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Jiang L, Jia L, Wang Y, Wu Y, Yue J. Adap-BDCM: Adaptive Bilinear Dynamic Cascade Model for Classification Tasks on CNV Datasets. Interdiscip Sci 2024:10.1007/s12539-024-00635-w. [PMID: 38758306 DOI: 10.1007/s12539-024-00635-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Copy number variation (CNV) is an essential genetic driving factor of cancer formation and progression, making intelligent classification based on CNV feasible. However, there are a few challenges in the current machine learning and deep learning methods, such as the design of base classifier combination schemes in ensemble methods and the selection of layers of neural networks, which often result in low accuracy. Therefore, an adaptive bilinear dynamic cascade model (Adap-BDCM) is developed to further enhance the accuracy and applicability of these methods for intelligent classification on CNV datasets. In this model, a feature selection module is introduced to mitigate the interference of redundant information, and a bilinear model based on the gated attention mechanism is proposed to extract more beneficial deep fusion features. Furthermore, an adaptive base classifier selection scheme is designed to overcome the difficulty of manually designing base classifier combinations and enhance the applicability of the model. Lastly, a novel feature fusion scheme with an attribute recall submodule is constructed, effectively avoiding getting stuck in local solutions and missing some valuable information. Numerous experiments have demonstrated that our Adap-BDCM model exhibits optimal performance in cancer classification, stage prediction, and recurrence on CNV datasets. This study can assist physicians in making diagnoses faster and better.
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Affiliation(s)
- Liancheng Jiang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China
| | - Liye Jia
- College of Computer Science and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Yizhen Wang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China
| | - Yongfei Wu
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China
| | - Junhong Yue
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China.
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Arnau-Collell C, Díez-Villanueva A, Bellosillo B, Augé JM, Muñoz J, Guinó E, Moreira L, Serradesanferm A, Pozo À, Torà-Rocamora I, Bonjoch L, Ibañez-Sanz G, Obon-Santacana M, Moratalla-Navarro F, Sanz-Pamplona R, Márquez Márquez C, Rueda Miret R, Pérez Berbegal R, Piquer Velasco G, Hernández Rodríguez C, Grau J, Castells A, Borràs JM, Bessa X, Moreno V, Castellví-Bel S. Evaluating the Potential of Polygenic Risk Score to Improve Colorectal Cancer Screening. Cancer Epidemiol Biomarkers Prev 2022; 31:1305-1312. [PMID: 35511747 PMCID: PMC9355543 DOI: 10.1158/1055-9965.epi-22-0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/14/2022] [Accepted: 04/26/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Colorectal cancer has high incidence and associated mortality worldwide. Screening programs are recommended for men and women over 50. Intermediate screens such as fecal immunochemical testing (FIT) select patients for colonoscopy with suboptimal sensitivity. Additional biomarkers could improve the current scenario. METHODS We included 2,893 individuals with a positive FIT test. They were classified as cases when a high-risk lesion for colorectal cancer was detected after colonoscopy, whereas the control group comprised individuals with low-risk or no lesions. 65 colorectal cancer risk genetic variants were genotyped. Polygenic risk score (PRS) and additive models for risk prediction incorporating sex, age, FIT value, and PRS were generated. RESULTS Risk score was higher in cases compared with controls [per allele OR = 1.04; 95% confidence interval (CI), 1.02-1.06; P < 0.0001]. A 2-fold increase in colorectal cancer risk was observed for subjects in the highest decile of risk alleles (≥65), compared with those in the first decile (≤54; OR = 2.22; 95% CI, 1.59-3.12; P < 0.0001). The model combining sex, age, FIT value, and PRS reached the highest accuracy for identifying patients with a high-risk lesion [cross-validated area under the ROC curve (AUROC): 0.64; 95% CI, 0.62-0.66]. CONCLUSIONS This is the first investigation analyzing PRS in a two-step colorectal cancer screening program. PRS could improve current colorectal cancer screening, most likely for higher at-risk subgroups. However, its capacity is limited to predict colorectal cancer risk status and should be complemented by additional biomarkers. IMPACT PRS has capacity for risk stratification of colorectal cancer suggesting its potential for optimizing screening strategies alongside with other biomarkers.
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Affiliation(s)
- Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Josep M. Augé
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Elisabet Guinó
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Anna Serradesanferm
- Department of Preventive Medicine and Epidemiology, Clinical Institute of Internal Medicine and Dermatology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona,Barcelona, Spain
| | - Àngels Pozo
- Department of Preventive Medicine and Epidemiology, Clinical Institute of Internal Medicine and Dermatology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona,Barcelona, Spain
| | - Isabel Torà-Rocamora
- Department of Preventive Medicine and Epidemiology, Clinical Institute of Internal Medicine and Dermatology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona,Barcelona, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Gemma Ibañez-Sanz
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain
| | - Mireia Obon-Santacana
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain
| | - Ferran Moratalla-Navarro
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain
| | - Carmen Márquez Márquez
- Gastroenterology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Rebeca Rueda Miret
- Pathology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Rocio Pérez Berbegal
- Gastroenterology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Gabriel Piquer Velasco
- Pathology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Cristina Hernández Rodríguez
- Unitat de Prevenció i Registre del Càncer, Servei d'Epidemiologia i Avaluació, Hospital del Mar, Barcelona, Spain
| | - Jaume Grau
- Department of Preventive Medicine and Epidemiology, Clinical Institute of Internal Medicine and Dermatology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona,Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Josep M. Borràs
- Department of Clinical Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Bessa
- Gastroenterology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Victor Moreno
- Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Barcelona, Spain.,Corresponding Authors: Victor Moreno, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Avinguda de la Granvia de l'Hospitalet, 199, L'Hospitalet de Llobregat 08908, Barcelona, Spain. Phone: 349-3260-7434; E-mail: ; and Sergi Castellví-Bel, Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Rosselló 149-153, Barcelona 08036, Spain. Phone: 349-3227-5707; E-mail:
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Corresponding Authors: Victor Moreno, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and University of Barcelona, Avinguda de la Granvia de l'Hospitalet, 199, L'Hospitalet de Llobregat 08908, Barcelona, Spain. Phone: 349-3260-7434; E-mail: ; and Sergi Castellví-Bel, Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Rosselló 149-153, Barcelona 08036, Spain. Phone: 349-3227-5707; E-mail:
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Polymorphisms within Autophagy-Related Genes Influence the Risk of Developing Colorectal Cancer: A Meta-Analysis of Four Large Cohorts. Cancers (Basel) 2021; 13:cancers13061258. [PMID: 33809172 PMCID: PMC7998818 DOI: 10.3390/cancers13061258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary We investigated the influence of autophagy-related variants in modulating colorectal cancer (CRC) risk through a meta-analysis of genome-wide association study (GWAS) data from four large European cohorts. We found that genetic variants within the DAPK2 and ATG5 loci were associated with CRC risk. This study also shed some light onto the functional mechanisms behind the observed associations and demonstrated the impact of DAPK2rs11631973 and ATG5rs546456 polymorphisms on the modulation of host immune responses, blood derived-cell counts and serum inflammatory protein levels, which might be involved in promoting cancer development. No effect of the DAPK2 and ATG5 polymorphisms on the autophagy flux was observed. Abstract The role of genetic variation in autophagy-related genes in modulating autophagy and cancer is poorly understood. Here, we comprehensively investigated the association of autophagy-related variants with colorectal cancer (CRC) risk and provide new insights about the molecular mechanisms underlying the associations. After meta-analysis of the genome-wide association study (GWAS) data from four independent European cohorts (8006 CRC cases and 7070 controls), two loci, DAPK2 (p = 2.19 × 10−5) and ATG5 (p = 6.28 × 10−4) were associated with the risk of CRC. Mechanistically, the DAPK2rs11631973G allele was associated with IL1 β levels after the stimulation of peripheral blood mononuclear cells (PBMCs) with Staphylococcus aureus (p = 0.002), CD24 + CD38 + CD27 + IgM + B cell levels in blood (p = 0.0038) and serum levels of en-RAGE (p = 0.0068). ATG5rs546456T allele was associated with TNF α and IL1 β levels after the stimulation of PBMCs with LPS (p = 0.0088 and p = 0.0076, respectively), CD14+CD16− cell levels in blood (p = 0.0068) and serum levels of CCL19 and cortisol (p = 0.0052 and p = 0.0074, respectively). Interestingly, no association with autophagy flux was observed. These results suggested an effect of the DAPK2 and ATG5 loci in the pathogenesis of CRC, likely through the modulation of host immune responses.
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Gargallo-Puyuelo CJ, Lanas Á, Carrera-Lasfuentes P, Ferrández Á, Quintero E, Carrillo M, Alonso-Abreu I, García-González MA. Familial Colorectal Cancer and Genetic Susceptibility: Colorectal Risk Variants in First-Degree Relatives of Patients With Colorectal Cancer. Clin Transl Gastroenterol 2021; 12:e00301. [PMID: 33534415 PMCID: PMC7861964 DOI: 10.14309/ctg.0000000000000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/18/2020] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Epidemiological studies estimate that having a first-degree relative (FDR) with colorectal cancer (CRC) increases 2-fold to 3-fold the risk of developing the disease. Because FDRs of CRC patients are more likely to co-inherit CRC risk variants, we aimed to evaluate potential differences in genotype distribution of single nucleotide polymorphisms (SNPs) related to CRC risk between FDRs of patients with nonsyndromic CRC (cases) and individuals with no family history of CRC (controls). METHODS We designed a case-control study comprising 750 cases and 750 Spanish Caucasian controls matched by sex, age, and histological findings after colonoscopy. Genomic DNA from all participants was genotyped for 88 SNPs associated with CRC risk using the MassArray (Sequenom) platform. RESULTS Ten of the 88 SNPs analyzed revealed significant associations (P < 0.05) with a family history of CRC in our population. The most robust associations were found for the rs17094983G>A SNP in the long noncoding RNA LINC01500 (odds ratio = 0.72; 95% confidence interval: 0.58-0.88, log-additive model), and the rs11255841T>A SNP in the long noncoding RNA LINC00709 (odds ratio = 2.04; 95% confidence interval: 1.19-3.51, dominant model). Of interest, the observed associations were in the same direction than those reported for CRC risk. DISCUSSION FDRs of CRC patients show significant differences in genotype distribution of SNPs related to CRC risk as compared to individuals with no family history of CRC. Genotyping of CRC risk variants in FDRs of CRC patients may help to identify subjects at risk that would benefit from stricter surveillance and CRC screening programs.
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Affiliation(s)
- Carla J. Gargallo-Puyuelo
- Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- University of Zaragoza School of Medicine, Zaragoza, Spain
| | - Ángel Lanas
- Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- University of Zaragoza School of Medicine, Zaragoza, Spain
- CIBERehd, Zaragoza, Spain
| | | | - Ángel Ferrández
- Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Enrique Quintero
- Department of Gastroenterology, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
- University of La Laguna, School of Medicine, Canary Islands, Spain
| | - Marta Carrillo
- Department of Gastroenterology, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - Inmaculada Alonso-Abreu
- Department of Gastroenterology, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - María Asunción García-González
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- CIBERehd, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
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Gyimesi G, Pujol-Giménez J, Kanai Y, Hediger MA. Sodium-coupled glucose transport, the SLC5 family, and therapeutically relevant inhibitors: from molecular discovery to clinical application. Pflugers Arch 2020; 472:1177-1206. [PMID: 32767111 PMCID: PMC7462921 DOI: 10.1007/s00424-020-02433-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023]
Abstract
Sodium glucose transporters (SGLTs) belong to the mammalian solute carrier family SLC5. This family includes 12 different members in human that mediate the transport of sugars, vitamins, amino acids, or smaller organic ions such as choline. The SLC5 family belongs to the sodium symporter family (SSS), which encompasses transporters from all kingdoms of life. It furthermore shares similarity to the structural fold of the APC (amino acid-polyamine-organocation) transporter family. Three decades after the first molecular identification of the intestinal Na+-glucose cotransporter SGLT1 by expression cloning, many new discoveries have evolved, from mechanistic analysis to molecular genetics, structural biology, drug discovery, and clinical applications. All of these advances have greatly influenced physiology and medicine. While SGLT1 is essential for fast absorption of glucose and galactose in the intestine, the expression of SGLT2 is largely confined to the early part of the kidney proximal tubules, where it reabsorbs the bulk part of filtered glucose. SGLT2 has been successfully exploited by the pharmaceutical industry to develop effective new drugs for the treatment of diabetic patients. These SGLT2 inhibitors, termed gliflozins, also exhibit favorable nephroprotective effects and likely also cardioprotective effects. In addition, given the recent finding that SGLT2 is also expressed in tumors of pancreas and prostate and in glioblastoma, this opens the door to potential new therapeutic strategies for cancer treatment by specifically targeting SGLT2. Likewise, further discoveries related to the functional association of other SGLTs of the SLC5 family to human pathologies will open the door to potential new therapeutic strategies. We furthermore hope that the herein summarized information about the physiological roles of SGLTs and the therapeutic benefits of the gliflozins will be useful for our readers to better understand the molecular basis of the beneficial effects of these inhibitors, also in the context of the tubuloglomerular feedback (TGF), and the renin-angiotensin system (RAS). The detailed mechanisms underlying the clinical benefits of SGLT2 inhibition by gliflozins still warrant further investigation that may serve as a basis for future drug development.
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Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Office D845, Freiburgstrasse 15, CH-3010, Bern, Switzerland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Office D845, Freiburgstrasse 15, CH-3010, Bern, Switzerland
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Office D845, Freiburgstrasse 15, CH-3010, Bern, Switzerland.
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Montazeri Z, Li X, Nyiraneza C, Ma X, Timofeeva M, Svinti V, Meng X, He Y, Bo Y, Morgan S, Castellví-Bel S, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo Á, Castells A, Bishop T, Buchanan D, Jenkins MA, Keku TO, Lindblom A, van Duijnhoven FJB, Wu A, Farrington SM, Dunlop MG, Campbell H, Theodoratou E, Zheng W, Little J. Systematic meta-analyses, field synopsis and global assessment of the evidence of genetic association studies in colorectal cancer. Gut 2020; 69:1460-1471. [PMID: 31818908 PMCID: PMC7398467 DOI: 10.1136/gutjnl-2019-319313] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To provide an understanding of the role of common genetic variations in colorectal cancer (CRC) risk, we report an updated field synopsis and comprehensive assessment of evidence to catalogue all genetic markers for CRC (CRCgene2). DESIGN We included 869 publications after parallel literature review and extracted data for 1063 polymorphisms in 303 different genes. Meta-analyses were performed for 308 single nucleotide polymorphisms (SNPs) in 158 different genes with at least three independent studies available for analysis. Scottish, Canadian and Spanish data from genome-wide association studies (GWASs) were incorporated for the meta-analyses of 132 SNPs. To assess and classify the credibility of the associations, we applied the Venice criteria and Bayesian False-Discovery Probability (BFDP). Genetic associations classified as 'positive' and 'less-credible positive' were further validated in three large GWAS consortia conducted in populations of European origin. RESULTS We initially identified 18 independent variants at 16 loci that were classified as 'positive' polymorphisms for their highly credible associations with CRC risk and 59 variants at 49 loci that were classified as 'less-credible positive' SNPs; 72.2% of the 'positive' SNPs were successfully replicated in three large GWASs and the ones that were not replicated were downgraded to 'less-credible' positive (reducing the 'positive' variants to 14 at 11 loci). For the remaining 231 variants, which were previously reported, our meta-analyses found no evidence to support their associations with CRC risk. CONCLUSION The CRCgene2 database provides an updated list of genetic variants related to CRC risk by using harmonised methods to assess their credibility.
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Affiliation(s)
- Zahra Montazeri
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Xue Li
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Christine Nyiraneza
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, Chongqing, China
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Xiangrui Meng
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Yazhou He
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Yacong Bo
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Shenzhen, Hong Kong
| | - Samuel Morgan
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Ceres Fernández-Rozadilla
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Ángel Carracedo
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Daniel Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Genetic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Anna Wu
- University of Southern California, Preventative Medicine, Los Angeles, California, USA
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Julian Little
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Shen N, Wang P, Li Y, Zhu Y, Gong Y, Zhong R, Lu Y, Cheng L. Nonreceptor protein tyrosine phosphatases (NRPTPs) gene family associates with the risk of hepatocellular carcinoma in a Chinese hepatitis B virus-related subjects. Mol Carcinog 2020; 59:980-988. [PMID: 32484301 DOI: 10.1002/mc.23228] [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: 03/19/2020] [Revised: 05/09/2020] [Accepted: 05/18/2020] [Indexed: 11/07/2022]
Abstract
Nonreceptor protein tyrosine phosphatases (NRPTPs) are reported to be associated with several human cancers, but their roles in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remain unclear. Here, we integrated bioinformatics tools, population association analyses, and biological assays to systematically screen for potentially functional single nucleotide polymorphisms (SNPs) within the 17 NRPTPs genes and evaluate the effects of candidate SNPs on the risk of HCC or persistent HBV infection. A total of 790 HBV-related HCC cases and 1454 cancer-free controls were enrolled. Controls included 711 HBV persistent carriers and 743 spontaneously recovered subjects. Results demonstrated that PTPN4 rs9308777 (odds ratio [OR] = 1.25, 95% confidence interval [CI] = 1.06-1.49, P = .009) and PTPN12 rs350050 (OR = 1.26, 95% CI = 1.10-1.45, P = .001), were significantly associated with HCC risk, but not with persistent HBV infection risk. The cumulative risk effect of these two SNPs was more significantly increased the susceptibility to HCC (OR = 1.27, 95% CI = 1.14-1.41, P = 2.40 × 10-5 ). Subsequent biological assays further revealed the potential pathogenesis that PTPN4 rs9308777 might decrease the gene expression, and PTPN12 rs3750050 might promote cell proliferation by attenuating PTPN12's inhibitory activity on EGFR/ERK pathway. In summary, our integrative study highlights that PTPN4 and PTPN12 are significantly associated with HBV-related HCC risk, but do not influence persistent HBV infection. These findings shed light on the importance of the synergistic effects of regulatory and missense variants on the risk for HCC, and provide data to support personalized cancer medicine in the future.
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Affiliation(s)
- Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Wang
- Institute and Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Single nucleotide polymorphisms associated with susceptibility for development of colorectal cancer: Case-control study in a Basque population. PLoS One 2019; 14:e0225779. [PMID: 31821333 PMCID: PMC6903717 DOI: 10.1371/journal.pone.0225779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/12/2019] [Indexed: 02/07/2023] Open
Abstract
Given the significant population diversity in genetic variation, we aimed to investigate whether single nucleotide polymorphisms (SNPs) previously identified in studies of colorectal cancer (CRC) susceptibility were also relevant to the population of the Basque Country (North of Spain). We genotyped 230 CRC cases and 230 healthy controls for 48 previously reported CRC-susceptibility SNPs. Only the rs6687758 in DUPS10 exhibited a statistically significant association with CRC risk based on the crude analysis. The rs6687758 AG genotype conferred about 2.13-fold increased risk for CRC compared to the AA genotype. Moreover, we found significant associations in cases between smoking status, physical activity, and the rs6687758 SNP. The results of a Genetic Risk Score (GRS) showed that the risk alleles were more frequent in cases than controls and the score was associated with CRC in crude analysis. In conclusion, we have confirmed a CRC susceptibility locus and the existence of associations between modifiable factors and the rs6687758 SNP; moreover, the GRS was associated with CRC. However, further experimental validations are needed to establish the role of this SNP, the function of the gene identified, as well as the contribution of the interaction between environmental factors and this locusto the risk of CRC.
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9
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Toma C, Díaz-Gay M, Franch-Expósito S, Arnau-Collell C, Overs B, Muñoz J, Bonjoch L, Soares de Lima Y, Ocaña T, Cuatrecasas M, Castells A, Bujanda L, Balaguer F, Cubiella J, Caldés T, Fullerton JM, Castellví-Bel S. Using linkage studies combined with whole-exome sequencing to identify novel candidate genes for familial colorectal cancer. Int J Cancer 2019; 146:1568-1577. [PMID: 31525256 PMCID: PMC7004061 DOI: 10.1002/ijc.32683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/23/2019] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is a complex disorder for which the majority of the underlying germline predisposition factors remain still unidentified. Here, we combined whole‐exome sequencing (WES) and linkage analysis in families with multiple relatives affected by CRC to identify candidate genes harboring rare variants with potential high‐penetrance effects. Forty‐seven affected subjects from 18 extended CRC families underwent WES. Genome‐wide linkage analysis was performed under linear and exponential models. Suggestive linkage peaks were identified on chromosomes 1q22–q24.2 (maxSNP = rs2134095; LODlinear = 2.38, LODexp = 2.196), 7q31.2–q34 (maxSNP = rs6953296; LODlinear = 2.197, LODexp = 2.149) and 10q21.2–q23.1 (maxSNP = rs1904589; LODlinear = 1.445, LODexp = 2.195). These linkage signals were replicated in 10 independent sets of random markers from each of these regions. To assess the contribution of rare variants predicted to be pathogenic, we performed a family‐based segregation test with 89 rare variants predicted to be deleterious from 78 genes under the linkage intervals. This analysis showed significant segregation of rare variants with CRC in 18 genes (weighted p‐value > 0.0028). Protein network analysis and functional evaluation were used to suggest a plausible candidate gene for germline CRC predisposition. Etiologic rare variants implicated in cancer germline predisposition may be identified by combining traditional linkage with WES data. This approach can be used with already available NGS data from families with several sequenced members to further identify candidate genes involved germline predisposition to disease. This approach resulted in one candidate gene associated with increased risk of CRC but needs evidence from further studies. What's new? Inherited genetic factors are thought to account for more than one‐third of colorectal cancer (CRC) cases. Most predisposing genetic factors, however, remain unidentified. Here, genome‐wide linkage analysis using whole‐exome sequencing (WES) data was performed in families with marked CRC aggregation. The combined linkage‐sequencing approach identified possible linkage peaks on chromosomes 1q22‐q24.2, 7q31.2‐q34, and 10q21.2‐q23.1. Analyses of potentially pathogenic variants revealed significant segregation of rare variants in 18 genes, while functional analyses identified a plausible candidate gene for germline CRC predisposition. The findings underscore the utility of linkage analysis employing WES for the discovery of candidate genes for disease predisposition.
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Affiliation(s)
- Claudio Toma
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Bronwyn Overs
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - 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), San Sebastian, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, 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), Ourense, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, CIBERONC (Centro de Investigacion Biomedica en Red de Cancer), IdISSC, Madrid, Spain
| | - Janice M Fullerton
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
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10
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Toma C, Díaz-Gay M, Soares de Lima Y, Arnau-Collell C, Franch-Expósito S, Muñoz J, Overs B, Bonjoch L, Carballal S, Ocaña T, Cuatrecasas M, Díaz de Bustamante A, Castells A, Bujanda L, Cubiella J, Balaguer F, Rodríguez-Alcalde D, Fullerton JM, Castellví-Bel S. Identification of a Novel Candidate Gene for Serrated Polyposis Syndrome Germline Predisposition by Performing Linkage Analysis Combined With Whole-Exome Sequencing. Clin Transl Gastroenterol 2019; 10:e00100. [PMID: 31663907 PMCID: PMC6919450 DOI: 10.14309/ctg.0000000000000100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/19/2019] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Serrated polyposis syndrome (SPS) is a complex disorder with a high risk of colorectal cancer for which the germline factors remain largely unknown. Here, we combined whole-exome sequencing (WES) and linkage studies in families with multiple members affected by SPS to identify candidate genes harboring rare variants with higher penetrance effects. METHODS Thirty-nine affected subjects from 16 extended SPS families underwent WES. Genome-wide linkage analysis was performed under linear and exponential models. The contribution of rare coding variants selected to be highly pathogenic was assessed using the gene-based segregation test. RESULTS A significant linkage peak was identified on chromosome 3p25.2-p22.3 (maxSNP = rs2293787; LODlinear = 2.311, LODexp = 2.11), which logarithm of the odds (LOD) score increased after fine mapping for the same marker (maxSNP = rs2293787; LODlinear = 2.4, LODexp = 2.25). This linkage signal was replicated in 10 independent sets of random markers from this locus. To assess the contribution of rare variants predicted to be pathogenic, we performed a family-based segregation test with 11 rare variants predicted to be deleterious from 10 genes under the linkage intervals. This analysis showed significant segregation of rare variants with SPS in CAPT7, TMEM43, NGLY1, and FBLN2 genes (weighted P value > 0.007). DISCUSSION Protein network analysis suggested FBLN2 as the most plausible candidate genes for germline SPS predisposition. Etiologic rare variants implicated in disease predisposition may be identified by combining traditional linkage with WES data. This powerful approach was effective for the identification of a new candidate gene for hereditary SPS.
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Affiliation(s)
- Claudio Toma
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Bronwyn Overs
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | | | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - 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), 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), Ourense, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
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11
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Cannizzaro M, Jarošová J, De Paepe B. Relevance of solute carrier family 5 transporter defects to inherited and acquired human disease. J Appl Genet 2019; 60:305-317. [PMID: 31286439 DOI: 10.1007/s13353-019-00502-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 06/21/2019] [Accepted: 06/30/2019] [Indexed: 01/12/2023]
Abstract
The solute carrier (SLC) group of membrane transport proteins is crucial for cells via their control of import and export of vital molecules across the cellular membrane. Defects in these transporters with narrow substrate specificities cause monogenic disorders, giving us essential clues of their precise roles in cellular functioning. The SLC5 family in particular has been linked to various human diseases, of mild and severe phenotype as well as high and low prevalence. In this review, we describe the effects on health of SLC5 dysfunction and dysregulation by summarizing findings in patients with transporter gene defects. Patients display a plethora of pathologies which include glucose/galactose malabsorption, familiar renal glycosuria, thyroid dyshormonogenesis, and distal hereditary motor neuronopathies. In addition, the therapeutic potential of intervening in transporter activities for treating common diseases such as diabetes and cancer is explored.
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Affiliation(s)
- Miryam Cannizzaro
- Department of Neurology & Neuromuscular Reference Center, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Jana Jarošová
- Department of Neurology & Neuromuscular Reference Center, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Boel De Paepe
- Department of Neurology & Neuromuscular Reference Center, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
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12
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Pimenta J, Lopes AM, Carracedo A, Arenas M, Amorim A, Comas D. Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula. Sci Rep 2019; 9:7825. [PMID: 31127131 PMCID: PMC6534591 DOI: 10.1038/s41598-019-44121-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.
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Affiliation(s)
- João Pimenta
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Institute of Evolutionary Biology (CSIC-UPF). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Faculty of Sciences, University of Porto, Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Angel Carracedo
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, CIBERER, Santiago de Compostela, Spain
| | - Miguel Arenas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310, Vigo, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.
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13
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Shen N, Li L, Xu W, Tian J, Yang Y, Zhu Y, Gong Y, Ke J, Gong J, Chang J, Zhong R, Miao X. A missense variant in PTPN12 associated with the risk of colorectal cancer by modifying Ras/MEK/ERK signaling. Cancer Epidemiol 2019; 59:109-114. [PMID: 30731403 DOI: 10.1016/j.canep.2019.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND The classical protein tyrosine phosphatases (PTPs) have been widely reported to be associated with various human malignancies including colorectal cancer (CRC). However, there are few comprehensive analyses of the association between the classical PTP genes and CRC risk. METHODS First, a bioinformatics analysis was performed to identify missense variants within the classical PTP gene family. Second, exome-wide association data and an independent population study were conducted to evaluate effects of candidate variants on CRC risk. Finally, functional assays based on signaling pathways were applied to uncover the potential pathogenic mechanism. RESULTS We identified that PTPN12 rs3750050 G allele presented a 19% increase the risk of CRC, with an OR of 1.19 (95% CI = 1.09-1.30, P = 1.015×10-4) under an additive model in the combined analysis. Furthermore, biochemical assays illustrated that rs3750050 could impair the inhibitory effect of PTPN12 on Ras/MEK/ERK signaling by impeding SHC dephosphorylation, increase the expression of cyclin D1 and ultimately lead to aberrant cell proliferation, thus contributing to CRC pathogenesis. CONCLUSION Our study highlights that PTPN12 rs3750050 could increase CRC risk by modifying Ras/MEK/ERK signaling. This work provides a novel insight into the roles of genetic variants within PTP genes in the pathogenesis of CRC.
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Affiliation(s)
- Na Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lu Li
- Research Center for Translational Medicine, Shantou University Medical College, North Dongxia Road, Shantou, 515041, Guangdong Province, China
| | - Wang Xu
- Research Center for Translational Medicine, Shantou University Medical College, North Dongxia Road, Shantou, 515041, Guangdong Province, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula. Nat Commun 2019; 10:551. [PMID: 30710075 PMCID: PMC6358624 DOI: 10.1038/s41467-018-08272-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022] Open
Abstract
The Iberian Peninsula is linguistically diverse and has a complex demographic history, including a centuries-long period of Muslim rule. Here, we study the fine-scale genetic structure of its population, and the genetic impacts of historical events, leveraging powerful, haplotype-based statistical methods to analyse 1413 individuals from across Spain. We detect extensive fine-scale population structure at extremely fine scales (below 10 Km) in some regions, including Galicia. We identify a major east-west axis of genetic differentiation, and evidence of historical north to south population movement. We find regionally varying fractions of north-west African ancestry (0–11%) in modern-day Iberians, related to an admixture event involving European-like and north-west African-like source populations. We date this event to 860–1120 CE, implying greater genetic impacts in the early half of Muslim rule in Iberia. Together, our results indicate clear genetic impacts of population movements associated with both the Muslim conquest and the subsequent Reconquista. The Iberian Peninsula has a complex history. Here, the authors analyse the genetic structure of the modern Iberian population at fine scale, revealing historical population movements associated with the time of Muslim rule.
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Torabi K, Erola P, Alvarez-Mora MI, Díaz-Gay M, Ferrer Q, Castells A, Castellví-Bel S, Milà M, Lozano JJ, Miró R, Ried T, Ponsa I, Camps J. Quantitative analysis of somatically acquired and constitutive uniparental disomy in gastrointestinal cancers. Int J Cancer 2018; 144:513-524. [PMID: 30350313 PMCID: PMC6635747 DOI: 10.1002/ijc.31936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/31/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022]
Abstract
Somatically acquired uniparental disomies (aUPDs) are frequent events in solid tumors and have been associated with cancer‐related genes. Studies assessing their functional consequences across several cancer types are therefore necessary. Here, we aimed at integrating aUPD profiles with the mutational status of cancer‐related genes in a tumor‐type specific manner. Using TCGA datasets for 1,032 gastrointestinal cancers, including colon (COAD), rectum (READ), stomach (STAD), esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), we show a non‐random distribution of aUPD, suggesting the existence of a cancer‐specific landscape of aUPD events. Our analysis indicates that aUPD acts as a “second hit” in Knudson's model in order to achieve biallelic inactivation of tumor suppressor genes. In particular, APC, ARID1A and NOTCH1 were recurrently inactivated by the presence of homozygous mutation as a consequence of aUPD in COAD and READ, STAD and ESCC, respectively. Furthermore, while TP53 showed inactivation caused by aUPD at chromosome arm 17p across all tumor types, copy number losses at this genomic position were also frequent. By experimental and computationally inferring genome ploidy, we demonstrate that an increased number of aUPD events, both affecting the whole chromosome or segments of it, were present in highly aneuploid genomes compared to near‐diploid tumors. Finally, the presence of mosaic UPD was detected at a higher frequency in DNA extracted from peripheral blood lymphocytes of patients with colorectal cancer compared to healthy individuals. In summary, our study defines specific profiles of aUPD in gastrointestinal cancers and provides unequivocal evidence of their relevance in cancer. What's new? Somatically acquired uniparental disomies (aUPDs), in which two copies of a chromosome originate from the same parent, have been documented in various human cancers. Here, the authors examined the frequency of aUPDs in different gastrointestinal cancer types. Events involving aUPDs were found to occur at high incidence in gastrointestinal cancers and at increased frequency particularly in highly aneuploid genomes. The data also reveal a nonrandom distribution of aUPDs, with evidence of biallelic inactivation of tumor suppressor genes and activation of oncogenes in a tumor type‐specific manner. The findings suggest that aUPDs are functionally relevant in gastrointestinal malignancies.
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Affiliation(s)
- Keyvan Torabi
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pau Erola
- Bioinformatics Unit, CIBEREHD, Barcelona, Catalonia, Spain.,Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Maria Isabel Alvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Catalonia, Spain
| | - Marcos Díaz-Gay
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Queralt Ferrer
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Montserrat Milà
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Catalonia, Spain
| | | | - Rosa Miró
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Immaculada Ponsa
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
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Gargallo CJ, Lanas Á, Carrera‐Lasfuentes P, Ferrandez Á, Quintero E, Carrillo M, Alonso‐Abreu I, García‐Gonzalez MA. Genetic susceptibility in the development of colorectal adenomas according to family history of colorectal cancer. Int J Cancer 2018; 144:489-502. [PMID: 30194776 PMCID: PMC6587859 DOI: 10.1002/ijc.31858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/30/2018] [Accepted: 08/29/2018] [Indexed: 12/25/2022]
Abstract
Our study aimed to evaluate the relevance of genetic susceptibility in the development of colorectal adenomas (CRA) and its relationship with the presence of family history of colorectal cancer (CRC). Genomic DNA from 750 cases (first degree relatives of patients with CRC) and 750 controls (subjects with no family history of CRC) was genotyped for 99 single nucleotide polymorphisms (SNPs) previously associated with CRC/CRA risk by GWAS and candidate gene studies by using the MassArray™ (Sequenom) platform. Cases and controls were matched by gender, age and histological lesion. Eight hundred and fifty‐eight patients showed no neoplastic lesions, whereas 288 patients showed low‐risk adenomas, and 354 patients presented high‐risk adenomas. Two SNPs (rs10505477, rs6983267) in the CASC8 gene were associated with a reduced risk of CRA in controls (log‐additive models, OR: 0.67, 95%CI:0.54–0.83, and OR:0.66, 95%CI:0.54–0.84, respectively). Stratified analysis by histological lesion revealed the association of rs10505477 and rs6983267 variants with reduced risk of low‐ and high‐risk adenomas in controls, being this effect stronger in low‐risk adenomas (log‐additive models, OR:0.63, 95%CI:0.47–0.84 and OR:0.64, 95%CI:0.47–0.86, respectively). Moreover, 2 SNPs (rs10795668, rs11255841) in the noncoding LINC00709 gene were significantly associated with a reduced risk of low‐risk adenomas in cases (recessive models, OR:0.22, 95%CI:0.06–0.72, and OR:0.08, 95%CI:0.03–0.61) and controls (dominant models, OR:0.50, 95%CI:0.34–0.75, and OR:0.52, 95%CI:0.35–0.78, respectively). In conclusion, some variants associated with CRC risk (rs10505477, rs6983267, rs10795668 and rs11255841) are also involved in the susceptibility to CRA and specific subtypes. These associations are influenced by the presence of family history of CRC. What's new? While numerous candidate gene variants have been associated with colorectal cancer, little is known about the relevance of genetic susceptibility or influence of family history in the development of precancerous colorectal adenomas. In the present study, certain genetic variants previously associated with colorectal cancer risk, including two variants in the CASC8 gene and two in the lnc‐RNA LINC00709 gene, were found to be also involved in susceptibility to colorectal adenomas. The associations were modified by family history of colorectal cancer. The results could have implications for colorectal cancer screening and the identification of individuals at increased risk of colorectal adenoma.
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Affiliation(s)
- Carla J. Gargallo
- Department of GastroenterologyHospital Clínico Universitario Lozano BlesaZaragozaSpain
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
| | - Ángel Lanas
- Department of GastroenterologyHospital Clínico Universitario Lozano BlesaZaragozaSpain
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
- University of Zaragoza School of MedicineZaragozaSpain
- CIBERehdZaragozaSpain
| | | | - Ángel Ferrandez
- Department of GastroenterologyHospital Clínico Universitario Lozano BlesaZaragozaSpain
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
| | - Enrique Quintero
- University of La Laguna, School of MedicineCanary IslandsSpain
- Hospital Universitario de CanariasCanary IslandsSpain
| | | | | | - María Asunción García‐Gonzalez
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
- CIBERehdZaragozaSpain
- Aragon Institute of Health Sciences (IACS)ZaragozaSpain
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Franch-Expósito S, Esteban-Jurado C, Garre P, Quintanilla I, Duran-Sanchon S, Díaz-Gay M, Bonjoch L, Cuatrecasas M, Samper E, Muñoz J, Ocaña T, Carballal S, López-Cerón M, Castells A, Vila-Casadesús M, Derdak S, Laurie S, Beltran S, Carvajal J, Bujanda L, Ruiz-Ponte C, Camps J, Gironella M, Lozano JJ, Balaguer F, Cubiella J, Caldés T, Castellví-Bel S. Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis. J Genet Genomics 2017; 45:41-45. [PMID: 29396139 DOI: 10.1016/j.jgg.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Clara Esteban-Jurado
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Isabel Quintanilla
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Saray Duran-Sanchon
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clinic de Barcelona, Barcelona 08036, Spain
| | - Esther Samper
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Sabela Carballal
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - María López-Cerón
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | | | - Maria Vila-Casadesús
- Bioinformatics Platform, CIBER of Hepatic and Digestive Diseases, Barcelona 08036, Spain
| | - Sophia Derdak
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Steven Laurie
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Sergi Beltran
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Jaime Carvajal
- Andalusian Developmental Biology Institute, CSIC-Pablo de Olavide University-Andalusian Regional Government, Sevilla 41013, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Biodonostia Institute, CIBER of Hepatic and Digestive Diseases, University of the Basque Country (UPV/EHU), San Sebastián 20080, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), CIBER of Rare Diseases, Genomics Medicine Group, Hospital Clínico Universitario, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
| | - Jordi Camps
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Meritxell Gironella
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Juan José Lozano
- Bioinformatics Platform, CIBER of Hepatic and Digestive Diseases, Barcelona 08036, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Ourense Biomedical Research Institute, Ourense 32005, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain.
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The genetic heterogeneity of colorectal cancer predisposition - guidelines for gene discovery. Cell Oncol (Dordr) 2016; 39:491-510. [PMID: 27279102 PMCID: PMC5121185 DOI: 10.1007/s13402-016-0284-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 12/22/2022] Open
Abstract
Background Colorectal cancer (CRC) is a cumulative term applied to a clinically and genetically heterogeneous group of neoplasms that occur in the bowel. Based on twin studies, up to 45 % of the CRC cases may involve a heritable component. Yet, only in 5–10 % of these cases high-penetrant germline mutations are found (e.g. mutations in APC and DNA mismatch repair genes) that result in a familial aggregation and/or an early onset of the disease. Genome-wide association studies have revealed that another ~5 % of the CRC cases may be explained by a cumulative effect of low-penetrant risk factors. Recent attempts to identify novel genetic factors using whole exome and whole genome sequencing has proven to be difficult since the remaining, yet to be discovered, high penetrant CRC predisposing genes appear to be rare. In addition, most of the moderately penetrant candidate genes identified so far have not been confirmed in independent cohorts. Based on literature examples, we here discuss how careful patient and cohort selection, candidate gene and variant selection, and corroborative evidence may be employed to facilitate the discovery of novel CRC predisposing genes. Conclusions The picture emerges that the genetic predisposition to CRC is heterogeneous, involving complex interplays between common and rare (inter)genic variants with different penetrances. It is anticipated, however, that the use of large clinically well-defined patient and control datasets, together with improved functional and technical possibilities, will yield enough power to unravel this complex interplay and to generate accurate individualized estimates for the risk to develop CRC.
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SYNJ2 Variant Rs9365723 is Associated with Colorectal Cancer Risk in Chinese Han Population. Int J Biol Markers 2016; 31:e138-43. [PMID: 26616230 DOI: 10.5301/jbm.5000182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2015] [Indexed: 12/17/2022]
Abstract
Purpose Colorectal cancer (CRC) is the third most common cancer and fourth leading cause of cancer mortality, and twin studies have shown that approximately 35% of the variation in susceptibility to CRC involves inherited genetic differences. We sought to investigate potential genetic associations between some single nucleotide polymorphisms (SNPs) and the risk of CRC in the Chinese Han population. Methods We conducted a case-control study including 269 cases and 309 controls. Sixteen SNPs associated with CRC risk were selected from previous genome-wide association studies and genotyped using Sequenom MassARRAY technology. Odds ratios and 95% confidence intervals (CIs) were calculated by unconditional logistic regression adjusting for age and gender. Results Using the chi-squared test we found that rs9365723 was associated with CRC risk (p = 0.012). With genetic model analysis, the genotype A/G-G/G (OR = 1.50; 95% CI 1.02-2.21; p = 0.038) of rs9365723 showed an increased risk of CRC in the dominant model. Furthermore, we found that rs9365723 was associated with an increased risk only for colon cancer but not rectal cancer (p = 0.009 and p = 0.414, respectively). Conclusions Our results, combined with previous studies, suggest that rs9365723, located on SYNJ2, is associated with the risk of CRC in a Chinese population. Thus, SYNJ2 may play a role in the development of CRC, especially colon cancer.
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Distinct NF-κB and MAPK Activation Thresholds Uncouple Steady-State Microbe Sensing from Anti-pathogen Inflammatory Responses. Cell Syst 2016; 2:378-90. [PMID: 27237739 DOI: 10.1016/j.cels.2016.04.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/29/2016] [Accepted: 04/22/2016] [Indexed: 12/30/2022]
Abstract
The innate immune system distinguishes low-level homeostatic microbial stimuli from those of invasive pathogens, yet we lack understanding of how qualitatively similar microbial products yield context-specific macrophage functional responses. Using quantitative approaches, we found that NF-κB and MAPK signaling was activated at different concentrations of a stimulatory TLR4 ligand in both mouse and human macrophages. Above a threshold of ligand, MAPK were activated in a switch-like manner, facilitating production of inflammatory mediators. At ligand concentrations below this threshold, NF-κB signaling occurred, promoting expression of a restricted set of genes and macrophage priming. Among TLR-induced genes, we observed an inverse correlation between MAPK dependence and ligand sensitivity, highlighting the role of this signaling dichotomy in partitioning innate responses downstream of a single receptor. Our study reveals an evolutionarily conserved innate immune response system in which danger discrimination is enforced by distinct thresholds for NF-κB and MAPK activation, which provide sequential barriers to inflammatory mediator production.
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Identification of a Potential Regulatory Variant for Colorectal Cancer Risk Mapping to 3p21.31 in Chinese Population. Sci Rep 2016; 6:25194. [PMID: 27120998 PMCID: PMC4848543 DOI: 10.1038/srep25194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/12/2016] [Indexed: 01/30/2023] Open
Abstract
Genome-wide association studies (GWAS) have established chromosome 3p21.31 as a susceptibility locus for colorectal cancer (CRC) that lacks replication and exploration in the Chinese population. We searched potentially functional single nucleotide polymorphisms (SNPs) in the linkage disequilibrium (LD) block of 3p21.31 with chromatin immunoprecipitation-sequencing (ChIP-seq) data of histone modification, and tested their association with CRC via a case-control study involving 767 cases and 1397 controls in stage 1 and 528 cases and 678 controls in stage 2. In addition to the tag SNP rs8180040 (odds ratio (OR) = 0.875, 95% confidence interval (95% CI) = 0.793−0.966, P = 0.008, P-FDR (false discovery rate) = 0.040), rs1076394 presented consistently significant associations with CRC risk at both stages with OR = 0.850 (95% CI = 0.771−0.938, P = 0.001, P-FDR = 0.005) under the additive model in combined analyses. Supported by the analyses of data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), it was suggested that rs1076394 served as an expression Quantitative Trait Loci (eQTL) for gene CCDC12 and NME6, while NME6’s expression was obviously higher in CRC tissues. Using biofeature information such as ChIP-seq and RNA sequencing (RNA-seq) data might help researchers to interpret GWAS results and locate functional variants for diseases in the post-GWAS era.
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22
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Abulí A, Castells A, Bujanda L, Lozano JJ, Bessa X, Hernández C, Álvarez-Urturi C, Pellisé M, Esteban-Jurado C, Hijona E, Burón A, Macià F, Grau J, Guayta R, Castellví-Bel S, Andreu M. Genetic Variants Associated with Colorectal Adenoma Susceptibility. PLoS One 2016; 11:e0153084. [PMID: 27078840 PMCID: PMC4831735 DOI: 10.1371/journal.pone.0153084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/23/2016] [Indexed: 01/11/2023] Open
Abstract
Background Common low-penetrance genetic variants have been consistently associated with colorectal cancer risk. Aim To determine if these genetic variants are associated also with adenoma susceptibility and may improve selection of patients with increased risk for advanced adenomas and/or multiplicity (≥ 3 adenomas). Methods We selected 1,326 patients with increased risk for advanced adenomas and/or multiplicity and 1,252 controls with normal colonoscopy from population-based colorectal cancer screening programs. We conducted a case-control association study analyzing 30 colorectal cancer susceptibility variants in order to investigate the contribution of these variants to the development of subsequent advanced neoplasia and/or multiplicity. Results We found that 14 of the analyzed genetic variants showed a statistically significant association with advanced adenomas and/or multiplicity: the probability of developing these lesions increased with the number of risk alleles reaching a 2.3-fold risk increment in individuals with ≥ 17 risk alleles. Conclusions Nearly half of the genetic variants associated with colorectal cancer risk are also related to advanced adenoma and/or multiplicity predisposition. Assessing the number of risk alleles in individuals within colorectal cancer screening programs may help to identify better a subgroup with increased risk for advanced neoplasia and/or multiplicity in the general population.
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Affiliation(s)
- Anna Abulí
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), Doctor Begiristain Kalea, 20014, Donostia/Gipuzkoa, Spain
| | - Juan José Lozano
- Plataforma de Bioinformática, CIBERehd, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Xavier Bessa
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Cristina Hernández
- Department of Epidemiology and Evaluation, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Cristina Álvarez-Urturi
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Maria Pellisé
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Clara Esteban-Jurado
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Elizabeth Hijona
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), Doctor Begiristain Kalea, 20014, Donostia/Gipuzkoa, Spain
| | - Andrea Burón
- Department of Epidemiology and Evaluation, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Francesc Macià
- Department of Epidemiology and Evaluation, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Jaume Grau
- Unitat d’Avaluació, Suport i Preventiva, Hospital Clínic, Roselló 138, 08036, Barcelona, Catalonia, Spain
| | - Rafael Guayta
- Planning and Research Unit, Consell de Collegis Farmacèutics de Catalunya, Girona 64, 08009, Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Montserrat Andreu
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
- * E-mail:
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Polymorphisms of PRLHR and HSPA12A and risk of gastric and colorectal cancer in the Chinese Han population. BMC Gastroenterol 2015; 15:107. [PMID: 26302849 PMCID: PMC4548694 DOI: 10.1186/s12876-015-0336-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/12/2015] [Indexed: 12/14/2022] Open
Abstract
Background Gastric and colorectal cancers have a major impact on public health, and are the most common malignant tumors in China. The aim of this research was to study whether polymorphisms of CHCHD3P1-HSP90AB7P, GRID1, HSPA12A, PRLHR, SBF2, POLD3 and C11orf93-C11orf92 genes are associated with the risk of gastric and colorectal cancers in the Chinese Han population. Methods We genotyped seven single nucleotide polymorphisms (SNPs) from seven genes. We selected 588 patients with gastric cancer and 449 with colorectal cancer, along with 703 healthy controls. All these SNPs were evaluated using the χ2 test and genetic model analysis. Results The genotype “A/T” of rs12413624 in PRLHR gene was associated with a decreased risk of colorectal cancer in allele model analysis [odds ratio (OR) = 0.81; 95 % confidence interval (CI) = 0.68–0.97; p = 0.018] and log-additive model analysis (OR = 0.81; 95 % CI = 0.66–0.98; p = 0.032). The genotype “A/G” of rs1665650 in HSPA12A gene was associated with a decreased risk of gastric cancer in overdominant model analysis (OR = 0.77; 95 % CI = 0.60–0.99; p = 0.038). Conclusions Our results provide evidence that variants of PRLHR gene are a protective factor in colorectal cancer and variants of HSPA12A gene are a protective factor in gastric cancer in the Chinese Han population.
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Hulur I, Gamazon ER, Skol AD, Xicola RM, Llor X, Onel K, Ellis NA, Kupfer SS. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics 2015; 16:138. [PMID: 25766683 PMCID: PMC4351699 DOI: 10.1186/s12864-015-1292-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/29/2015] [Indexed: 12/20/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases. Results 8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn’s disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2). Enrichment of colon eQTL near transcription start sites and for active histone marks was demonstrated, and eQTL with high population differentiation were identified. Conclusions Through the comprehensive study of eQTL in the human colon, this study identified novel target genes for IBD- and CRC-associated genetic variants. Moreover, bioinformatic characterization of colon eQTL provides a tissue-specific tool to improve understanding of biological differences in diseases between different ethnic groups. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1292-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imge Hulur
- Committee on Genetics, Genomics and Systems Biology, Chicago, IL, 60637, USA.
| | - Eric R Gamazon
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Andrew D Skol
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
| | - Rosa M Xicola
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Xavier Llor
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Kenan Onel
- Department of Pediatrics, University of Chicago, Chicago, IL, 60637, USA.
| | - Nathan A Ellis
- University of Arizona Cancer Center, Tucson, AZ, 85724, USA.
| | - Sonia S Kupfer
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
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Shaik AP, Shaik AS, Al-Sheikh YA. Colorectal cancer: A review of the genome-wide association studies in the kingdom of Saudi Arabia. Saudi J Gastroenterol 2015; 21:123-8. [PMID: 26021770 PMCID: PMC4455141 DOI: 10.4103/1319-3767.157548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-wise association studies (GWAS) identify risk variants and modifiers that can influence the pathophysiological processes involved in colorectal cancer (CRC) and thus are important to detect associations between disease phenotypes. Our literature review, performed as per PRISMA statement indicates a significant lack of GWAS functional studies in Saudi Arabia. Therefore, studies on sequencing and mapping are needed to identify gene variants that play a role in the pathophysiology of CRC in this specific population. Because it is not apt to generalize disease associations found in other racial and/or ethnic groups to the Arabic or Middle Eastern population, it is very important to conduct GWAS taking into account multiple ethnicities in this region. In addition, linkage studies and case-control studies that include the various confounding and epigenetic factors are needed for appropriate diagnosis of CRC. We recommend that studies in this region be conducted to understand the role of gene-environment interactions across the various ethnic groups, stages of cancer, tumor type, clinical variables, and the population risk to CRC.
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Affiliation(s)
- Abjal P. Shaik
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Asma S. Shaik
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Yazeed A. Al-Sheikh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia,Address for correspondence: Dr. Yazeed A. Al-Sheikh, Molecular Genetics Chair, Clinical Lab Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia. E-mail:
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26
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Real LM, Ruiz A, Gayán J, González-Pérez A, Sáez ME, Ramírez-Lorca R, Morón FJ, Velasco J, Marginet-Flinch R, Musulén E, Carrasco JM, Moreno-Rey C, Vázquez E, Chaves-Conde M, Moreno-Nogueira JA, Hidalgo-Pascual M, Ferrero-Herrero E, Castellví-Bel S, Castells A, Fernandez-Rozadilla C, Ruiz-Ponte C, Carracedo A, González B, Alonso S, Perucho M. A colorectal cancer susceptibility new variant at 4q26 in the Spanish population identified by genome-wide association analysis. PLoS One 2014; 9:e101178. [PMID: 24978480 PMCID: PMC4076321 DOI: 10.1371/journal.pone.0101178] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/03/2014] [Indexed: 11/28/2022] Open
Abstract
Background Non-hereditary colorectal cancer (CRC) is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome–wide association studies (GWAS) are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population. Results A total of 801 controls and 500 CRC cases were included in the discovery GWAS dataset. 77 single nucleotide polymorphisms (SNP)s from single-locus and 243 SNPs from two-locus association analyses were selected for replication in 423 additional CRC cases and 1382 controls. In the meta-analysis, one SNP, rs3987 at 4q26, reached GWAS significant p-value (p = 4.02×10−8), and one SNP pair, rs1100508 CG and rs8111948 AA, showed a trend for two-locus association (p = 4.35×10−11). Additionally, our GWAS confirmed the previously reported association with CRC of five SNPs located at 3q36.2 (rs10936599), 8q24 (rs10505477), 8q24.21(rs6983267), 11q13.4 (rs3824999) and 14q22.2 (rs4444235). Conclusions Our GWAS for CRC patients from Spain confirmed some previously reported associations for CRC and yielded a novel candidate risk SNP, located at 4q26. Epistasis analyses also yielded several novel candidate susceptibility pairs that need to be validated in independent analyses.
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Affiliation(s)
- Luis M. Real
- Department of Structural Genomics, Neocodex, Seville, Spain
- Infectious Diseases and Microbiology Unit, Hospital Nuestra Señora de Valme, Seville, Spain
- Institute of Biomedicine of Seville (IBIS), Seville, Spain
| | - Agustín Ruiz
- Department of Structural Genomics, Neocodex, Seville, Spain
- Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Javier Gayán
- Department of Structural Genomics, Neocodex, Seville, Spain
- Bioinfosol, Seville, Spain
| | - Antonio González-Pérez
- Department of Structural Genomics, Neocodex, Seville, Spain
- Andalusian Center for Bioinformatic Studies (CAEBI), Seville, Spain
| | - María E. Sáez
- Department of Structural Genomics, Neocodex, Seville, Spain
- Andalusian Center for Bioinformatic Studies (CAEBI), Seville, Spain
| | - Reposo Ramírez-Lorca
- Department of Structural Genomics, Neocodex, Seville, Spain
- Institute of Biomedicine of Seville (IBIS), Seville, Spain
| | - Francisco J. Morón
- Department of Structural Genomics, Neocodex, Seville, Spain
- Institute of Biomedicine of Seville (IBIS), Seville, Spain
| | - Juan Velasco
- Department of Structural Genomics, Neocodex, Seville, Spain
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Ruth Marginet-Flinch
- Department of Structural Genomics, Neocodex, Seville, Spain
- Department of Pathology, Hospital Universitario Germans Trias i Pujol (HUGTP), Badalona, Barcelona, Spain
| | - Eva Musulén
- Department of Pathology, Hospital Universitario Germans Trias i Pujol (HUGTP), Badalona, Barcelona, Spain
| | | | - Concha Moreno-Rey
- Department of Structural Genomics, Neocodex, Seville, Spain
- Department of Oncology, Hospital Virgen del Rocío, Seville, Spain
| | | | | | | | | | | | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, University of Barcelona, CIBEREHD, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, University of Barcelona, CIBEREHD, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ceres Fernandez-Rozadilla
- Galician Public Foundation of Genomic Medicine, Centro de Investigación Biomédica en Red de Enfermedades Raras, Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, A Coruña, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine, Centro de Investigación Biomédica en Red de Enfermedades Raras, Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, A Coruña, Spain
| | - Angel Carracedo
- Galician Public Foundation of Genomic Medicine, Centro de Investigación Biomédica en Red de Enfermedades Raras, Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, A Coruña, Spain
| | - Beatriz González
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Sergio Alonso
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Manuel Perucho
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
- Sanford-Burnham Medical Research Institute (SBMRI), La Jolla, California United States of America
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail:
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Fernandez-Rozadilla C, Cazier JB, Tomlinson I, Brea-Fernández A, Lamas MJ, Baiget M, López-Fernández LA, Clofent J, Bujanda L, Gonzalez D, de Castro L, Hemminki K, Bessa X, Andreu M, Jover R, Xicola R, Llor X, Moreno V, Castells A, Castellví-Bel S, Carracedo A, Ruiz-Ponte C. A genome-wide association study on copy-number variation identifies a 11q11 loss as a candidate susceptibility variant for colorectal cancer. Hum Genet 2014; 133:525-34. [PMID: 24218287 DOI: 10.1007/s00439-013-1390-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/24/2013] [Indexed: 11/30/2022]
Abstract
Colorectal cancer (CRC) is a complex disease, and therefore its development is determined by the combination of both environmental factors and genetic variants. Although genome-wide association studies (GWAS) of SNP variation have conveniently identified 20 genetic variants so far, a significant proportion of the observed heritability is yet to be explained. Common copy-number variants (CNVs) are one of the most important genomic sources of variability, and hence a potential source to explain part of this missing genetic fraction. Therefore, we have performed a GWAS on CNVs to explore the relationship between common structural variation and CRC development. Phase 1 of the GWAS consisted of 881 cases and 667 controls from a Spanish cohort. Copy-number status was validated by quantitative PCR for each of those common CNVs potentially associated with CRC in phase I. Subsequently, SNPs were chosen as proxies for the validated CNVs for phase II replication (1,342 Spanish cases and 1,874 Spanish controls). Four common CNVs were found to be associated with CRC and were further replicated in Phase II. Finally, we found that SNP rs1944682, tagging a 11q11 CNV, was nominally associated with CRC susceptibility (p value = 0.039; OR = 1.122). This locus has been previously related to extreme obesity phenotypes, which could suggest a relationship between body weight and CRC susceptibility.
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Affiliation(s)
- C Fernandez-Rozadilla
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica, IDIS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer), Complexo Hospitalario Universitario de Santiago, Choupana s/n, 15706, Santiago, Spain
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Abulí A, Bujanda L, Muñoz J, Buch S, Schafmayer C, Valeria Maiorana M, Veneroni S, van Wezel T, Liu T, Westers H, Esteban-Jurado C, Ocaña T, Piqué JM, Andreu M, Jover R, Carracedo A, Xicola RM, Llor X, Castells A, Dunlop M, Hofstra R, Lindblom A, Wijnen J, Peterlongo P, Hampe J, Ruiz-Ponte C, Castellví-Bel S. The MLH1 c.1852_1853delinsGC (p.K618A) variant in colorectal cancer: genetic association study in 18,723 individuals. PLoS One 2014; 9:e95022. [PMID: 24743384 PMCID: PMC3990597 DOI: 10.1371/journal.pone.0095022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/21/2014] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer is one of the most frequent neoplasms and an important cause of mortality in the developed world. Mendelian syndromes account for about 5% of the total burden of CRC, being Lynch syndrome and familial adenomatous polyposis the most common forms. Lynch syndrome tumors develop mainly as a consequence of defective DNA mismatch repair associated with germline mutations in MLH1, MSH2, MSH6 and PMS2. A significant proportion of variants identified by screening these genes correspond to missense or noncoding changes without a clear pathogenic consequence, and they are designated as “variants of uncertain significance”, being the c.1852_1853delinsGC (p.K618A) variant in the MLH1 gene a clear example. The implication of this variant as a low-penetrance risk variant for CRC was assessed in the present study by performing a case-control study within a large cohort from the COGENT consortium-COST Action BM1206 including 18,723 individuals (8,055 colorectal cancer cases and 10,668 controls) and a case-only genotype-phenotype correlation with several clinical and pathological characteristics restricted to the Epicolon cohort. Our results showed no involvement of this variant as a low-penetrance variant for colorectal cancer genetic susceptibility and no association with any clinical and pathological characteristics including family history for this neoplasm or Lynch syndrome.
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Affiliation(s)
- Anna Abulí
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
- Department of Gastroenterology, Hospital del Mar-IMIM (Hospital del Mar Medical Research Centre), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia, Networked Biomedical Research Centre for Hepatic and Digestive Diseases (CIBEREHD), Basque Country University, San Sebastián, Spain
| | - Jenifer Muñoz
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Stephan Buch
- Department of Medine I, University Hospital Dresden, Dresden, Germany
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Silvia Veneroni
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Helga Westers
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Clara Esteban-Jurado
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Teresa Ocaña
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep M. Piqué
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Montserrat Andreu
- Department of Gastroenterology, Hospital del Mar-IMIM (Hospital del Mar Medical Research Centre), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Rodrigo Jover
- Department of Gastroenterology, Hospital General d'Alacant, Alicante, Spain
| | - Angel Carracedo
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Rosa M. Xicola
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Xavier Llor
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | | | - Malcolm Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, United Kingdom
| | - Robert Hofstra
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Juul Wijnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Jochen Hampe
- Department of Medine I, University Hospital Dresden, Dresden, Germany
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
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29
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Esteban-Jurado C, Garre P, Vila M, Lozano JJ, Pristoupilova A, Beltrán S, Abulí A, Muñoz J, Balaguer F, Ocaña T, Castells A, Piqué JM, Carracedo A, Ruiz-Ponte C, Bessa X, Andreu M, Bujanda L, Caldés T, Castellví-Bel S. New genes emerging for colorectal cancer predisposition. World J Gastroenterol 2014; 20:1961-1971. [PMID: 24587672 PMCID: PMC3934466 DOI: 10.3748/wjg.v20.i8.1961] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/20/2013] [Accepted: 01/15/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent neoplasms and an important cause of mortality in the developed world. This cancer is caused by both genetic and environmental factors although 35% of the variation in CRC susceptibility involves inherited genetic differences. Mendelian syndromes account for about 5% of the total burden of CRC, with Lynch syndrome and familial adenomatous polyposis the most common forms. Excluding hereditary forms, there is an important fraction of CRC cases that present familial aggregation for the disease with an unknown germline genetic cause. CRC can be also considered as a complex disease taking into account the common disease-commom variant hypothesis with a polygenic model of inheritance where the genetic components of common complex diseases correspond mostly to variants of low/moderate effect. So far, 30 common, low-penetrance susceptibility variants have been identified for CRC. Recently, new sequencing technologies including exome- and whole-genome sequencing have permitted to add a new approach to facilitate the identification of new genes responsible for human disease predisposition. By using whole-genome sequencing, germline mutations in the POLE and POLD1 genes have been found to be responsible for a new form of CRC genetic predisposition called polymerase proofreading-associated polyposis.
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Biancolella M, Fortini BK, Tring S, Plummer SJ, Mendoza-Fandino GA, Hartiala J, Hitchler MJ, Yan C, Schumacher FR, Conti DV, Edlund CK, Noushmehr H, Coetzee SG, Bresalier RS, Ahnen DJ, Barry EL, Berman BP, Rice JC, Coetzee GA, Casey G. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. Hum Mol Genet 2013; 23:2198-209. [PMID: 24256810 DOI: 10.1093/hmg/ddt584] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies of colorectal cancer (CRC) have identified a number of common variants associated with modest risk, including rs3802842 at chromosome 11q23.1. Several genes map to this region but rs3802842 does not map to any known transcribed or regulatory sequences. We reasoned, therefore, that rs3802842 is not the functional single-nucleotide polymorphism (SNP), but is in linkage disequilibrium (LD) with a functional SNP(s). We performed ChIP-seq for histone modifications in SW480 and HCT-116 CRC cells, and incorporated ChIP-seq and DNase I hypersensitivity data available through ENCODE within a 137-kb genomic region containing rs3802842 on 11q23.1. We identified SNP rs10891246 in LD with rs3802842 that mapped within a bidirectional promoter region of genes C11orf92 and C11orf93. Following mutagenesis to the risk allele, the promoter demonstrated lower levels of reporter gene expression. A second SNP rs7130173 was identified in LD with rs3802842 that mapped to a candidate enhancer region, which showed strong unidirectional activity in both HCT-116 and SW480 CRC cells. The risk allele of rs7130173 demonstrated reduced enhancer activity compared with the common allele, and reduced nuclear protein binding affinity in electromobility shift assays compared with the common allele suggesting differential transcription factor (TF) binding. SNPs rs10891246 and rs7130173 are on the same haplotype, and expression quantitative trait loci (eQTL) analyses of neighboring genes implicate C11orf53, C11orf92 and C11orf93 as candidate target genes. These data imply that rs10891246 and rs7130173 are functional SNPs mapping to 11q23.1 and that C11orf53, C11orf92 and C11orf93 represent novel candidate target genes involved in CRC etiology.
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Wang H, Haiman CA, Burnett T, Fortini BK, Kolonel LN, Henderson BE, Signorello LB, Blot WJ, Keku TO, Berndt SI, Newcomb PA, Pande M, Amos CI, West DW, Casey G, Sandler RS, Haile R, Stram DO, Le Marchand L. Fine-mapping of genome-wide association study-identified risk loci for colorectal cancer in African Americans. Hum Mol Genet 2013; 22:5048-55. [PMID: 23851122 DOI: 10.1093/hmg/ddt337] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies of colorectal cancer (CRC) in Europeans and Asians have identified 21 risk susceptibility regions [29 index single-nucleotide polymorphisms (SNPs)]. Characterizing these risk regions in diverse racial groups with different linkage disequilibrium (LD) structure can help localize causal variants. We examined associations between CRC and all 29 index SNPs in 6597 African Americans (1894 cases and 4703 controls). Nine SNPs in eight regions (5q31.1, 6q26-q27, 8q23.3, 8q24.21, 11q13.4, 15q13.3, 18q21.1 and 20p12.3) formally replicated in our data with one-sided P-values <0.05 and the same risk directions as reported previously. We performed fine-mapping of the 21 risk regions (including 250 kb on both sides of the index SNPs) using genotyped and imputed markers at the density of the 1000 Genomes Project to search for additional or more predictive risk markers. Among the SNPs correlated with the index variants, two markers, rs12759486 (or rs7547751, a putative functional variant in perfect LD with it) in 1q41 and rs7252505 in 19q13.1, were more strongly and statistically significantly associated with CRC (P < 0.0006). The average per allele risk was improved using the replicated index variants and the two new markers (odds ratio = 1.14, P = 6.5 × 10(-16)) in African Americans, compared with using all index SNPs (odds ratio = 1.07, P = 3.4 × 10(-10)). The contribution of the two new risk SNPs to CRC heritability was estimated to be 1.5% in African Americans. This study highlights the importance of fine-mapping in diverse populations.
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Affiliation(s)
- Hansong Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
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Saigusa S, Inoue Y, Tanaka K, Toiyama Y, Okugawa Y, Shimura T, Hiro J, Uchida K, Mohri Y, Kusunoki M. Decreased expression of DUSP4 is associated with liver and lung metastases in colorectal cancer. Med Oncol 2013; 30:620. [PMID: 23749251 DOI: 10.1007/s12032-013-0620-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 05/24/2013] [Indexed: 01/05/2023]
Abstract
Dual-specificity protein phosphatase 4 (DUSP4), a negative regulator of extracellular-regulated kinase activity, is a potential mediator of resistance to chemotherapy and a tumor suppressor. The aim of this study is to clarify the association between DUSP4 gene expression and clinical outcome in patients with colorectal cancer. Patients who underwent surgery for colorectal cancer were enrolled in this study (n = 212). We investigated DUSP4 gene expression by real-time reverse transcription polymerase chain reaction in colorectal cancer tissue and paired normal mucosa. Immunohistochemical analyses of DUSP4 and ERK1/2 were also conducted. Additionally, we examined the relationship between gene expression and KRAS mutation in 74 of the 212 patients. DUSP4 expression in tumor tissues was significantly higher than that in matched normal mucosa (P < 0.0001). Decreased DUSP4 expression was significantly associated with advanced T classification, lymphatic invasion, vascular invasion, advanced stage, and liver and lung metastases. Logistic regression analysis revealed that decreased DUSP4 expression was an independent risk factor for synchronous distant metastases (P = 0.006). Increased DUSP4 expression was significantly associated with better prognosis (P = 0.0162). Immunohistochemical examination showed DUSP4 expression in the nucleus and cytoplasm of cancer cells, and no correlation was observed between DUSP4 and ERK1/2 expression. There was no significant correlation between DUSP4 expression and KRAS mutation. In conclusion, DUSP4 expression in colorectal cancer was negatively correlated with factors reflecting tumor progression, including distant metastases. Our data suggest that DUSP4 may act as a tumor suppressor in colorectal cancer.
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Affiliation(s)
- Susumu Saigusa
- Department of Gastrointestinal and Pediatric Surgery, Mie Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507, Japan.
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Sipos F, Mũzes G, Patai AV, Fũri I, Péterfia B, Hollósi P, Molnár B, Tulassay Z. Genome-wide screening for understanding the role of DNA methylation in colorectal cancer. Epigenomics 2013; 5:569-81. [PMID: 24059802 DOI: 10.2217/epi.13.52] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation analysis methods have undergone an impressive revolution over the past 15 years. Regarding colorectal cancer (CRC), the localization and distribution of several differently methylated genes have been determined by genome-wide DNA methylation assays. These genes do not just influence the pathogenesis of CRC, but can be used further as diagnostic or prognostic markers. Moreover, the identified four DNA methylation-based subgroups of CRC have important clinical and therapeutic merit. Since genome-wide DNA methylation analyzes result in a large amount of data, there is a need for complex bioinformatic and pathway analysis. Future challenges in epigenetic alterations of CRC include the demand for comprehensive identification and experimental validation of gene abnormalities. By introduction of genome-wide DNA methylation profiling into clinical practice not only the patients' risk stratification but development of targeted therapies will also be possible.
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Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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