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Zhang M, Wang X, Yang N, Zhu X, Lu Z, Cai Y, Li B, Zhu Y, Li X, Wei Y, Zhang S, Tian J, Miao X. Prioritization of risk genes in colorectal cancer by integrative analysis of multi-omics data and gene networks. SCIENCE CHINA. LIFE SCIENCES 2024; 67:132-148. [PMID: 37747674 DOI: 10.1007/s11427-023-2439-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/26/2023] [Indexed: 09/26/2023]
Abstract
Genome-wide association studies (GWASs) have identified over 140 colorectal cancer (CRC)-associated loci; however, target genes at the majority of loci and underlying molecular mechanisms are poorly understood. Here, we utilized a Bayesian approach, integrative risk gene selector (iRIGS), to prioritize risk genes at CRC GWAS loci by integrating multi-omics data. As a result, a total of 105 high-confidence risk genes (HRGs) were identified, which exhibited strong gene dependencies for CRC and enrichment in the biological processes implicated in CRC. Among the 105 HRGs, CEBPB, located at the 20q13.13 locus, acted as a transcription factor playing critical roles in cancer. Our subsequent assays indicated the tumor promoter function of CEBPB that facilitated CRC cell proliferation by regulating multiple oncogenic pathways such as MAPK, PI3K-Akt, and Ras signaling. Next, by integrating a fine-mapping analysis and three independent case-control studies in Chinese populations consisting of 8,039 cases and 12,775 controls, we elucidated that rs1810503, a putative functional variant regulating CEBPB, was associated with CRC risk (OR=0.90, 95%CI=0.86-0.93, P=1.07×10-7). The association between rs1810503 and CRC risk was further validated in three additional multi-ancestry populations consisting of 24,254 cases and 58,741 controls. Mechanistically, the rs1810503 A to T allele change weakened the enhancer activity in an allele-specific manner to decrease CEBPB expression via long-range promoter-enhancer interactions, mediated by the transcription factor, REST, and thus decreased CRC risk. In summary, our study provides a genetic resource and a generalizable strategy for CRC etiology investigation, and highlights the biological implications of CEBPB in CRC tumorigenesis, shedding new light on the etiology of CRC.
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Affiliation(s)
- Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Cancer Epidemiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Zhengzhou, 450008, China
| | - Nan Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiangpan Li
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430062, China
| | - Shaokai Zhang
- Department of Cancer Epidemiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Zhengzhou, 450008, China.
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China.
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China.
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430073, China.
- Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
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Mieno MN, Yamasaki M, Kuchiba A, Yamaji T, Ide K, Tanaka N, Sawada N, Inoue M, Tsugane S, Sawabe M, Iwasaki M. Lack of significant associations between single nucleotide polymorphisms in LPAL2-LPA genetic region and all cancer incidence and mortality in Japanese population: The Japan public health center-based prospective study. Cancer Epidemiol 2023; 85:102395. [PMID: 37321067 DOI: 10.1016/j.canep.2023.102395] [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: 01/24/2023] [Revised: 05/02/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND High lipoprotein (a) level is an established cardiovascular risk, but its association with non-cardiovascular diseases, especially cancer, is controversial. Serum lipoprotein (a) levels vary widely by genetic backgrounds and are largely determined by the genetic variations of apolipoprotein (a) gene, LPA. In this study, we investigate the association between SNPs in LPA region and cancer incidence and mortality in Japanese. METHODS A genetic cohort study was conducted utilizing the data from 9923 participants in the Japan Public Health Center-based Prospective Study (JPHC Study). Twenty-five SNPs in the LPAL2-LPA region were selected from the genome-wide genotyped data. Cox regression analysis adjusted for the covariates and competing risks of death from other causes, were used to estimate the relative risk (hazard ratios (HR) with 95% confidence intervals (CI)) of overall and site-specific cancer incidence and mortality, for each SNP. RESULTS No significant association was found between SNPs in the LPAL2-LPA region and cancer incidence or mortality (overall/site-specific cancer). In men, however, HRs for stomach cancer incidence of 18SNPs were estimated higher than 1.5 (e.g., 2.15 for rs13202636, model free, 95%CI: 1.28-3.62) and those for stomach cancer mortality of 2SNPs (rs9365171, rs1367211) were estimated 2.13 (recessive, 95%CI:1.04-4.37) and 1.61 (additive, 95%CI: 1.00-2.59). Additionally, the minor allele for SNP rs3798220 showed increased death risk from colorectal cancer (CRC) in men (HR: 3.29, 95% CI:1.59 - 6.81) and decreased CRC incidence risk in women (HR: 0.46, 95%CI: 0.22-0.94). Minor allele carrier of any of 4SNPs could have risk of prostate cancer incidence (e.g., rs9365171 dominant, HR: 1.71, 95%CI: 1.06-2.77). CONCLUSIONS None of the 25 SNPs in the LPAL2-LPA region was found to be significantly associated with cancer incidence or mortality. Considering the possible association between SNPs in LPAL2-LPA region and colorectal, prostate and stomach cancer incidence or mortality, further analysis using different cohorts is warranted.
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Affiliation(s)
- Makiko Naka Mieno
- Department of Medical Informatics, Center for Information, Jichi Medical University, Shimotsuke 329-0498, Japan; Health Data Science Research Section, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Research Institute, Tokyo 173-0015, Japan
| | - Maria Yamasaki
- Health Data Science Research Section, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Research Institute, Tokyo 173-0015, Japan
| | - Aya Kuchiba
- Biostatistics Division, Center for Research Administration and Support/Division of Biostatistical Research, Institute for Cancer Control, National Cancer Center, Tokyo 104-0045, Japan; Graduate School of Health Innovation, Kanagawa University of Human Services, Kanagawa, 210-0821, Japan
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan.
| | - Keigo Ide
- Health Data Science Research Section, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Research Institute, Tokyo 173-0015, Japan; Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Noriko Tanaka
- Health Data Science Research Section, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Research Institute, Tokyo 173-0015, Japan.
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan
| | - Manami Inoue
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan; Division of Prevention, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan
| | - Shoichiro Tsugane
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan; National Institute of Health and Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo 162-8636, Japan
| | - Motoji Sawabe
- Department of Molecular Pathology, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan; Division of Cohort Research, National Cancer Center Institute for Cancer Control, Tokyo 104-0045, Japan
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Lin TC, Chuang MH, Hsiung CN, Chang PK, Sun CA, Yang T, Chou YC, Hu JM, Hsu CH. Susceptibility to Colorectal Cancer Based on HSD17B4 rs721673 and rs721675 Polymorphisms and Alcohol Intake among Taiwan Biobank Participants: A Retrospective Case Control Study Using the Nationwide Claims Data. J Pers Med 2023; 13:jpm13040576. [PMID: 37108962 PMCID: PMC10146027 DOI: 10.3390/jpm13040576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
Colorectal cancer (CRC) is a major public health issue, and there are limited studies on the association between 17β-hydroxysteroid dehydrogenase type 4 (HSD17B4) polymorphism and CRC. We used two national databases from Taiwan to examine whether HSD17B4 rs721673, rs721675, and alcohol intake were independently and interactively correlated with CRC development. We linked the Taiwan Biobank (TWB) participants’ health and lifestyle information and genotypic data from 2012 to 2018 to the National Health Insurance Database (NHIRD) to confirm their medical records. We performed a genome-wide association study (GWAS) using data from 145 new incident CRC cases and matched 1316 healthy, non-CRC individuals. We calculated the odds ratios (OR) and 95% confidence intervals (CI) for CRC based on multiple logistic regression analyses. HSD17B4 rs721673 and rs721675 on chromosome 5 were significantly and positively correlated with CRC (rs721673 A > G, aOR = 2.62, p = 2.90 × 10−8; rs721675 A > T, aOR = 2.61, p = 1.01 × 10−6). Within the high-risk genotypes, significantly higher ORs were observed among the alcohol intake group. Our results demonstrated that the rs721673 and rs721675 risk genotypes of HSD17B4 might increase the risk of CRC development in Taiwanese adults, especially those with alcohol consumption habits.
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Affiliation(s)
- Tzu-Chiao Lin
- School of Medicine, National Defense Medical Center, Taipei 114, Taiwan
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Min-Hua Chuang
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Chia-Ni Hsiung
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 300, Taiwan
- Data Science Statistical Cooperation Center, Institute of Statistical Science, Academia Sinica, Taipei 114, Taiwan
| | - Pi-Kai Chang
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-An Sun
- Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
| | - Tsan Yang
- Department of Health Business Administration, Meiho University, Pingtung County 912, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Je-Ming Hu
- School of Medicine, National Defense Medical Center, Taipei 114, Taiwan
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Chih-Hsiung Hsu
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
- Health Service and Readiness Section, Armed Forces Taoyuan General Hospital, Taoyuan 325, Taiwan
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Xiao Q, Chen J, Zhu J, Zeng S, Cai H, Zhu G. Association of several loci of SMAD7 with colorectal cancer: A meta-analysis based on case-control studies. Medicine (Baltimore) 2023; 102:e32631. [PMID: 36607878 PMCID: PMC9829263 DOI: 10.1097/md.0000000000032631] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Sma-and mad-related protein 7 (SMAD7) can affect tumor progression by closing transforming growth factor-beta intracellular signaling channels. Despite the extensive research on the correlation between SMAD7 polymorphisms and colorectal cancer (CRC), the conclusions of studies are still contradictory. We conducted a study focusing on the association of SMAD7 polymorphisms rs4939827, rs4464148, and rs12953717 with CRC. METHODS We searched through 5 databases for articles and used odd ratios (ORs) and 95% confidence intervals (CIs) to discuss the correlation of SMAD7 polymorphisms with CRC risk. The heterogeneity will be appraised by subgroup analysis and meta-regression. Contour-enhanced funnel plot, Begg test and Egger test were utilized to estimate publication bias, and the sensitivity analysis illustrates the reliability of the outcomes. We performed False-positive report probability and trial sequential analysis methods to verify results. We also used public databases for bioinformatics analysis. RESULTS We conclusively included 34 studies totaling 173251 subjects in this study. The minor allele (C) of rs4939827 is a protective factor of CRC (dominant, OR/[95% CI] = 0.89/[0.83-0.97]; recessive, OR/[95% CI] = 0.89/[0.83-0.96]; homozygous, OR/[95% CI] = 0.84/[0.76-0.93]; heterozygous, OR/[95% CI] = 0.91/[0.85-0.97]; additive, OR/[95% CI] = 0.91/[0.87-0.96]). the T allele of rs12953717 (recessive, OR/[95% CI] = 1.22/[1.15-1.28]; homozygous, OR/[95% CI] = 1.25/[1.13-1.38]; additive, OR/[95% CI] = 1.11/[1.05-1.17]) and the C allele of rs4464148 (heterozygous, OR/[95% CI] = 1.13/[1.04-1.24]) can enhance the risk of CRC. CONCLUSION Rs4939827 (T > C) can decrease the susceptibility to CRC. However, the rs4464148 (T > C) and rs12953717 (C > T) variants were connected with an enhanced risk of CRC.
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Affiliation(s)
- Qiang Xiao
- General Surgery Department, First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Jian Chen
- General Surgery Department, First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Jia Zhu
- General Surgery Department, First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Shukun Zeng
- General Surgery Department, First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Hu Cai
- General Surgery Department, First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Guomin Zhu
- General Surgery Department, First Affiliated Hospital of Nanchang University, Jiangxi, China
- * Correspondence: Guomin Zhu, First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China (e-mail: )
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Cheng X, Zhang F, Gong J, Li Y, Zhou D, Wang J, Vong EG, Yuan Y, Lai M, Zhang D. Identification of potential functional variants and genes at 18q21.1 associated with the carcinogenesis of colorectal cancer. PLoS Genet 2022; 18:e1010050. [PMID: 35108261 PMCID: PMC8870576 DOI: 10.1371/journal.pgen.1010050] [Citation(s) in RCA: 3] [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: 07/21/2021] [Revised: 02/24/2022] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 160 susceptibility loci for colorectal cancer (CRC). The effects of these variants, particularly their mechanisms, however, remain unclear. In this study, a comprehensive functional annotation of CRC-related GWAS signals was firstly conducted to identify the potential causal variants. We found that the SNP rs7229639 in intron 3 of SMAD7 at 18q21.1 might serve as a putative functional variant in CRC. The SNP rs7229639 is located in a region with evidence of regulatory potential. Dual-luciferase reporter assays revealed that three other SNPs (rs77544449, rs60385309 and rs72917785), in strong linkage disequilibrium (LD) with rs7229639, exhibited allele-specific enhancer activity, of which one of the target genes may conceivably be LIPG, as suggested by eQTL association data and Hi-C data. We also verified that LIPG promoted malignancy of CRC cells in vitro, with supporting clinical data indicating that LIPG is upregulated and correlated with a poor prognosis in CRC. Finally, pitavastatin was observed to exhibit an anti-CRC activity and modest inhibition of LIPG mRNA levels. Collectively, our data suggest that these functional variants at 18q21.1 are involved in the pathogenesis of CRC by modulating enhancer activity, and possibly LIPG expression, thus indicating a promising therapeutic target for CRC. The results of functional annotation in our investigation could also serve as an inventory for CRC susceptibility SNPs and offer guides for post-GWAS downstream functional studies. In the latest statistics, the incidence and mortality rate of colorectal cancer (CRC) remains high. Genome-wide association studies (GWAS) have become a powerful tool for identifying genetic susceptibility loci that confer significant risk on disease, and have identified more than 160 risk loci associated with CRC. However, it has proven quite difficult to identify the regulatory variants and target genes involved behind these GWAS signals. Here, we take advantage of multi-omics data and multiple biological experiments to reveal new biological pathways affecting susceptibility to CRC. We show that a specific genetic variant, rs7229639, and three other high linked functional variants (rs77544449, rs60385309 and rs72917785) at 18q21.1 might regulate the expression of LIPG, a gene that was shown to exhibit an oncogenic function by our in-vitro experiments and clinical data analysis. The link between genetic variants, gene expression and CRC phenotype established by us could provide references for follow-up basic and clinical studies.
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Affiliation(s)
- Xiaoqing Cheng
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fenglan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jingwen Gong
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yige Li
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dan Zhou
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Wang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
| | - Eu Gene Vong
- Department of Biochemistry and Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Department of Medical Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- * E-mail: (YY); (ML); (DZ)
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
- * E-mail: (YY); (ML); (DZ)
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, China
- * E-mail: (YY); (ML); (DZ)
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Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle ADL, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W. Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. Gastroenterology 2021; 160:1164-1178.e6. [PMID: 33058866 PMCID: PMC7956223 DOI: 10.1053/j.gastro.2020.08.062] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes. METHODS Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted. RESULTS We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis. CONCLUSIONS Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Weiqiang Lin
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeroen Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Tabitha Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yuan Yuan
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangqin Wang
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqiu Bai
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | | | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - David V Conti
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Mark Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | | | - Soo Chin Lee
- National University Cancer Institute, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Neil Murphy
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; School of Public Health, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Xiaoliang Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St John's, Newfoundland and Labrador, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen B Gruber
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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7
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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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8
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Fortini BK, Tring S, Devall MA, Ali MW, Plummer SJ, Casey G. SNPs associated with colorectal cancer at 15q13.3 affect risk enhancers that modulate GREM1 gene expression. Hum Mutat 2021; 42:237-245. [PMID: 33476087 PMCID: PMC7898835 DOI: 10.1002/humu.24166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/12/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Several genome wide association studies of colorectal cancer (CRC) have identified single nucleotide polymorphisms (SNPs) on chromosome 15q13.3 associated with CRC risk. To identify functional variant(s) underlying this association, we investigated SNPs in linkage disequilibrium with the risk‐associated SNP rs4779584 that overlapped regulatory regions/enhancer elements characterized in colon‐related tissues and cells. We identified several SNP‐containing regulatory regions that exhibited enhancer activity in vitro, including one SNP (rs1406389) that correlated with allele‐specific effects on enhancer activity. Deletion of either this enhancer or another enhancer that had previously been reported in this region correlated with decreased expression of GREM1 following CRISPR/Cas9 genome editing. That GREM1 is one target of these enhancers was further supported by an expression quantitative trait loci correlation between rs1406389 and GREM1 expression in the transverse but not sigmoid colon in the Genotype‐Tissue Expression dataset. Taken together, we conclude that the 15q13.3 region contains at least two functional variants that map to distinct enhancers and impact CRC risk through modulation of GREM1 expression.
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Affiliation(s)
| | - Stephanie Tring
- Molecular Genomics Core, University of Southern California, Los Angeles, California, USA
| | - Matthew A Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Mourad Wagdy Ali
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Sarah J Plummer
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
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9
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Yuan Y, Bao J, Chen Z, Villanueva AD, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu XO, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Hum Mol Genet 2021; 30:321-330. [PMID: 33481017 DOI: 10.1093/hmg/ddab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 02/05/2023] Open
Abstract
Most genetic variants for colorectal cancer (CRC) identified in genome-wide association studies (GWAS) are located in intergenic regions, implying pathogenic dysregulations of gene expression. However, comprehensive assessments of target genes in CRC remain to be explored. We conducted a multi-omics analysis using transcriptome and/or DNA methylation data from the Genotype-Tissue Expression, The Cancer Genome Atlas and the Colonomics projects. We identified 116 putative target genes for 45 GWAS-identified variants. Using summary-data-based Mendelian randomization approach (SMR), we demonstrated that the CRC susceptibility for 29 out of the 45 CRC variants may be mediated by cis-effects on gene regulation. At a cutoff of the Bonferroni-corrected PSMR < 0.05, we determined 66 putative susceptibility genes, including 39 genes that have not been previously reported. We further performed in vitro assays for two selected genes, DIP2B and SFMBT1, and provide functional evidence that they play a vital role in colorectal carcinogenesis via disrupting cell behavior, including migration, invasion and epithelial-mesenchymal transition. Our study reveals a large number of putative novel susceptibility genes and provides additional insight into the underlying mechanisms for CRC genetic risk loci.
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Affiliation(s)
- Yuan Yuan
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 322000, China
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Anna Díez Villanueva
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO); Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL); Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP); Faculty of Medicine, Department of Clinical Sciences, University of Barcelona, Barcelona 08908, Spain
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Fangqin Wang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 322000, China
| | - Dejian Zhao
- Departments of Genetics, Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xianghui Fu
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy, West China Hospital, Chengdu, Sichuan 610041, China
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Deyou Zheng
- Departments of Genetics, Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO); Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL); Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP); Faculty of Medicine, Department of Clinical Sciences, University of Barcelona, Barcelona 08908, Spain
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Weiqiang Lin
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 322000, China
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
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10
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Tian J, Lou J, Cai Y, Rao M, Lu Z, Zhu Y, Zou D, Peng X, Wang H, Zhang M, Niu S, Li Y, Zhong R, Chang J, Miao X. Risk SNP-Mediated Enhancer-Promoter Interaction Drives Colorectal Cancer through Both FADS2 and AP002754.2. Cancer Res 2020; 80:1804-1818. [PMID: 32127356 DOI: 10.1158/0008-5472.can-19-2389] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/06/2019] [Accepted: 02/27/2020] [Indexed: 01/17/2023]
Abstract
Although genome-wide association studies (GWAS) have identified more than 100 colorectal cancer risk loci, most of the biological mechanisms associated with these loci remain unclear. Here we first performed a comprehensive expression quantitative trait loci analysis in colorectal cancer tissues adjusted for multiple confounders to test the determinants of germline variants in established GWAS susceptibility loci on mRNA and long noncoding RNA (lncRNA) expression. Combining integrative functional genomic/epigenomic analyses and a large-scale population study consisting of 6,024 cases and 10,022 controls, we then prioritized rs174575 with a C>G change as a potential causal candidate for colorectal cancer at 11q12.2, as its G allele was associated with an increased risk of colorectal cancer (OR = 1.26; 95% confidence interval = 1.17-1.36; P = 2.57 × 10-9). rs174575 acted as an allele-specific enhancer to distally facilitate expression of both FADS2 and lncRNA AP002754.2 via long-range enhancer-promoter interaction loops, which were mediated by E2F1. AP002754.2 further activated a transcriptional activator that upregulated FADS2 expression. FADS2, in turn, was overexpressed in colorectal cancer tumor tissues and functioned as a potential oncogene that facilitated colorectal cancer cell proliferation and xenograft growth in vitro and in vivo by increasing the metabolism of PGE2, an oncogenic molecule involved in colorectal cancer tumorigenesis. Our findings represent a novel mechanism by which a noncoding variant can facilitate long-range genome interactions to modulate the expression of multiple genes including not only mRNA, but also lncRNA, which provides new insights into the understanding of colorectal cancer etiology. SIGNIFICANCE: This study provides an oncogenic regulatory circuit among several oncogenes including E2F1, FADS2, and AP002754.2 underlying the association of rs174575 with colorectal cancer risk, which is driven by long-range enhancer-promoter interaction loops. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/9/1804/F1.large.jpg.
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Affiliation(s)
- Jianbo Tian
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.,Department of Quality Management, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Meilin Rao
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Haoxue Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Siyuan Niu
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yue Li
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.
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11
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Lu Y, Kweon SS, Cai Q, Tanikawa C, Shu XO, Jia WH, Xiang YB, Huyghe JR, Harrison TA, Kim J, Shin A, Kim DH, Matsuo K, Jee SH, Guo X, Wen W, Shi J, Li B, Wang N, Shin MH, Li HL, Ren Z, Oh JH, Oze I, Ahn YO, Jung KJ, Gao J, Gao YT, Pan ZZ, Kamatani Y, Chan AT, Gsur A, Hampe J, Le Marchand L, Li L, Lindblom A, Moreno V, Newcomb PA, Offit K, Pharoah PDP, van Duijnhoven FJB, Van Guelpen B, Vodicka P, Weinstein SJ, Wolk A, Wu AH, Hsu L, Zeng YX, Long J, Peters U, Matsuda K, Zheng W. Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians. Cancer Epidemiol Biomarkers Prev 2020; 29:477-486. [PMID: 31826910 PMCID: PMC7571256 DOI: 10.1158/1055-9965.epi-19-0755] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/30/2019] [Accepted: 12/04/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Risk variants identified so far for colorectal cancer explain only a small proportion of familial risk of this cancer, particularly in Asians. METHODS We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, including 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 promising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls of European descent. To identify additional risk variants in known colorectal cancer loci, we performed conditional analyses in East Asians. RESULTS An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk at P = 3.9 × 10-8 in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This association was replicated in European descendants using a variant (rs2938616) in complete linkage disequilibrium with rs67052019 (P = 7.7 × 10-3). Of the remaining 59 variants, 12 showed an association at P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 × 10-8 and two variants with an association near the genome-wide significance level (rs60911071, P = 5.8 × 10-8; rs62558833, P = 7.5 × 10-8) in the combined analyses of Asian- and European-ancestry data. In addition, using data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS. CONCLUSIONS In this large GWAS, we identified three novel risk loci and two highly suggestive loci for colorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the etiology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal cancer risk loci identified previously. IMPACT Our study provides novel data to improve the understanding of the genetic basis for colorectal cancer risk.
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Affiliation(s)
- Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, Seoul, Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, Korea
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nan Wang
- General Surgery Department, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Hong-Lan Li
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Isao Oze
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Jing Gao
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhi-Zhong Pan
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Andrew T Chan
- Division of Gastroenterology, and Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Epidemiology, and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | | | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- School of Public Health, University of Washington, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, California
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
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12
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Evaluating the predictive value of genetic risk score in colorectal cancer among Chinese Han population. J Hum Genet 2019; 65:271-279. [PMID: 31857674 DOI: 10.1038/s10038-019-0703-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/11/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Increasing single nucleotide polymorphisms (SNPs) have been identified to be associated with colorectal cancer (CRC). We aimed to investigate whether genetic risk scores (GRS) that aggregate information from multiple genetic variants can predict the risk of CRC in a Chinese population. Fifty candidate SNPs were selected to explore the associations with CRC in a discovery sample with 1002 CRC cases and 999 healthy controls. We modeled the significant SNPs identified by the case-control study as a multilocus weighted GRS and estimated the association of GRS with CRC. Furthermore, 300 pairs of cases and controls were included as a validation sample to confirm the finding. Area under the receiver operating characteristic curve (AUROC) was used to evaluate the predictive power of GRS in CRC. A total of seven SNPs were found to increase the risk of CRC, and two SNPs were found to be negatively associated with CRC in the discovery sample. Relative to participants with the lowest quartile of GRS, those with the highest quartile had a 2.64-fold (95% CI: 1.99-3.51) higher risk for CRC. For every 0.1 point of GRS increase, the risk of CRC increase by 11% (95% CI: 8-14%). AUROC for GRS alone were 0.59 (95% CI: 0.57-0.62) and 0.52 (95% CI: 0.46-0.58) in the discovery and validation sample, respectively. AUROC increased to 0.62 (95% CI: 0.59-0.64) and 0.71 (95% CI: 0.65-0.76) by combining environmental risk factors. Our findings support an association between GRS and risk of CRC, which provides evidence of improved prediction model for CRC in China.
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13
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Three functional variants were identified to affect RPS24 expression and significantly associated with risk of colorectal cancer. Arch Toxicol 2019; 94:295-303. [DOI: 10.1007/s00204-019-02600-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/15/2019] [Indexed: 10/25/2022]
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14
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Fedirko V, Mandle HB, Zhu W, Hughes DJ, Siddiq A, Ferrari P, Romieu I, Riboli E, Bueno-de-Mesquita B, van Duijnhoven FJB, Siersema PD, Tjønneland A, Olsen A, Perduca V, Carbonnel F, Boutron-Ruault MC, Kühn T, Johnson T, Krasimira A, Trichopoulou A, Makrythanasis P, Thanos D, Panico S, Krogh V, Sacerdote C, Skeie G, Weiderpass E, Colorado-Yohar S, Sala N, Barricarte A, Sanchez MJ, Quirós R, Amiano P, Gylling B, Harlid S, Perez-Cornago A, Heath AK, Tsilidis KK, Aune D, Freisling H, Murphy N, Gunter MJ, Jenab M. Vitamin D-Related Genes, Blood Vitamin D Levels and Colorectal Cancer Risk in Western European Populations. Nutrients 2019; 11:E1954. [PMID: 31434255 PMCID: PMC6722852 DOI: 10.3390/nu11081954] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Higher circulating 25-hydroxyvitamin D levels (25(OH)D) have been found to be associated with lower risk for colorectal cancer (CRC) in prospective studies. Whether this association is modified by genetic variation in genes related to vitamin D metabolism and action has not been well studied in humans. We investigated 1307 functional and tagging single-nucleotide polymorphisms (SNPs; individually, and by gene/pathway) in 86 vitamin D-related genes in 1420 incident CRC cases matched to controls from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. We also evaluated the association between these SNPs and circulating 25(OH)D in a subset of controls. We confirmed previously reported CRC risk associations between SNPs in the VDR, GC, and CYP27B1 genes. We also identified additional associations with 25(OH)D, as well as CRC risk, and several potentially novel SNPs in genes related to vitamin D transport and action (LRP2, CUBN, NCOA7, and HDAC9). However, none of these SNPs were statistically significant after Benjamini-Hochberg (BH) multiple testing correction. When assessed by a priori defined functional pathways, tumor growth factor β (TGFβ) signaling was associated with CRC risk (P ≤ 0.001), with most statistically significant genes being SMAD7 (PBH = 0.008) and SMAD3 (PBH = 0.008), and 18 SNPs in the vitamin D receptor (VDR) binding sites (P = 0.036). The 25(OH)D-gene pathway analysis suggested that genetic variants in the genes related to VDR complex formation and transcriptional activity are associated with CRC depending on 25(OH)D levels (interaction P = 0.041). Additional studies in large populations and consortia, especially with measured circulating 25(OH)D, are needed to confirm our findings.
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Affiliation(s)
- Veronika Fedirko
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
| | - Hannah B Mandle
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Wanzhe Zhu
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - David J Hughes
- Cancer Biology and Therapeutics Group (CBT), Conway Institute, School of Biomolecular and Biomedical Science (SBBS), University College Dublin, Dublin, Ireland
| | - Afshan Siddiq
- Genomics England, London EC1M 6BQ, UK
- Imperial College London, London SW7 2AZ, UK
| | - Pietro Ferrari
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France
| | - Isabelle Romieu
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Bas Bueno-de-Mesquita
- Division of Human Nutrition & Health, Wageningen University & Research, 6700 AA Wageningen, The Netherlands
| | - Fränzel J B van Duijnhoven
- Division of Human Nutrition & Health, Wageningen University & Research, 6700 AA Wageningen, The Netherlands
| | - Peter D Siersema
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Anne Tjønneland
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Anja Olsen
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5, Université Paris Descartes, 75006 Paris, France
- CESP, Fac. de médecine-Univ. Paris-Sud, Fac. de médecine-UVSQ, INSERM, Université Paris-Saclay, F-94805 Villejuif, France
- Gustave Roussy, F-94805 Villejuif, France
| | - Franck Carbonnel
- CESP, Fac. de médecine-Univ. Paris-Sud, Fac. de médecine-UVSQ, INSERM, Université Paris-Saclay, F-94805 Villejuif, France
- Gustave Roussy, F-94805 Villejuif, France
- Department of Gastroenterology, Bicêtre University Hospital, Assistance Publique des Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France
| | - Marie-Christine Boutron-Ruault
- CESP, Fac. de médecine-Univ. Paris-Sud, Fac. de médecine-UVSQ, INSERM, Université Paris-Saclay, F-94805 Villejuif, France
- Gustave Roussy, F-94805 Villejuif, France
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Theron Johnson
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Aleksandrova Krasimira
- Nutrition, Immunity and Metabolism, Department of Epidemiology, German Institute for Human Nutrition Potsdam-Rehbrücke, Arthur-Scheunert Allee, 14558 Nuthetal, Germany
| | | | - Periklis Makrythanasis
- Hellenic Health Foundation, 115 27 Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Dimitris Thanos
- Hellenic Health Foundation, 115 27 Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico Ii University, 80138 Naples, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, 20133 Milano, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), 10126 Turin, Italy
| | - Guri Skeie
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, 9019 Tromsø, Norway
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, 9019 Tromsø, Norway
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, N-0304 Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institut, SE-171 77 Stockholm, Sweden
- Genetic Epidemiology Group, Folkhälsan Research Center and Faculty of Medicine, Helsinki University, Helsinki 00014, Finland
- International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France
| | - Sandra Colorado-Yohar
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia 30008, Spain
- CIBER Epidemiology and Public Healh (CIBERESP), Madrid 28029, Spain
- Research Group on Demography and Health, National Faculty of Public Health, University of Antioquia, Cl. 67 ##53-108 Medellín, Colombia
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, and Translational Research Laboratory, Catalan Institute of Oncology (ICO)-IDIBELL, 08908 Barcelona, Spain
| | - Aurelio Barricarte
- CIBER Epidemiology and Public Healh (CIBERESP), Madrid 28029, Spain
- Navarra Public Health Institute, Pamplona 31008, Spain
| | - Maria-Jose Sanchez
- CIBER Epidemiology and Public Healh (CIBERESP), Madrid 28029, Spain
- Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria (ibs.GRANADA), Granada 18012, Spain
| | - Ramón Quirós
- Public Health Directorate, Asturias 33006, Spain
| | - Pilar Amiano
- CIBER Epidemiology and Public Healh (CIBERESP), Madrid 28029, Spain
- Public Health Division of Gipuzkoa, BioDonostia Research Institute, San Sebastian 20014, Spain
| | - Björn Gylling
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Alicia K Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece
| | - Dagfinn Aune
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
- Department of Nutrition, Bjørknes University College, 0456 Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Heinz Freisling
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France
| | - Mazda Jenab
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon 69372, France.
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15
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Tian J, Chang J, Gong J, Lou J, Fu M, Li J, Ke J, Zhu Y, Gong Y, Yang Y, Zou D, Peng X, Yang N, Mei S, Wang X, Zhong R, Cai K, Miao X. Systematic Functional Interrogation of Genes in GWAS Loci Identified ATF1 as a Key Driver in Colorectal Cancer Modulated by a Promoter-Enhancer Interaction. Am J Hum Genet 2019; 105:29-47. [PMID: 31204011 DOI: 10.1016/j.ajhg.2019.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/06/2019] [Indexed: 01/02/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified approximately 100 colorectal cancer (CRC) risk loci. However, the causal genes in these loci have not been systematically interrogated. We conducted a high-throughput RNA-interference functional screen to identify the genes essential for proliferation in the CRC risk loci of Asian populations. We found that ATF1, located in the 12q13.12 region, functions as an oncogene that facilitates cell proliferation; ATF1 has the most significant effect of the identified genes and promotes CRC xenograft growth by affecting cell apoptosis. Next, by integrating a fine-mapping analysis, a two-stage affected-control study consisting of 6,213 affected individuals and 10,388 controls, and multipronged experiments, we elucidated that two risk variants, dbSNP: rs61926301 and dbSNP: rs7959129, that located in the ATF1 promoter and first intron, respectively, facilitate a promoter-enhancer interaction, mediated by the synergy of SP1 and GATA3, to upregulate ATF1 expression, thus synergistically predisposing to CRC risk (OR = 1.77, 95% CI = 1.42-2.21, p = 3.16 × 10-7; Pmultiplicative-interaction = 1.20 × 10-22; Padditive-interaction = 6.50 × 10-3). Finally, we performed RNA-seq and ChIP-seq assays in CRC cells treated with ATF1 overexpression in order to dissect the target programs of ATF1. Results showed that ATF1 activates a subset of genes, including BRAF, NRAS, MYC, BIRC2, DAAM1, MAML2, STAT1, ID1, and NKD2, related to apoptosis, Wnt, TGF-β, and MAPK pathways, and these effects could cooperatively increase the risk of CRC. These findings reveal the clinical potential of ATF1 in CRC development and illuminate a promoter-enhancer interaction module between the ATF1 regulatory elements dbSNP: rs61926301 and dbSNP: rs7959129, and they bring us closer to understanding the molecular drivers of cancer.
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16
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Lu Y, Kweon SS, Tanikawa C, Jia WH, Xiang YB, Cai Q, Zeng C, Schmit SL, Shin A, Matsuo K, Jee SH, Kim DH, Kim J, Wen W, Shi J, Guo X, Li B, Wang N, Zhang B, Li X, Shin MH, Li HL, Ren Z, Oh JH, Oze I, Ahn YO, Jung KJ, Conti DV, Schumacher FR, Rennert G, Jenkins MA, Campbell PT, Hoffmeister M, Casey G, Gruber SB, Gao J, Gao YT, Pan ZZ, Kamatani Y, Zeng YX, Shu XO, Long J, Matsuda K, Zheng W. Large-Scale Genome-Wide Association Study of East Asians Identifies Loci Associated With Risk for Colorectal Cancer. Gastroenterology 2019; 156:1455-1466. [PMID: 30529582 PMCID: PMC6441622 DOI: 10.1053/j.gastro.2018.11.066] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Genome-wide association studies (GWASs) have associated approximately 50 loci with risk of colorectal cancer (CRC)-nearly one third of these loci were initially associated with CRC in studies conducted in East Asian populations. We conducted a GWAS of East Asians to identify CRC risk loci and evaluate the generalizability of findings from GWASs of European populations to Asian populations. METHODS We analyzed genetic data from 22,775 patients with CRC (cases) and 47,731 individuals without cancer (controls) from 14 studies in the Asia Colorectal Cancer Consortium. First, we performed a meta-analysis of 7 GWASs (10,625 cases and 34,595 controls) and identified 46,554 promising risk variants for replication by adding them to the Multi-Ethnic Global Array (MEGA) for genotype analysis in 6445 cases and 7175 controls. These data were analyzed, along with data from an additional 5705 cases and 5961 controls genotyped using the OncoArray. We also obtained data from 57,976 cases and 67,242 controls of European descent. Variants at identified risk loci were functionally annotated and evaluated in correlation with gene expression levels. RESULTS A meta-analyses of all samples from people of Asian descent identified 13 loci and 1 new variant at a known locus (10q24.2) associated with risk of CRC at the genome-wide significance level of P < 5 × 10-8. We did not perform experiments to replicate these associations in additional individuals of Asian ancestry. However, the lead risk variant in 6 of these loci was also significantly associated with risk of CRC in European descendants. A strong association (44%-75% increase in risk per allele) was found for 2 low-frequency variants: rs201395236 at 1q44 (minor allele frequency, 1.34%) and rs77969132 at 12p11.21 (minor allele frequency, 1.53%). For 8 of the 13 associated loci, the variants with the highest levels of significant association were located inside or near the protein-coding genes L1TD1, EFCAB2, PPP1R21, SLCO2A1, HLA-G, NOTCH4, DENND5B, and GNAS. For other intergenic loci, we provided evidence for the possible involvement of the genes ALDH7A1, PRICKLE1, KLF5, WWOX, and GLP2R. We replicated findings for 41 of 52 previously reported risk loci. CONCLUSIONS We showed that most of the risk loci previously associated with CRC risk in individuals of European descent were also associated with CRC risk in East Asians. Furthermore, we identified 13 loci significantly associated with risk for CRC in Asians. Many of these loci contained genes that regulate the immune response, Wnt signaling to β-catenin, prostaglandin E2 catabolism, and cell pluripotency and proliferation. Further analyses of these genes and their variants is warranted, particularly for the 8 loci for which the lead CRC risk variants were not replicated in persons of European descent.
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Affiliation(s)
- Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea; Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Chenjie Zeng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, Seoul, Korea
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan; Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nan Wang
- General Surgery Department, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics First Affiliated Hospital, Army Medical University, Shapingba District, Chongqing, China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Hong-Lan Li
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Isao Oze
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - David V Conti
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel; Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel; Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen B Gruber
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jing Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhi-Zhong Pan
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan; Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
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17
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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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18
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Song N, Kim K, Shin A, Park JW, Chang HJ, Shi J, Cai Q, Kim DY, Zheng W, Oh JH. Colorectal cancer susceptibility loci and influence on survival. Genes Chromosomes Cancer 2018; 57:630-637. [DOI: 10.1002/gcc.22674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Nan Song
- Cancer Research Institute; Seoul National University College of Medicine; Seoul South Korea
| | - Kyeezu Kim
- Division of Epidemiology and Biostatistics; University of Illinois at Chicago School of Public Health; Chicago Illinois
| | - Aesun Shin
- Cancer Research Institute; Seoul National University College of Medicine; Seoul South Korea
- Department of Preventive Medicine; Seoul National University College of Medicine; Seoul South Korea
- Molecular Epidemiology Branch, National Cancer Center; Goyang South Korea
| | - Ji Won Park
- Department of Surgery; Seoul National University College of Medicine and Hospital; Seoul South Korea
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
| | - Hee Jin Chang
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Dae Yong Kim
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center; Goyang South Korea
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19
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Chang J, Tian J, Yang Y, Zhong R, Li J, Zhai K, Ke J, Lou J, Chen W, Zhu B, Shen N, Zhang Y, Gong Y, Zhu Y, Zou D, Peng X, Huang K, Miao X. A Rare Missense Variant in TCF7L2 Associates with Colorectal Cancer Risk by Interacting with a GWAS-Identified Regulatory Variant in the MYC Enhancer. Cancer Res 2018; 78:5164-5172. [DOI: 10.1158/0008-5472.can-18-0910] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/16/2018] [Accepted: 07/10/2018] [Indexed: 11/16/2022]
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20
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Wang S, Zhang Y, Chen M, Wang Y, Feng Y, Xu Z, Zhang D, Sun Y, Fu Z. Association of genetic variants in ATR-CHEK1 and ATM-CHEK2 pathway genes with risk of colorectal cancer in a Chinese population. Oncotarget 2018; 9:26616-26624. [PMID: 29928473 PMCID: PMC6003554 DOI: 10.18632/oncotarget.24299] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/04/2017] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE The ATR-CHEK1 and ATM-CHEK2 pathway have been confirmed to be related with the DNA damage response (DDR). Many studies have reported that genetic variants in ATR/CHEK1 and ATM/CHEK2 are associated with cancer risk. However, the association between genetic variants in ATR-CHEK1, ATM-CHEK2 pathway genes and colorectal cancer susceptibility is still unknown. In this study, we aim to explore whether these variants are correlated with the risk of colorectal cancer in a Chinese population. METHODS A hospital-based case-control study, including 1,121 cases and 1,056 controls was conducted to evaluate the association between eight selected single nucleotide polymorphisms (SNPs) (rs35514263 in ATR; rs492510, rs558351 in CHKE1; rs189037 in ATM; rs2236141, rs5762748, rs2236142 and rs9620817 in CHEK2) in ATR-CHEK1 and ATM-CHEK2 pathways and the risk of colorectal cancer in a Chinese population by using TaqMan method. RESULTS Individuals with rs189037 A allele were found to have a significantly increased risk of colorectal cancer, compared to those carrying G allele [odds ratio(OR) = 1.23, 95% confidence interval (CI) = 1.02-1.47 in dominant model and OR= 1.14, 95%CI= 1.01-1.29 in additive model]. And this risk is more pronounced in elder people (>69), rectum, early stage and poorly grade. In addition, bioinformatic analysis showed that rs189037 may change the secondary structure. CONCLUSIONS Our results provide the evidence that rs189037 in ATM may increase the susceptibility of colorectal cancer in a Chinese population.
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Affiliation(s)
- Shijia Wang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yue Zhang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Min Chen
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yong Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yifei Feng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ziwei Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dongsheng Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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21
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Hong Y, Wu G, Li W, Liu D, He K. A comprehensive meta-analysis of genetic associations between five key SNPs and colorectal cancer risk. Oncotarget 2018; 7:73945-73959. [PMID: 27661122 PMCID: PMC5342026 DOI: 10.18632/oncotarget.12154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) on colorectal cancer (CRC) have identified dozens of single nucleotide polymorphisms (SNPs) in more than 19 independent loci associated with CRC. Due to the heterogeneity of the studied subjects and the contrary results, it is challenging to verify the certainty of the association between these loci and CRC.We conducted a critical review of the published studies of SNPs associated with CRC. Five most frequently reported SNPs, which are rs6983267/8q24.21, rs4939827/18q21.1, rs10795668/10p14, rs4444235/14q22.2 and rs4779584/ 15q13.3, were selected for the current study from the qualified studies. Then meta-analyses based on larger sample sizes with average of 33,000 CRC cases and 34,000 controls were performed to assess the association between SNPs and CRC risk. Heterogeneity among studies and publication bias were assessed by the χ2-based Q statistic test Begg's funnel plot or Egger's test, respectively.Our meta-analysis confirmed significant associations of the five SNPs with CRC risk under different genetic models. Two risk variants at rs6983267 {Odds Ratio (OR) 1.388, 95% Confidence Interval (CI) 1.180-1.8633} and rs10795668 (OR 1.323, 95% CI 1.062-1.648) had the highest ORs in homogeneous model. While ORs of the other three variants at rs4939827 {OR 1.298, 95% CI 1.135-1.483}, rs4779584 (OR 1.261, 95% CI 1.146-1.386) and rs4444235 (OR 1.160, 95% CI 1.106-1.216) were also statistically significant. Sensitivity analyses and publication bias assessment indicated the robust stability and reliability of the results.
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Affiliation(s)
- Yi Hong
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Guoying Wu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Wei Li
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Dahai Liu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
| | - Kan He
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China.,Department of Biostatistics, School of Life Sciences, Anhui University, Hefei City, Anhui 230601, P. R. China
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22
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SMAD7 polymorphisms and colorectal cancer risk: a meta-analysis of case-control studies. Oncotarget 2018; 7:75561-75570. [PMID: 28070019 PMCID: PMC5342761 DOI: 10.18632/oncotarget.12285] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/14/2016] [Indexed: 01/29/2023] Open
Abstract
Mothers against decapentaplegic homolog 7 (SMAD7) inhibits the transforming growth factor-β (TGF-β) signaling pathway, which regulates carcinogenesis and cancer progression. A number of studies have reported that SMAD7 polymorphisms (rs4464148, rs4939827, and rs12953717) are associated with colorectal cancer (CRC) risk, but the results from these studies remain conflicting. To determine a more precise estimation of the relationship between SMAD7 and CRC, we undertook a large-scale meta-analysis of 63 studies, which included a total of 187,181 subjects (86,585 cases and 100,596 controls). The results of our meta-analysis revealed that the C allele of rs4464148 [CC vs. TT+TC, odds ratio (OR) =1.23, 95% confidence interval (CI): 1.14–1.33, P < 0.01], the T allele of rs4939827 [TT vs. CC+TC, odds ratio OR=1.15, 95%CI:1.07–1.22, P < 0.01] and the T allele of rs12953717 [TT vs. CC+TC, OR =1.22, 95%CI:1.16–1.29, P < 0.01] were all associated with the increased CRC risk. Subgroup analysis according to ethnicity showed rs4464148 and rs12953717 were associated with the risk of CRC in both Caucasians and Asians, whereas rs4939827 was a risk polymorphism for CRC specifically in Caucasians. In summary, this large-scale meta-analysis indicated that SMAD7 polymorphisms (rs4464148, rs4939827, and rs12953717) correlate with CRC.
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23
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Risk of eighteen genome-wide association study-identified genetic variants for colorectal cancer and colorectal adenoma in Han Chinese. Oncotarget 2018; 7:77651-77663. [PMID: 27769063 PMCID: PMC5363611 DOI: 10.18632/oncotarget.12750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 10/01/2016] [Indexed: 01/20/2023] Open
Abstract
Background Recent genome-wide association studies (GWAS) identified eighteen single-nucleotide polymorphisms (SNPs) to be significantly associated with the risk of colorectal cancer (CRC). However, overall results of the following replications are inconsistent and little is known about whether these associations also exit in colorectal adenomas (CRA). Methods The SNP genotyping was performed using a Sequenom MassARRAY to investigate the association of these eighteen SNPs with colorectal neoplasm in a case-control study consisted of 1049 colorectal cancers, 283 adenomas, and 1030 controls. Results Two of these SNPs, rs10505477 and rs719725, showed evidence of an association in both CRC and CRA in our study population. Besides, seven SNPs (rs10808555, rs7014346, rs7837328, rs704017, rs11196172, rs4779584, and rs7229639) were significantly associated with CRC, and another one SNP rs11903757 was over-represented in CRA compared with controls. The strongest association was provided by rs11196172 (OR = 2.02, 95% CI = 1.66 - 2.46, P < 0.0001) and rs11903757 (OR = 1.96, 95% CI = 1.28 - 3.00, P = 0.0026). Conclusion These results suggest that some previously reported SNP associations also have impact on CRC and CRA predispositions in the Han Chinese population. A part of genetic risk to CRC is possibly mediated by susceptibility to adenomas.
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24
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Ke J, Lou J, Chen X, Li J, Liu C, Gong Y, Yang Y, Zhu Y, Zhang Y, Tian J, Chang J, Zhong R, Gong J, Miao X. Identification of a functional variant for colorectal cancer risk mapping to chromosome 5q31.1. Oncotarget 2018; 7:35199-207. [PMID: 27177089 PMCID: PMC5085221 DOI: 10.18632/oncotarget.9298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWASs) have established chromosome 5q31.1 as a risk locus for colorectal cancer (CRC). We previously identified a potentially regulatory single nucleotide polymorphism (SNP) rs17716310 within 5q31.1. Now, we extended our study with another independent Chinese population, functional assays and analyses of TCGA (The Cancer Genome Atlas) data. Significant associations between rs17716310 and CRC risk were found in Present Study including 1075 CRC cases and 1999 controls (additive model: OR = 1.149, 95% CI = 1.027–1.286, P = 0.016), and in Combined Study including 1766 cases and 2708 controls (additive model: OR = 1.145, 95% CI = 1.045–1.254, P = 0.004). Dual luciferase reporter gene assays indicated that the variant C allele obviously increased transcriptional activity. Using TCGA datasets, we indicated rs17716310 as a cis expression quantitative trait locus (eQTL) for the gene SMAD5, whose expression was significantly higher in CRC tissues. These findings suggested that the functional polymorphism rs17716310 A > C might be a genetic modifier for CRC, promoting the expression of SMAD5 that belonged to the transforming growth factor beta (TGF-β) signaling pathway.
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Affiliation(s)
- Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueqin Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and 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.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and 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.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and 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.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and 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.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and 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.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and 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.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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25
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Shaker OG, Mohammed SR, Mohammed AM, Mahmoud Z. Impact of microRNA-375 and its target gene SMAD-7 polymorphism on susceptibility of colorectal cancer. J Clin Lab Anal 2018; 32:e22215. [PMID: 28374902 PMCID: PMC6817095 DOI: 10.1002/jcla.22215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/27/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) has a high morbidity and mortality. Many studies reported that mir-375 is frequently down-regulated in many cancers including esophageal cancer, hepatocellular carcinoma, breast cancer and leukemias. AIM Our aim was to study the expression of microRNA-375 and its target gene SMAD-7 polymorphisms (rs4939827) in CRC patients in comparison to control subjects and to correlate these results with clinical data of patients to elucidate their role in pathogenesis and early diagnosis of CRC. MATERIAL AND METHODS The present study was conducted on 122 subjects divided into 86 patients with CRC and 36 age- and sex-matched controls. The followings were done to all subjects: full history taking, full clinical examination, complete blood picture, serum (ALT, AST), serum albumin, CEA, TLC, PLT, and creatinine. Gene expression of miRNA-375 from serum was done by real-time PCR. Gene polymorphism SNPs of SMAD7 (rs4939827) was also done in DNA extracted from blood by real-time PCR. RESULTS As regards the polymorphism of SMAD7, we found that CC (wild) genotype has high percentage in controls compared to CRC cases (36.1% vs 15.1%). Meanwhile, the mutant and heterozygotes genotypes showed high percentage among cases compared to controls (33.7%, and 51.2% respectively) vs (22.2%, and 41.7% respectively) with no significant statistical analysis. There was a statistically significant high T-allelic frequency among cases and C-allelic frequency among controls. There was a statistically significant association between fold change in micro RNA (-375) and the susceptibility to CRC as there is down-regulation of the microRNA-375 in CRC group with fold change in 0.42±0.27. CONCLUSION Micro RNA-375 and rs4939827 SNP in SMAD7 could be considered as potential markers for detecting and early diagnosing CRC patients.
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Affiliation(s)
- Olfat Gamil Shaker
- Biochemistry and Molecular BiologyFaculty of MedicineCairo UniversityCairoEgypt
| | - Shereen Rashad Mohammed
- Departments of Medical Biochemistry and Molecular BiologyFaculty of MedicineFayoum UniversityAl FayoumEgypt
| | - Asmaa Mohammed Mohammed
- Departments of Medical Biochemistry and Molecular BiologyFaculty of MedicineFayoum UniversityAl FayoumEgypt
| | - Zeinab Mahmoud
- Departments of Tropical MedicineFaculty of MedicineCairo UniversityCairoEgypt
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26
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Alonso-Molero J, González-Donquiles C, Palazuelos C, Fernández-Villa T, Ramos E, Pollán M, Aragonés N, Llorca J, Henar Alonso M, Tardón A, Amiano P, Moleon JJJ, Pérez RP, Capelo R, Molina AJ, Acebo IG, Guevara M, Perez-Gomez B, Lope V, Huerta JM, Castaño-Vinyals G, Kogevinas M, Moreno V, Martín V. The RS4939827 polymorphism in the SMAD7 GENE and its association with Mediterranean diet in colorectal carcinogenesis. BMC MEDICAL GENETICS 2017; 18:122. [PMID: 29084532 PMCID: PMC5661920 DOI: 10.1186/s12881-017-0485-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 10/18/2017] [Indexed: 02/06/2023]
Abstract
Background The objective of our investigation is to study the relationship between the rs4939827 SNP in the SMAD7 gene, Mediterranean diet pattern and the risk of colorectal cancer. Methods We examined 1087 cases of colorectal cancer and 2409 population controls with available DNA samples from the MCC-Spain study, 2008–2012. Descriptive statistical analyses, and multivariate logistic mixed models were performed. The potential synergistic effect of rs4939827 and the Mediterranean diet pattern was evaluated with logistic regression in different strata of of adherence to the Mediterranean diet and the genotype. Results High adherence to Mediterrenean diet was statistically significantly associated with colorectal cancer risk. A decreased risk for CRC cancer was observed for the CC compared to the TT genotype (OR = 0.65 and 95% CI = 0.51–0.81) of the rs4939827 SNP Also, we could show an association between the Mediterranean diet pattern (protective factor) and rs4939827. Although the decreased risk for the CC genotype was slightly more pronounced in subjects with high adherence to Mediterrenean diet, there was no statistically significant synergistic effect between genotype CC and adherence to the Mediterranean dietary pattern factors. Conclusion The SMAD7 gene and specifically the allele C could be protective for colorectal cancer. An independent protective association was also observed between high adherence Mediterranean diet pattern and CRC risk. Findings form this study indicate that high adherence to Mediterranean diet pattern has a protective role for CRC cancer probably involving the Tumor Growth Factor- β pathway in this cancer. Electronic supplementary material The online version of this article (10.1186/s12881-017-0485-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jéssica Alonso-Molero
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud. Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Carmen González-Donquiles
- Centro de Investigación Biomédica en Red (CIBERESP) and Oviedo University; Departamento de Ciencias Biomédicas. Universidad de León. Campus de Vegazana, León, Spain.
| | | | - Tania Fernández-Villa
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud. Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Elena Ramos
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud. Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Marina Pollán
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Cancer and Environmental Epidemiology Unit, National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Nuria Aragonés
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Cancer and Environmental Epidemiology Unit, National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Javier Llorca
- Universidad de Cantabria, Santander, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - M Henar Alonso
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Cancer Prevention and Control Program, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
| | - Adonina Tardón
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Oncology Institute IUOPA, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Pilar Amiano
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Instituto de Salud Pública de Navarra, Pamplona, Navarra, Spain
| | - José Juan Jiménez Moleon
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - Rosana Peiró Pérez
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Dirección General de Salud Pública, Fundación para el fomento de la investigación sanitaria y biomédica de la Comunidad Valenciana, FISABIO-Salud Pública, Barcelona, Spain
| | - Rocío Capelo
- Centro de Investigación en Salud y Medio Ambiente (CYSMA), Universidad de Huelva, Huelva, Spain
| | - Antonio J Molina
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud. Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Inés Gómez Acebo
- Universidad de Cantabria, Santander, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marcela Guevara
- Instituto de Salud Pública de Navarra, Pamplona, Navarra, Spain
| | - Beatriz Perez-Gomez
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Cancer and Environmental Epidemiology Unit, National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Cancer Epidemiology Research Group, Oncology and Hematology Area, IIS Puerta De Hierro, Madrid, Spain
| | - Virginia Lope
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Cancer and Environmental Epidemiology Unit, National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - José María Huerta
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
| | - Gemma Castaño-Vinyals
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manolis Kogevinas
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,School of Public Health, Athens, Greece
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Cancer Prevention and Control Program, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Grupo de Investigación en Interacciones Gen-Ambiente y Salud de la Universidad de León, León, Spain
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27
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Wang N, Lu Y, Khankari NK, Long J, Li HL, Gao J, Gao YT, Xiang YB, Shu XO, Zheng W. Evaluation of genetic variants in association with colorectal cancer risk and survival in Asians. Int J Cancer 2017; 141:1130-1139. [PMID: 28567967 PMCID: PMC5524202 DOI: 10.1002/ijc.30812] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) have identified over 40 genetic loci associated with colorectal cancer (CRC) risk. The association of single nucleotide polymorphisms (SNPs) at these loci with CRC risk and survival has not been adequately evaluated in East Asians. GWAS-identified CRC risk variants were used to construct weighted genetic risk scores (GRSs). We evaluated these GRSs in association with CRC risk in 3,303 CRC cases and 3,553 controls using logistic regression models. Associations with overall and CRC-specific survival were assessed in 731 CRC patients using Cox regression models. The association between the GRSs (overall and Asian-specific) and CRC risk was approximately twofold (highest vs. lowest quintile), and the shape of the dose-response was linear (ptrend = 1.24 × 10-13 and 3.02 × 10-14 for overall GRS and Asian-specific GRS, respectively). The association of the GRS with CRC risk was stronger among those with a family history of CRC (pinteraction = 0.007). Asian-specific GRS using previously reported survival SNPs increased risk for mortality and the shape of the dose-response was linear for CRC-specific and all-cause mortality (ptrend = 0.01 and 0.006, respectively). Furthermore, the minor alleles of rs6983267 and rs1957636 were associated with worse CRC-specific and overall survival. We show that GRSs constructed using GWAS-identified common variants are strongly associated with CRC risk in Asians. We confirm previous findings for the possible association between some SNPs with survival, and provide evidence for two additional CRC risk variants that may be related to CRC survival.
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Affiliation(s)
- Nan Wang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nikhil K. Khankari
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hong-Lan Li
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jing Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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28
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Jiao W, Leng X, Zhou Q, Wu Y, Sun L, Tan Y, Ni H, Dong X, Shen T, Liu Y, Li J. Different miR-21-3p isoforms and their different features in colorectal cancer. Int J Cancer 2017; 141:2103-2111. [PMID: 28734015 DOI: 10.1002/ijc.30902] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 05/26/2017] [Accepted: 07/11/2017] [Indexed: 12/22/2022]
Abstract
MiR-21, the only microRNA (miRNA) found to be overexpressed in any type of solid tumor, its guide stand, miR-21-5p, has been studied a lot in colorectal cancer (CRC); however, few researchers focused on its passenger strand, miR-21-3p. In our study, based on The Cancer Genome Atlas (TCGA) data, we found that there were more varieties and quantities of miR-21-3p isoforms in microsatellite instability (MSI)-type CRC. We further examined the role of miR-21-3p by in vitro and in vivo studies. MiR-21-3p may be an oncogene in CRC by promoting cellular mobility through epithelial-mesenchymal transition. However, different isoforms, especially miR-21-3p 0 | 2, may be a favorable prognostic marker for CRC survival, probably due to increased complementary effect of miR-21-5p and/or target genes. Further study investigating the underlying mechanism of miRNA isoforms is needed.
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Affiliation(s)
- Weijuan Jiao
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Xueqin Leng
- Department of Bioinformatics, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Qun Zhou
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yayun Wu
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Lina Sun
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yan Tan
- Department of Pathology, the First People's Hospital of Changzhou, Changzhou, People's Republic of China
| | - Hengli Ni
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Xiaoqiang Dong
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Tong Shen
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yao Liu
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Jianming Li
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
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29
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Iwasaki M, Tanaka-Mizuno S, Kuchiba A, Yamaji T, Sawada N, Goto A, Shimazu T, Sasazuki S, Wang H, Marchand LL, Tsugane S. Inclusion of a Genetic Risk Score into a Validated Risk Prediction Model for Colorectal Cancer in Japanese Men Improves Performance. Cancer Prev Res (Phila) 2017; 10:535-541. [PMID: 28729251 DOI: 10.1158/1940-6207.capr-17-0141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/22/2017] [Accepted: 07/11/2017] [Indexed: 11/16/2022]
Abstract
We previously developed and validated a risk prediction model for colorectal cancer in Japanese men using modifiable risk factors. To further improve risk prediction, we evaluated the degree of improvement obtained by adding a genetic risk score (GRS) using genome-wide association study (GWAS)-identified risk variants to our validated model. We examined the association between 36 risk variants identified by GWAS and colorectal cancer risk using a weighted Cox proportional hazards model in a nested case-control study within the Japan Public Health Center-based Prospective Study. GRS was constructed using six variants associated with risk in this study of the 36 tested. We assessed three models: a nongenetic model that included the same variables used in our previously validated model; a genetic model that used GRS; and an inclusive model, which included both. The c-statistic, integrated discrimination improvement (IDI), and net reclassification improvement (NRI) were calculated by the 5-fold cross-validation method. We estimated 10-year absolute risks for developing colorectal cancer. A statistically significant association was observed between the weighted GRS and colorectal cancer risk. The mean c-statistic for the inclusive model (0.66) was slightly greater than that for the nongenetic model (0.60). Similarly, the mean IDI and NRI showed improvement when comparing the nongenetic and inclusive models. These models for colorectal cancer were well calibrated. The addition of GRS using GWAS-identified risk variants to our validated model for Japanese men improved the prediction of colorectal cancer risk. Cancer Prev Res; 10(9); 535-41. ©2017 AACR.
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Affiliation(s)
- Motoki Iwasaki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan.
| | - Sachiko Tanaka-Mizuno
- Division of Medical Statistics, Shiga University of Medical Science, Tsukinowa Seta-cho, Ohtsu, Shiga, Japan
| | - Aya Kuchiba
- Division of Biostatistical Research, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Atsushi Goto
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shizuka Sasazuki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Hansong Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
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30
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Park SL, Cheng I, Haiman CA. Genome-Wide Association Studies of Cancer in Diverse Populations. Cancer Epidemiol Biomarkers Prev 2017. [PMID: 28637795 DOI: 10.1158/1055-9965.epi-17-0169] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) of cancer have identified more than 700 risk loci, of which approximately 80% were first discovered in European ancestry populations, approximately 15% in East Asians, 3% in multiethnic scans, and less than 1% in African and Latin American populations. These percentages closely mirror the distribution of samples included in the discovery phase of cancer GWAS to date (84% European, 11% East Asian, 4% African, and 1% Latin American ancestry). GWAS in non-European ancestry populations have provided insight into ancestry-specific variation in cancer and have pointed to regions of susceptibility that are of particular importance in certain populations. Uncovering and characterizing cancer risk loci in diverse populations is critical for understanding underlying biological mechanisms and developing future genetic risk prediction models in non-European ancestry populations. New GWAS and continued collaborations will be required to eliminate population inequalities in the number of studies, sample sizes, and variant content on GWAS arrays, and to better align genetic research in cancer to the global distribution of race/ethnicity Cancer Epidemiol Biomarkers Prev; 27(4); 405-17. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Sungshim L Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California.,Stanford Cancer Institute, Palo Alto, California
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
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31
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Li J, Liu H, Zou L, Ke J, Zhang Y, Zhu Y, Yang Y, Gong Y, Tian J, Zou D, Peng X, Gong J, Zhong R, Huang K, Chang J, Miao X. A functional variant in GREM1 confers risk for colorectal cancer by disrupting a hsa-miR-185-3p binding site. Oncotarget 2017; 8:61318-61326. [PMID: 28977865 PMCID: PMC5617425 DOI: 10.18632/oncotarget.18095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022] Open
Abstract
The transforming growth factor beta (TGF-β) pathway has been implicated in carcinogenesis of intestinal canal. Except for common variants indentified by genome-wide association studies, variants with lower frequency can also explain a part of the disease heritability, especially those in gene regulatory regions. In this study, we searched for colorectal cancer (CRC) related functional low-frequency variants (minor allele frequency 1-5%) in untranslated regions (UTR) involved in the TGF-β signaling using a next-generation sequencing based approach. A case-control study including 1,841 CRC cases and 1,837 controls was performed to identify CRC associated variants and biological experiments were applied to further explore the potential functions of the significant variants. Three low-frequency UTR variants were selected as our candidates and subsequent association analyses showed that a low-frequency variant rs12915554 in the 3’ UTR of GREM1 was significantly associated with CRC risk (Additive model: OR=1.43, 95%CI: 1.04-1.95, P=0.026). Functional annotations suggested that rs12915554 variation increased the expression of GREM1 by perturbing a hsa-miR-185-3p binding site. Moreover, higher expression level of GREM1 was investigated in colon tumor tissues compared with adjacent normal tissues using TCGA data. In conclusion, low-frequency UTR variant rs12915554 in the gene GREM1 was in relation to CRC susceptibility in a Chinese population and this variation might promote CRC development through enhancing GREM1 expression in a miRNA-mediated posttranscriptional manner.
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Affiliation(s)
- Jiaoyuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Li Zou
- Department of Health Care, Bao'an Maternal and Child Health Hospital, Shenzhen, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhang
- 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
| | - Yang Yang
- 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
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- 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
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Huang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, 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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32
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Ke J, Tian J, Li J, Gong Y, Yang Y, Zhu Y, Zhang Y, Zhong R, Chang J, Gong J. Identification of a functional polymorphism affecting microRNA binding in the susceptibility locus 1q25.3 for colorectal cancer. Mol Carcinog 2017; 56:2014-2021. [PMID: 28277607 DOI: 10.1002/mc.22649] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/12/2017] [Accepted: 03/03/2017] [Indexed: 01/02/2023]
Abstract
Genome-wide association studies (GWASs) have identified dozens of susceptibility loci for colorectal cancer (CRC). However, most of them lack functional genetic variants and clear biological mechanisms. MicroRNAs (miRNAs) are small noncoding RNAs involved in a variety of physiological and tumorigenic processes. Here we hypothesized that single nucleotide polymorphisms (SNPs) that affect miRNAs biogenesis and binding, could contribute to CRC risk in the Chinese population. To locate miRNA-related SNPs in established GWAS loci, we initially screened out five candidate SNPs using a systematic bioinformatics analysis. Then, we performed a two-stage case-control study consisting of 2347 cases and 3390 controls, and found a positive polymorphism rs1062044, which presented consistently significant associations with CRC in both stages, and with an odds ratio (OR) = 1.32 (95% confidence interval (95%CI) = 1.18-1.49, P = 3.43E-06) under the dominant model in the combined study. Further luciferase reporter gene assays indicated that the variant G allele obviously improved the specific binding between miR-423-5p and the gene LAMC1. These findings suggested that the functional SNP rs1062044 at 1q25.3 might be a genetic modifier for the occurrence and development of CRC.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Jing Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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33
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Li J, Zou L, Zhou Y, Li L, Zhu Y, Yang Y, Gong Y, Lou J, Ke J, Zhang Y, Tian J, Zou D, Peng X, Chang J, Gong J, Zhong R, Zhou X, Miao X. A low-frequency variant in SMAD7 modulates TGF-β signaling and confers risk for colorectal cancer in Chinese population. Mol Carcinog 2017; 56:1798-1807. [PMID: 28218435 DOI: 10.1002/mc.22637] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/08/2017] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
The TGF-β pathway plays an essential role in regulating cell proliferation and differentiation. GWASs and candidate approaches have identified a battery of genetic variants in the TGF-β pathway contributing to colorectal cancer (CRC). However, most of the significant variants are common variants and their functions remain ambiguous. To identify causal variants with low-frequency in the TGF-β pathway contributing to CRC susceptibility in Chinese population, we performed targeted sequencing of 12 key genes in TGF-β signaling in CRC patients followed by a two-stage case-control study with a total of 5109 cases and 5169 controls. Bioinformatic annotations and biochemical experiments were applied to reveal the potential functions of significant variants. Seven low-frequency genetic variants were captured through targeted sequencing. The two stage association studies showed that missense variant rs3764482 (c. 83C>T; p. S28F) in the gene SMAD7 was consistently and significantly associated with CRC risk. Compared with the wild type, the ORs for variant allele were 1.37 (95%CI: 1.10-1.70, P = 0.005), 1.55 (95%CI: 1.30-1.86, P = 1.15 × 106 ), and 1.48 (1.29-1.70, P = 2.44 × 10;8 ) in stage 1, stage 2, and the combined analyses, respectively. Functional annotations revealed that the minor allele T of rs3764482 was more effective than the major allele C in blocking the TGF-β signaling and inhibiting the phosphorylation of receptor-regulated SMADs (R-SMADs). In conclusion, low-frequency coding variant rs3764482 in SMAD7 is associated with CRC risk in Chinese population. The rs3764482 variant may block the TGF-β signaling via impeding the activation of downstream genes, leading to cancer cell proliferation, thus contributing to CRC pathogenesis.
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Affiliation(s)
- Jiaoyuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Li Zou
- Department of Health Care, Bao'an Maternal and Child Health Hospital, Shenzhen, China
| | - Ying Zhou
- Institute of Orthopaedics, the First Affiliated Hospital of Chinese PLA General Hospial, Beijing, China
| | - Lu Li
- Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Yi Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jiang Chang
- Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Jing Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
| | - Xiaobo Zhou
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, Massachusetts
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Environment and Health, Tongji Medical College, Huazhong University of Science and Technology, Ministry of Education & Ministry of Environmental Protection, Wuhan, China
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34
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Common risk variants for colorectal cancer: an evaluation of associations with age at cancer onset. Sci Rep 2017; 7:40644. [PMID: 28084440 PMCID: PMC5233996 DOI: 10.1038/srep40644] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/09/2016] [Indexed: 12/18/2022] Open
Abstract
Common genetic risk variants for colorectal cancer (CRC) have been identified at approximately 40 loci by genome-wide association studies (GWAS). We investigated the association of these risk variants by age at onset of CRC using case-only and case-control analysis. A total of 1,962 CRC cases and 2,668 controls from two independent case-control studies conducted by Korea’s National Cancer Center were included in this study. We genotyped 33 GWAS-identified single-nucleotide polymorphisms (SNPs) associated with CRC risk. The risk allele in SNP rs704017, located at 10q22.3 in the ZMIZ1-AS1 gene, was consistently less frequent among CRC patients aged <50 years than among CRC patients aged ≥50 years in the case-only analysis (odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.66–0.92, P = 2.7 × 10−3, in an additive model), although this did not surpass the threshold for multiple testing. The direction of associations between rs704017 and CRC risk differed by age group in the combined case-control analysis (<50 years: OR = 0.77, 95% CI = 0.60–0.98, P = 0.03 and ≥50 years: OR = 1.13, 95% CI = 0.98–1.29, P = 0.09, in a dominant model); the p-values for heterogeneity (Pheterogeneity = 7.5 × 10−3) and for interaction were statistically significant (Pinteraction = 7.8 × 10−3, in the dominant model). Our results suggest that the CRC susceptibility SNP rs704017 has a hereditary effect on onset age of CRC.
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Hahn MM, de Voer RM, Hoogerbrugge N, Ligtenberg MJL, Kuiper RP, van Kessel AG. 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] [MESH Headings] [Grants] [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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Affiliation(s)
- M M Hahn
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R M de Voer
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - M J L Ligtenberg
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R P Kuiper
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - A Geurts van Kessel
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
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36
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Xu C, Zhou D, Pan F, Liu Y, Zhang D, Lin A, Miao X, Ni Y, Lv D, Zhang S, Li X, Zhu Y, Lai M. A novel variant on chromosome 6p21.1 is associated with the risk of developing colorectal cancer: a two-stage case-control study in Han Chinese. BMC Cancer 2016; 16:807. [PMID: 27756247 PMCID: PMC5069896 DOI: 10.1186/s12885-016-2843-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/06/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genes in inflammatory pathways play a pivotal role in the development of colorectal cancer. We conducted a two-stage case-control study and aimed at screening the colorectal cancer-associated genetic variations in inflammatory genes. METHODS Twenty-three candidate variants were genotyped in 952 primary colorectal cancer cases and 875 cancer-free controls from eastern China. Promising single nucleotide polymorphisms were further genotyped in 518 cases and 554 controls from middle China. Expression quantitative trait loci and differential gene expression analyses were performed for the associated gene. RESULTS rs2282151 presented consistently significant associations with the risk of colorectal cancer in both stages (odds ratio (95 % confidence interval) = 1.30 (1.16-1.46), risk allele = C, P combined = 8.9E-6). Gene expression quantitative trait loci analyzes uncovered consistent cis-regulatory signals which showed that the C allele of rs2282151 was associated with increased expression level of heat shock protein 90 alpha family class B member 1 (HSP90AB1). Then we found that the mRNA expression levels of HSP90AB1 were significantly higher in tumor tissues than normal tissues (fold-change = 1.83) in 28 pairs of colorectal tissue samples. The expression difference was consistent with data from online datasets. Additionally, we observed notable peaks of H3K27ac and H3K4me3 near the first intron of HSP90AB1 using ChIP-seq data from multiple cell lines (including HCT116). CONCLUSIONS Our findings indicate that the C allele of the novel colorectal cancer-associated variant rs2282151 is associated with increased expression levels of HSP90AB1, which is expressed higher in colorectal tumor tissues than in normal tissues.
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Affiliation(s)
- Chunxiao Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.,Department of Chronic Non-Communicable Diseases Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Dan Zhou
- Department of Pathology, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Feixia Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Yi Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Dandan Zhang
- Department of Pathology, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Aifen Lin
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Zhejiang, China.,Medical Research Center, Taizhou Hospital of Zhejiang Province, Zhejiang, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yaqin Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Duo Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Shuai Zhang
- Department of Pathology, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaobo Li
- Department of Computer Science and Technology, College of Engineering, Lishui University, Lishui, Zhejiang, China
| | - Yimin Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
| | - Maode Lai
- Department of Pathology, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, China.
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37
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Hua RX, Zhuo ZJ, Zhu J, Zhang SD, Xue WQ, Zhang JB, Xu HM, Li XZ, Zhang PF, He J, Jia WH. XPG Gene Polymorphisms Contribute to Colorectal Cancer Susceptibility: A Two-Stage Case-Control Study. J Cancer 2016; 7:1731-1739. [PMID: 27698911 PMCID: PMC5039395 DOI: 10.7150/jca.15602] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/09/2016] [Indexed: 02/07/2023] Open
Abstract
Previous studies have reported that xeroderma pigmentosum group G (XPG) gene polymorphisms may modulate colorectal cancer (CRC) susceptibility. In this study, we performed a two-stage case-control study to comprehensively investigate the associations of five polymorphisms in the XPG gene with CRC risk in 1,901 cases and 1,976 controls from Southern China, including rs2094258 C>T, rs751402 C>T, rs2296147 T>C, rs1047768 T>C and rs873601 G>A. After combining data from two stages, we found that three of the studied polymorphisms (rs2094258 C>T, rs751402 C>T, and rs873601 G>A) were significantly associated with CRC susceptibility. After adjustment for age and gender, multivariate logistic regression analysis indicated that carriers of the rs2094258 T alleles had an increased CRC risk [CT vs. CC: adjusted odds ratio (OR)=1.17, 95% confidence interval (CI)=1.01-1.36; TT vs. CC: adjusted OR=1.49, 95% CI=1.18-1.89; TT vs. CT/CC: adjusted OR=1.38, 95% CI=1.10-1.72]. Likely, rs873601 A allele also conferred increased CRC susceptibility. In contrast, a protective association was identified between rs751402 C>T polymorphism and the risk of CRC. In summary, our results indicated that these three polymorphisms were found to associate with CRC susceptibility in a Southern Chinese population.
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Affiliation(s)
- Rui-Xi Hua
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhen-Jian Zhuo
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jinhong Zhu
- Molecular Epidemiology Laboratory and Department of Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Shao-Dan Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Wen-Qiong Xue
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Jiang-Bo Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Hong-Mei Xu
- Reproductive Medical Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Guangzhou 510120, Guangdong, China
| | - Xi-Zhao Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Pei-Fen Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Jing He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wei-Hua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
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38
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Wang M, Gu D, Du M, Xu Z, Zhang S, Zhu L, Lu J, Zhang R, Xing J, Miao X, Chu H, Hu Z, Yang L, Tang C, Pan L, Du H, Zhao J, Du J, Tong N, Sun J, Shen H, Xu J, Zhang Z, Chen J. Common genetic variation in ETV6 is associated with colorectal cancer susceptibility. Nat Commun 2016; 7:11478. [PMID: 27145994 PMCID: PMC4858728 DOI: 10.1038/ncomms11478] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/31/2016] [Indexed: 01/04/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified multiple susceptibility loci for colorectal cancer, but much of heritability remains unexplained. To identify additional susceptibility loci for colorectal cancer, here we perform a GWAS in 1,023 cases and 1,306 controls and replicate the findings in seven independent samples from China, comprising 5,317 cases and 6,887 controls. We find a variant at 12p13.2 associated with colorectal cancer risk (rs2238126 in ETV6, P=2.67 × 10(-10)). We replicate this association in an additional 1,046 cases and 1,076 controls of European ancestry (P=0.034). The G allele of rs2238126 confers earlier age at onset of colorectal cancer (P=1.98 × 10(-6)) and reduces the binding affinity of transcriptional enhancer MAX. The mRNA level of ETV6 is significantly lower in colorectal tumours than in paired normal tissues. Our findings highlight the potential importance of genetic variation in ETV6 conferring susceptibility to colorectal cancer.
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Affiliation(s)
- Meilin Wang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Genetic Toxicology, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Mulong Du
- Department of Genetic Toxicology, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhi Xu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Suzhan Zhang
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Lingjun Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jiachun Lu
- Institute for Chemical Carcinogenesis, State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510182, China
| | - Rui Zhang
- Department of Colorectal Surgery, Liaoning Cancer Hospital and Institute, Shenyang 110042, China
| | - Jinliang Xing
- Department of Cell Biology and Cell Engineering Research Center, State Key Laboratory of Cancer Biology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Haiyan Chu
- Department of Genetic Toxicology, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Lei Yang
- Institute for Chemical Carcinogenesis, State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510182, China
| | - Cuiju Tang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Lei Pan
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Haina Du
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jian Zhao
- Department of Colorectal Surgery, Liaoning Cancer Hospital and Institute, Shenyang 110042, China
| | - Jiangbo Du
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Na Tong
- Department of Genetic Toxicology, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jielin Sun
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois 60201, USA
| | - Hongbing Shen
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois 60201, USA
| | - Zhengdong Zhang
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Genetic Toxicology, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
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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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Schmit SL, Schumacher FR, Edlund CK, Conti DV, Ihenacho U, Wan P, Van Den Berg D, Casey G, Fortini BK, Lenz HJ, Tusié-Luna T, Aguilar-Salinas CA, Moreno-Macías H, Huerta-Chagoya A, Ordóñez-Sánchez ML, Rodríguez-Guillén R, Cruz-Bautista I, Rodríguez-Torres M, Muñóz-Hernández LL, Arellano-Campos O, Gómez D, Alvirde U, González-Villalpando C, González-Villalpando ME, Le Marchand L, Haiman CA, Figueiredo JC. Genome-wide association study of colorectal cancer in Hispanics. Carcinogenesis 2016; 37:547-556. [PMID: 27207650 PMCID: PMC4876992 DOI: 10.1093/carcin/bgw046] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/13/2016] [Indexed: 01/01/2023] Open
Abstract
This manuscript describes the first large-scale genome-wide association study of colorectal cancer in Hispanics and Latinos. Our results demonstrate the broad replication of known susceptibility regions and the importance of fine-mapping in ethnic minority populations. Genome-wide association studies (GWAS) have identified 58 susceptibility alleles across 37 regions associated with the risk of colorectal cancer (CRC) with P < 5×10−8. Most studies have been conducted in non-Hispanic whites and East Asians; however, the generalizability of these findings and the potential for ethnic-specific risk variation in Hispanic and Latino (HL) individuals have been largely understudied. We describe the first GWAS of common genetic variation contributing to CRC risk in HL (1611 CRC cases and 4330 controls). We also examine known susceptibility alleles and implement imputation-based fine-mapping to identify potential ethnicity-specific association signals in known risk regions. We discovered 17 variants across 4 independent regions that merit further investigation due to suggestive CRC associations (P < 1×10−6) at 1p34.3 (rs7528276; Odds Ratio (OR) = 1.86 [95% confidence interval (CI): 1.47–2.36); P = 2.5×10−7], 2q23.3 (rs1367374; OR = 1.37 (95% CI: 1.21–1.55); P = 4.0×10−7), 14q24.2 (rs143046984; OR = 1.65 (95% CI: 1.36–2.01); P = 4.1×10−7) and 16q12.2 [rs142319636; OR = 1.69 (95% CI: 1.37–2.08); P=7.8×10−7]. Among the 57 previously published CRC susceptibility alleles with minor allele frequency ≥1%, 76.5% of SNPs had a consistent direction of effect and 19 (33.3%) were nominally statistically significant (P < 0.05). Further, rs185423955 and rs60892987 were identified as novel secondary susceptibility variants at 3q26.2 (P = 5.3×10–5) and 11q12.2 (P = 6.8×10−5), respectively. Our findings demonstrate the importance of fine mapping in HL. These results are informative for variant prioritization in functional studies and future risk prediction modeling in minority populations.
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Affiliation(s)
- Stephanie L Schmit
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Christopher K Edlund
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - David V Conti
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Ugonna Ihenacho
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Peggy Wan
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Graham Casey
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Barbara K Fortini
- Department of Biology, Claremont McKenna College, Claremont, CA 91711, USA
| | - Heinz-Josef Lenz
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Sección XVI, Tlalpan, 14000 México City, México.,Instituto de Investigaciones Biomédicas, UNAM. Unidad de Biología Molecular y Medicina Genómica, UNAM/INCMNSZ, Coyoacán, 04510 México City, México
| | - Carlos A Aguilar-Salinas
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Sección XVI, Tlalpan, 14000 México City, México
| | | | - Alicia Huerta-Chagoya
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Sección XVI, Tlalpan, 14000 México City, México.,Instituto de Investigaciones Biomédicas, UNAM. Unidad de Biología Molecular y Medicina Genómica, UNAM/INCMNSZ, Coyoacán, 04510 México City, México
| | | | | | | | | | | | - Olimpia Arellano-Campos
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Sección XVI, Tlalpan, 14000 México City, México
| | - Donají Gómez
- Universidad Autónoma Metropolitana, Tlalpan 14387, México City, México
| | - Ulices Alvirde
- Universidad Autónoma Metropolitana, Tlalpan 14387, México City, México
| | - Clicerio González-Villalpando
- Unidad de Investigación en Diabetes, Instituto Nacional de Salud Pública, México City, México.,Centro de Estudios en Diabetes, 01120 México City, México and
| | | | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Christopher A Haiman
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine.,University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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Jenkins MA, Makalic E, Dowty JG, Schmidt DF, Dite GS, MacInnis RJ, Ait Ouakrim D, Clendenning M, Flander LB, Stanesby OK, Hopper JL, Win AK, Buchanan DD. Quantifying the utility of single nucleotide polymorphisms to guide colorectal cancer screening. Future Oncol 2016; 12:503-13. [PMID: 26846999 DOI: 10.2217/fon.15.303] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM To determine whether single nucleotide polymorphisms (SNPs) can be used to identify people who should be screened for colorectal cancer. METHODS We simulated one million people with and without colorectal cancer based on published SNP allele frequencies and strengths of colorectal cancer association. We estimated 5-year risks of colorectal cancer by number of risk alleles. RESULTS We identified 45 SNPs with an average 1.14-fold increase colorectal cancer risk per allele (range: 1.05-1.53). The colorectal cancer risk for people in the highest quintile of risk alleles was 1.81-times that for the average person. CONCLUSION We have quantified the extent to which known susceptibility SNPs can stratify the population into clinically useful colorectal cancer risk categories.
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Affiliation(s)
- Mark A Jenkins
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Enes Makalic
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - James G Dowty
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Gillian S Dite
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Robert J MacInnis
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia.,Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Driss Ait Ouakrim
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, School of Medicine, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Louisa B Flander
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Oliver K Stanesby
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - John L Hopper
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Aung K Win
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Daniel D Buchanan
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia.,Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, School of Medicine, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
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Yao K, Hua L, Wei L, Meng J, Hu J. Correlation Between CASC8, SMAD7 Polymorphisms and the Susceptibility to Colorectal Cancer: An Updated Meta-Analysis Based on GWAS Results. Medicine (Baltimore) 2015; 94:e1884. [PMID: 26579801 PMCID: PMC4652810 DOI: 10.1097/md.0000000000001884] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWASs) and a number of case-control studies have suggested that several single nucleotide polymorphisms (SNPs), rs7837328, rs7014346, rs6983267, rs10505477 on CASC8 gene and rs4939827, rs4464148, rs12953717 on SMAD7 gene are significantly correlated with the susceptibility to colorectal cancer (CRC). For the sake of clarifying the association, a meta-analysis was conducted and population heterogeneity was considered in the study.A total of 34 articles including 90 studies (168,471 cases and 163,223 controls) that evaluated the relationship between the CASC8, SMAD7 genes and the risk of CRC under the allelic model were reviewed. Also subgroup analysis was performed by ethnicity (Caucasian, Asian, and African) and all of the analyses were implemented in R 3.2.1 software.Pooled data from the meta-analysis revealed that the A allele of rs7837328, the A allele of rs7014346, the G allele of rs6983267, the A allele of rs10505477, the T allele of rs4939827, the T of rs4464148, and the T of rs12953717 were significantly associated with an increased risk of CRC under the allelic model. Additionally, subgroup analyses of 6 SNPs by ethnicity (rs4464148 excepted) witnessed that the A allele of rs7837328, the G allele of rs6983267, and the T of rs12953717 were notably associated with an increased risk of CRC among Caucasian and Asian. Furthermore, the A allele of rs7014346, the A allele of rs10505477, and the T allele of rs4939827 were significantly related with an elevated risk of CRC only among Caucasian.Our study suggested that for CASC8 gene, SNP of rs7837328 and rs6983267 are risk factors for CRC among both Caucasian and Asian whereas rs7014346 and rs10505477 are risky gene polymorphisms only among Caucasian. For SMAD7 gene, rs4939827 and rs4464148 are risk factors for CRC among Caucasian whereas rs12953717 could elevate the susceptibility to CRC in both Caucasian and Asian.
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Affiliation(s)
- Kunhou Yao
- From the Department of General Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China (KY, LH, JM, JH); and Department of Digestive Medicine, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China (LW)
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Abstract
Colorectal cancer (CRC) is a complex disease that develops as a consequence of both genetic and environmental risk factors. A small proportion (3-5%) of cases arise from hereditary syndromes predisposing to early onset CRC as a result of mutations in over a dozen well defined genes. In contrast, CRC is predominantly a late onset 'sporadic' disease, developing in individuals with no obvious hereditary syndrome. In recent years, genome wide association studies have discovered that over 40 genetic regions are associated with weak effects on sporadic CRC, and it has been estimated that increasingly large genome wide scans will identify many additional novel genetic regions. Subsequent experimental validations have identified the causally related variant(s) in a limited number of these genetic regions. Further biological insight could be obtained through ethnically diverse study populations, larger genetic sequencing studies and development of higher throughput functional experiments. Along with inherited variation, integration of the tumour genome may shed light on the carcinogenic processes in CRC. In addition to summarising the genetic architecture of CRC, this review discusses genetic factors that modify environmental predictors of CRC, as well as examples of how genetic insight has improved clinical surveillance, prevention and treatment strategies. In summary, substantial progress has been made in uncovering the genetic architecture of CRC, and continued research efforts are expected to identify additional genetic risk factors that further our biological understanding of this disease. Subsequently these new insights will lead to improved treatment and prevention of colorectal cancer.
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Affiliation(s)
- Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Stephanie Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Niha Zubair
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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44
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Ke J, Lou J, Chen X, Li J, Liu C, Gong Y, Yang Y, Zhu Y, Zhang Y, Gong J. Identification of a Potential Regulatory Variant for Colorectal Cancer Risk Mapping to Chromosome 5q31.1: A Post-GWAS Study. PLoS One 2015; 10:e0138478. [PMID: 26381143 PMCID: PMC4575091 DOI: 10.1371/journal.pone.0138478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/29/2015] [Indexed: 02/07/2023] Open
Abstract
Large-scale genome-wide association studies (GWAS) have established chromosome 5q31.1 as a susceptibility locus for colorectal cancer (CRC), which was still lack of causal genetic variants. We searched potentially regulatory single nucleotide polymorphisms (SNPs) in the overlap region between linkage disequilibrium (LD) block of 5q31.1 and regulatory elements predicted by histone modifications, then tested their association with CRC via a case-control study. Among three candidate common variants, we found rs17716310 conferred significantly (heterozygous model: OR = 1.273, 95% confidence interval (95%CI) = 1.016–1.595, P = 0.036) and marginally (dominant model: OR = 1.238, 95%CI = 1.000–1.532, P = 0.050) increase risk for CRC in a Chinese population including 695 cases and 709 controls. This variation was suggested to be regulatory altering the activity of enhancer that control PITX1 expression. Using epigenetic information such as chromatin immunoprecipitation-sequencing (ChIP-seq) data might help researchers to interpret the results of GWAS and locate causal variants for diseases in post-GWAS era.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueqin Chen
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Liu
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail:
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The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population. PLoS One 2015; 10:e0130377. [PMID: 26079486 PMCID: PMC4469430 DOI: 10.1371/journal.pone.0130377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Aberrant alternative splicing included alterations in components of the mRNA splicing machinery often occurred in colon cancer. However, the role of SF3A1, one key component of the mRNA splicing machinery, on colorectal cancer (CRC) risk was still not elucidated. METHOD AND FINDINGS We performed a hospital-based case-control study containing 801 CRC patients and 817 cancer-free controls to examine the association between SF3A1 polymorphisms and CRC risk in a Chinese population. Four candidate SNPs (rs10376, rs5753073, rs2839998 and rs2074733) were selected based on bioinformatics analysis and previous findings. The results showed no significant associations between these SNPs and CRC risk (P > 0.05). Besides, the stratified analysis based on the smoking and alcohol use status obtained no statistically significant results. CONCLUSION Our study was the first one to investigate the association between SF3A1 polymorphisms and CRC risk. The results suggested these four SNPs in SF3A1 were not associated with CRC risk in a Chinese population, however, further more studies are needed to confirm our findings.
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46
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Shu XO, Li H, Yang G, Gao J, Cai H, Takata Y, Zheng W, Xiang YB. Cohort Profile: The Shanghai Men's Health Study. Int J Epidemiol 2015; 44:810-8. [PMID: 25733578 DOI: 10.1093/ije/dyv013] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2015] [Indexed: 12/26/2022] Open
Abstract
The Shanghai Men's Health Study (SMHS) is a population-based cohort study of 61,480 men aged 40-74 years, launched in 2002 in urban Shanghai to investigate the contribution of lifestyle/environmental factors and genetic susceptibility to cancer and other non-communicable diseases (NCDs). At baseline, trained interviewers collected detailed information on personal and dietary habits, occupational/medical history and physical activity, and took anthropometric measurements (response rate: 74%). Blood, urine and DNA were collected from 75%, 89% and 89% of participants, respectively. The cohort has been followed up through a combination of in-person surveys every 3-4 years and annual record linkage with cancer and vital statistics registries. Response rates for in-person follow-up surveys were over 91% and coverage for mortality nearly 100%. SMHS participants have a high smoking rate (58.6%) and moderate alcohol-drinking rate (29.3%), but low obesity rate (2.6%). They have a low calorie intake from fat (16.2% of total calorie intake) and protein (16.4%), high calorie intake from carbohydrates (67.4%), and high intake of soy food, cruciferous vegetables and fish (156.5, 110.6 and 51.7 g/day, respectively). With its unique exposure pattern and wealth of data and biological samples, the SMHS is well positioned for long-term research into NCD aetiology and prognosis. Information about accessing the SMHS resources can be found at: http://www.mc.vanderbilt.edu/swhs-smhs/.
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Affiliation(s)
- Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, USA and
| | - Honglan Li
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gong Yang
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, USA and
| | - Jing Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hui Cai
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, USA and
| | - Yumie Takata
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, USA and
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, USA and
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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47
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Das S, Martinez LR, Ray S. Phospholipid remodeling and eicosanoid signaling in colon cancer cells. INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS 2014; 51:512-519. [PMID: 25823224 PMCID: PMC4460191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phospholipid remodeling and eicosanoid synthesis are central to lipid-based inflammatory reactions. Studies have revealed that membrane phospholipid remodeling by fatty acids through deacylation/reacylation reactions increases the risk of colorectal cancers (CRC) by allowing the cells to produce excess inflammatory eicosanoids, such as prostaglandins, thromboxanes and leukotrienes. Over the years, efforts have been made to understand the lipid remodeling pathways and to design anti-cancer drugs targeting the enzymes of eicosanoid biosynthesis. Here, we discuss the recent progress in phospholipid remodeling and eicosanoid biosynthesis in CRC.
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Affiliation(s)
- Siddhartha Das
- Infectious Disease and Immunology Cluster, the Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968-0519, USA
| | - Leobarda Robles Martinez
- Infectious Disease and Immunology Cluster, the Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968-0519, USA
| | - Suparna Ray
- Department of Biology, University of Erlangen-Nüremberg, Erlangen, Germany
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48
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Sherman SK, Maxwell JE, Qian Q, Bellizzi AM, Braun TA, Iannettoni MD, Darbro BW, Howe JR. Esophageal cancer in a family with hamartomatous tumors and germline PTEN frameshift and SMAD7 missense mutations. Cancer Genet 2014; 208:41-6. [PMID: 25554686 DOI: 10.1016/j.cancergen.2014.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 10/29/2014] [Accepted: 11/02/2014] [Indexed: 12/26/2022]
Abstract
Germline mutations in the PTEN tumor-suppressor gene cause autosomal-dominant conditions such as Cowden and Bannayan-Riley-Ruvalcaba syndromes with variable presentations, including hamartomatous gastrointestinal tumors, dermatologic abnormalities, neurologic symptoms, and elevated cancer risk. We describe a father and son with extensive hamartomatous gastrointestinal polyposis who both developed early-onset esophageal cancer. Exome sequencing identified a novel germline PTEN frameshift mutation (c.568_569insC, p.V191Sfs*11). In addition, a missense mutation of SMAD7 (c.115G>A, p.G39R) with an allele frequency of 0.3% in the Exome Variant Server was detected in both affected individuals. Fluorescence in situ hybridization for PTEN in the resected esophageal cancer specimen demonstrated no PTEN copy loss in malignant cells; however, results of an immunohistochemical analysis demonstrated a loss of PTEN protein expression. While the risks of many cancers are elevated in the PTEN hamartoma tumor syndromes, association between esophageal adenocarcinoma and these syndromes has not been previously reported. Esophageal adenocarcinoma and extensive polyposis/ganglioneuromatosis could represent less common features of these syndromes, potentially correlating with this novel PTEN frameshift and early protein termination genotype. Alternatively, because simultaneous disruption of both the PTEN and TGF-β/SMAD4 pathways is associated with development of esophageal cancer in a mouse model and because SMAD4 mutations cause gastrointestinal hamartomas in juvenile polyposis syndrome, the SMAD7 mutation may represent an additional modifier of these individuals' PTEN-mutant phenotype.
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Affiliation(s)
- Scott K Sherman
- Department of General Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Jessica E Maxwell
- Department of General Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Qining Qian
- Department of Cytogenetics/Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Terry A Braun
- Department of Ophthalmology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Mark D Iannettoni
- Department of Thoracic Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Benjamin W Darbro
- Department of Cytogenetics/Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - James R Howe
- Department of General Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
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Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. Nat Genet 2014; 46:533-42. [PMID: 24836286 PMCID: PMC4068797 DOI: 10.1038/ng.2985] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/21/2014] [Indexed: 12/15/2022]
Abstract
Known genetic loci explain only a small proportion of the familial relative risk of colorectal cancer (CRC). We conducted a genome-wide association study of CRC in East Asians with 14,963 cases and 31,945 controls and identified 6 new loci associated with CRC risk (P = 3.42 × 10(-8) to 9.22 × 10(-21)) at 10q22.3, 10q25.2, 11q12.2, 12p13.31, 17p13.3 and 19q13.2. Two of these loci map to genes (TCF7L2 and TGFB1) with established roles in colorectal tumorigenesis. Four other loci are located in or near genes involved in transcriptional regulation (ZMIZ1), genome maintenance (FEN1), fatty acid metabolism (FADS1 and FADS2), cancer cell motility and metastasis (CD9), and cell growth and differentiation (NXN). We also found suggestive evidence for three additional loci associated with CRC risk near genome-wide significance at 8q24.11, 10q21.1 and 10q24.2. Furthermore, we replicated 22 previously reported CRC-associated loci. Our study provides insights into the genetic basis of CRC and suggests the involvement of new biological pathways.
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