRC outcome.
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Affiliation(s)
- Dominique Scherer
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- Institute of Medical Biometry and Informatics, University of Heidelberg, 69117 Heidelberg, Germany;
| | - Heike Deutelmoser
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- Institute of Medical Biometry and Informatics, University of Heidelberg, 69117 Heidelberg, Germany;
| | - Yesilda Balavarca
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
| | - Reka Toth
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- Division of Cancer Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- European Molecular Biology Laboratory (EMBL), Genome Biology, 69117 Heidelberg, Germany
| | - Katharina Buck
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
| | - Elisabeth Johanna Kap
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (E.J.K.); (P.S.); (J.C.-C.)
| | - Akke Botma
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (E.J.K.); (P.S.); (J.C.-C.)
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (E.J.K.); (P.S.); (J.C.-C.)
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (L.J.); (K.W.); (M.H.)
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, 69117 Heidelberg, Germany;
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (L.J.); (K.W.); (M.H.)
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany;
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (L.J.); (K.W.); (M.H.)
| | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69117 Heidelberg, Germany;
- Chirurgische Klinik I, Lukaskrankenhaus Neuss, 41464 Neuss, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (L.J.); (K.W.); (M.H.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany;
- Division Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69117 Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (E.J.K.); (P.S.); (J.C.-C.)
- Cancer Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cornelia M. Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69117 Heidelberg, Germany; (D.S.); (H.D.); (Y.B.); (R.T.); (N.H.); (K.B.); (A.B.); (H.B.)
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
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