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Szuman M, Kaczmarek-Ryś M, Hryhorowicz S, Kryszczyńska A, Grot N, Pławski A. Low-Penetrance Susceptibility Variants in Colorectal Cancer-Current Outlook in the Field. Int J Mol Sci 2024; 25:8338. [PMID: 39125905 PMCID: PMC11313073 DOI: 10.3390/ijms25158338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/16/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent and mortality-causing neoplasia, with various distributions between populations. Strong hereditary predispositions are the causatives of a small percentage of CRC, and most cases have no transparent genetic background. This is a vast arena for exploring cancer low-susceptibility genetic variants. Nonetheless, the research that has been conducted to date has failed to deliver consistent conclusions and often features conflicting messages, causing chaos in this field. Therefore, we decided to organize the existing knowledge on this topic. We screened the PubMed and Google Scholar databases. We drew up markers by gene locus gathered by hallmark: oncogenes, tumor suppressor genes, genes involved in DNA damage repair, genes involved in metabolic pathways, genes involved in methylation, genes that modify the colonic microenvironment, and genes involved in the immune response. Low-penetration genetic variants increasing the risk of cancer are often population-specific, hence the urgent need for large-scale testing. Such endeavors can be successful only when financial decision-makers are united with social educators, medical specialists, genetic consultants, and the scientific community. Countries' policies should prioritize research on this subject regardless of cost because it is the best investment. In this review, we listed potential low-penetrance CRC susceptibility alleles whose role remains to be established.
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Affiliation(s)
- Marcin Szuman
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (M.S.); (M.K.-R.); (S.H.); (A.K.); (N.G.)
| | - Marta Kaczmarek-Ryś
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (M.S.); (M.K.-R.); (S.H.); (A.K.); (N.G.)
- University Clinical Hospital, Przybyszewskiego 49, 60-355 Poznań, Poland
| | - Szymon Hryhorowicz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (M.S.); (M.K.-R.); (S.H.); (A.K.); (N.G.)
| | - Alicja Kryszczyńska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (M.S.); (M.K.-R.); (S.H.); (A.K.); (N.G.)
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (M.S.); (M.K.-R.); (S.H.); (A.K.); (N.G.)
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (M.S.); (M.K.-R.); (S.H.); (A.K.); (N.G.)
- Department of General and Endocrine Surgery and Gastroenterological Oncology, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznań, Poland
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Ye J, Mu YY, Wang J, He XF. Individual effects of GSTM1 and GSTT1 polymorphisms on cervical or ovarian cancer risk: An updated meta-analysis. Front Genet 2023; 13:1074570. [PMID: 36712849 PMCID: PMC9879013 DOI: 10.3389/fgene.2022.1074570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Background: Studies have shown that glutathione S-transferase M1 (GSTM1) and. glutathione S-transferase T1 (GSTT1) null genotype may increase the risk of cervical cancer (CC) or ovarian cancer (OC), however, the results of published original studies and meta-analyses are inconsistent. Objectives: To investigate the association between GSTM1 present/null and GSTT1 present/null polymorphisms, with the risk of cervical cancer or ovarian cancer. Methods: The odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the association between GSTM1 present/null and GSTT1 present/null polymorphisms and the risk of cervical cancer or ovarian cancer. To assess the confidence of statistically significant associations, we applied false positive reporting probability (FPRP) and bayesian false discovery probability (BFDP) tests. Results: Overall analysis showed that GSTM1 null was associated with an increased risk of cervical cancer, and subgroup analysis showed a significant increase in cervical cancer risk in Indian and Chinese populations; GSTT1 was not found null genotype are significantly associated with cervical cancer. Overall analysis showed that GSTM1 and GSTT1 null were not associated with the risk of ovarian cancer, subgroup analysis showed that GSTM1 null was associated with an increased risk of OC in East Asia, and GSTT1 null was associated with an increased risk of OC in South America. However, when we used false positive reporting probability and bayesian false discovery probability to verify the confidence of a significant association, all positive results showed "low confidence" (FPRP > .2, BFDP > .8). Conclusion: Overall, this study strongly suggests that all positive results should be interpreted with caution and are likely a result of missing plausibility rather than a true association.
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Affiliation(s)
- Jing Ye
- The First People's Hospital of Bijie, Bijie, Guizhou, China
| | - Yi-Yang Mu
- Orthopedics, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Jiong Wang
- Department of Gynecology, Heji Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi
| | - Xiao-Feng He
- Institute of Evidence-based medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi,*Correspondence: Xiao-Feng He,
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Liu LS, Wang D, Tang R, Wang Q, Zheng L, Wei J, Li Y, He XF. Individual and combined effects of the GSTM1, GSTT1, and GSTP1 polymorphisms on type 2 diabetes mellitus risk: A systematic review and meta-analysis. Front Genet 2022; 13:959291. [PMID: 36419826 PMCID: PMC9676647 DOI: 10.3389/fgene.2022.959291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/14/2022] [Indexed: 10/13/2023] Open
Abstract
Backgrounds: Compared with previously published meta-analyses, this is the first study to investigate the combined effects of glutathione-S-transferase polymorphisms (GSTM1, GSTT1 and GSTP1 IIe105Val) and type 2 diabetes mellitus (T2DM) risk; moreover, the credibility of statistically significant associations was assessed; furthermore, many new original studies were published. Objectives: To determine the relationship between GSTM1, GSTT1, and GSTP1 polymorphisms with T2DM risk. Methods: PubMed, Embase, Wanfang, and China National Knowledge Infrastructure Databases were searched. We quantify the relationship using crude odds ratios and their 95% confidence intervals Moreover, the Venice criteria, false-positive report probability (FPRP), and Bayesian false discovery probability (BFDP) were used to validate the significance of the results. Results: Overall, significantly increased T2DM risk was found between individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on T2DM risk, but, combined effects of the GSTT1 and GSTP1 polymorphisms was not statistically significant. GSTT1 gene polymorphism significantly increases the risk of T2DM complications, while GSTM1 and GSTP1 polymorphisms had no statistical significance. The GSTM1 null genotype was linked to a particularly increased risk of T2DM in Caucasians; the GSTT1 null genotype was connected to a significantly higher risk of T2DM in Asians and Indians; and the GSTP1 IIe105Val polymorphism was related to a substantially increased T2DM risk in Indians. Moreover, the GSTM1 and GSTT1 double null genotype was associated with substantially increased T2DM risk in Caucasians and Indians; the combined effects of GSTM1 and GSTP1 polymorphisms was associated with higher T2DM risk in Caucasians. However, all significant results were false when the Venice criteria, FPRP, and BFDP test were used (any FPRP >0.2 and BFDP value >0.8). Conclusion: The current analysis strongly suggests that the individual and combined effects of GSTM1, GSTT1 and GSTP1 polymorphisms might not be connected with elevated T2DM risk.
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Affiliation(s)
| | - Di Wang
- Changzhi Medical College, Changzhi, Shanxi, China
| | - Ru Tang
- Changzhi Medical College, Changzhi, Shanxi, China
| | - Qi Wang
- Changzhi Medical College, Changzhi, Shanxi, China
| | - Lu Zheng
- Department of Endocrinology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Jian Wei
- Department of Endocrinology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Yan Li
- Department of Endocrinology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Xiao-feng He
- Department of Epidemiology, School of Public Health to Southern Medical University, Guangzhou, Guangdong, China
- Institute of Evidence-Based Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
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Zhao Y, Wang D, Zhang CY, Liu YJ, Wang XH, Shi MY, Wang W, Shen XL, He XF. Individual and combined effects of the GSTM1, GSTT1, and GSTP1 polymorphisms on leukemia risk: An updated meta-analysis. Front Genet 2022; 13:976673. [DOI: 10.3389/fgene.2022.976673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Several meta-analyses have analyzed the association of GSTM1 present/null, GSTT1 present/null, and GSTP1 IIe105Val polymorphisms with leukemia risk. However, the results of these meta-analyses have been conflicting. Moreover, they did not evaluate the combined effects of the three aforementioned gene polymorphisms. Furthermore, they did not appraise the credibility of the positive results. Finally, many new studies have been published. Therefore, an updated meta-analysis was conducted.Objectives: To further explore the relationship of the three aforementioned gene polymorphisms with leukemia risk.Methods: The crude odds ratios (ORs) and 95% confidence intervals (CIs) were applied to evaluate the association of the individual and combined effects of the three aforementioned genes. Moreover, the false-positive report probability (FPRP) and Bayesian false discovery probability (BFDP) were applied to verify the credibility of these statistically significant associations.Results: Overall, the individual GSTM1, GSTT1, and GSTP1 IIe105Val polymorphisms added leukemia risk. On combining GSTM1 and GSTT1, GSTM1 and GSTP1, and GSTT1 and GSTP1 polymorphisms, positive results were also observed. However, no significant association was observed between the combined effects of these three polymorphisms with leukemia risk in the overall analysis. Moreover, when only selecting Hardy–Weinberg equilibrium (HWE) and medium- and high-quality studies, we came to similar results. However, when the FPRP and BFDP values were applied to evaluate the credibility of positive results, the significant association was only observed for the GSTT1 null genotype with leukemia risk in Asians (BFDP = 0.367, FPRP = 0.009).Conclusion: This study strongly suggests a significant increase in the risk of leukemia in Asians for the GSTT1 null genotype.
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Cheng TYD, Ilozumba MN, Balavarca Y, Neuhouser ML, Miller JW, Beresford SAA, Zheng Y, Song X, Duggan DJ, Toriola AT, Bailey LB, Green R, Caudill MA, Ulrich CM. Associations between Genetic Variants and Blood Biomarkers of One-Carbon Metabolism in Postmenopausal Women from the Women's Health Initiative Observational Study. J Nutr 2022; 152:1099-1106. [PMID: 34967850 PMCID: PMC8971010 DOI: 10.1093/jn/nxab444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 12/24/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genetic variation in one-carbon metabolism may affect nutrient concentrations and biological functions. However, data on genetic variants associated with blood biomarkers of one-carbon metabolism in US postmenopausal women are limited, and whether these associations were affected by the nationwide folic acid (FA) fortification program is unclear. OBJECTIVES We investigated associations between genetic variants and biomarkers of one-carbon metabolism using data from the Women's Health Initiative Observational Study. METHODS In 1573 non-Hispanic White (NHW) and 282 Black/African American, American Indian/Alaska Native, Asian/Pacific Islander, and Hispanic/Latino women aged 50-79 y, 288 nonsynonymous and tagging single-nucleotide variants (SNVs) were genotyped. RBC folate, plasma folate, pyridoxal-5'-phosphate (PLP), vitamin B-12, homocysteine, and cysteine concentrations were determined in 12-h fasting blood. Multivariable linear regression tested associations per variant allele and for an aggregated genetic risk score. Effect modifications before, during, and after nationwide FA fortification were examined. RESULTS After correction for multiple comparisons, among NHW women, 5,10-methylenetetrahydrofolate reductase (MTHFR) rs1801133 (677C→T) variant T was associated with lower plasma folate (-13.0%; 95% CI: -17.3%, -8.6%) and higher plasma homocysteine (3.5%; 95% CI: 1.7%, 5.3%) concentrations. Other associations for nonsynonymous SNVs included DNMT3A rs11695471 (T→A) with plasma PLP; EHMT2 rs535586 (G→A), TCN2 rs1131603 (L349S A→G), and TCN2 rs35838082 (R188W G→A) with plasma vitamin B-12; CBS rs2851391 (G→A) with plasma homocysteine; and MTHFD1 rs2236224 (G→A) and rs2236225 (R653Q G→A) with plasma cysteine. The influence of FA fortification on the associations was limited. Highest compared with lowest quartiles of aggregated genetic risk scores from SNVs in MTHFR and MTRR were associated with 14.8% to 18.9% lower RBC folate concentrations. Gene-biomarker associations were similar in women of other races/ethnicities. CONCLUSIONS Our findings on genetic variants associated with several one-carbon metabolism biomarkers may help elucidate mechanisms of maintaining B vitamin status in postmenopausal women.
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Affiliation(s)
| | | | - Yesilda Balavarca
- Department of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Marian L Neuhouser
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Joshua W Miller
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Shirley A A Beresford
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Yingye Zheng
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xiaoling Song
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David J Duggan
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Adetunji T Toriola
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Lynn B Bailey
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Ralph Green
- Department of Pathology and Laboratory Medicine, University of California Davis, Davis, CA, USA
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
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Zhang WP, Yang C, Xu LJ, Wang W, Song L, He XF. Individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on lung cancer risk: A meta-analysis and re-analysis of systematic meta-analyses. Medicine (Baltimore) 2021; 100:e26104. [PMID: 34190143 PMCID: PMC8257913 DOI: 10.1097/md.0000000000026104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/12/2020] [Indexed: 01/04/2023] Open
Abstract
Thirty-five previous meta-analyses have been reported on the individual glutathione S-transferase M1 (GSTM1) present/null, glutathione S-transferase T1 (GSTT1) present/null, and glutathione S-transferase P1 (GSTP1) IIe105Val polymorphisms with lung cancer (LC) risk. However, they did not appraise the credibility and explore the combined effects between the 3 genes and LC risk.We performed a meta-analysis and re-analysis of systematic previous meta-analyses to solve the above problems.Meta-analyses of Observational Studies in Epidemiology guidelines were used. Moreover, we employed false-positive report probability (FPRP), Bayesian false discovery probability (BFDP), and the Venice criteria to verify the credibility of current and previous meta-analyses.Significantly increased LC risk was considered as "highly credible" or "positive" for GSTM1 null genotype in Japanese (odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.17-1.44, I2 = 0.0%, statistical power = 0.997, FPRP = 0.008, BFDP = 0.037, and Venice criteria: AAB), for GSTT1 null genotype in Asians (OR = 1.23, 95% CI = 1.12-1.36, I2 = 49.1%, statistical power = 1.000, FPRP = 0.051, BFDP = 0.771, and Venice criteria: ABB), especially Chinese populations (OR = 1.31, 95% CI = 1.16-1.49, I2 = 48.9%, Statistical power = 0.980, FPRP = 0.039, BFDP = 0.673, and Venice criteria: ABB), and for GSTP1 IIe105Val polymorphism in Asians (Val vs IIe: OR = 1.28, 95% CI = 1.17-1.42, I2 = 30.3%, statistical power = 0.999, FPRP = 0.003, BFDP = 0.183, and Venice criteria: ABB). Significantly increased lung adenocarcinoma (AC) risk was also considered as "highly credible" or "positive" in Asians for the GSTM1 (OR = 1.35, 95% CI = 1.22-1.48, I2 = 25.5%, statistical power = 0.988, FPRP < 0.001, BFDP < 0.001, and Venice criteria: ABB) and GSTT1 (OR = 1.36, 95% CI = 1.17-1.58, I2 = 30.2%, statistical power = 0.900, FPRP = 0.061, BFDP = 0.727, and Venice criteria: ABB) null genotype.This study indicates that GSTM1 null genotype is associated with increased LC risk in Japanese and lung AC risk in Asians; GSTT1 null genotype is associated with increased LC risk in Chinese, and GSTP1 IIe105Val polymorphism is associated with increased LC risk in Asians.
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Affiliation(s)
- Wen-Ping Zhang
- Department of Cardiothoracic Surgery, Heping Hospital Affiliated to Changzhi Medical College
| | - Chen Yang
- Teaching Reform Class of 2016 of the First Clinical College, Changzhi Medical College, Shanxi, Changzhi City
| | - Ling-Jun Xu
- Department of Pain Management, the First Affiliated Hospital, Jinan University, Guangzhou City
| | - Wei Wang
- Beijing Zhendong Guangming Pharmaceutical Research Institute Co Ltd, Beijing City
| | | | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi City, PR China
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Nam SW, Lee KS, Yang JW, Ko Y, Eisenhut M, Lee KH, Shin JI, Kronbichler A. Understanding the genetics of systemic lupus erythematosus using Bayesian statistics and gene network analysis. Clin Exp Pediatr 2021; 64:208-222. [PMID: 32683804 PMCID: PMC8103040 DOI: 10.3345/cep.2020.00633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
The publication of genetic epidemiology meta-analyses has increased rapidly, but it has been suggested that many of the statistically significant results are false positive. In addition, most such meta-analyses have been redundant, duplicate, and erroneous, leading to research waste. In addition, since most claimed candidate gene associations were false-positives, correctly interpreting the published results is important. In this review, we emphasize the importance of interpreting the results of genetic epidemiology meta-analyses using Bayesian statistics and gene network analysis, which could be applied in other diseases.
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Affiliation(s)
- Seoung Wan Nam
- Department of Rheumatology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Kwang Seob Lee
- Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Won Yang
- Department of Nephrology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Korea
| | - Michael Eisenhut
- Department of Pediatrics, Luton & Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
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Association between the combined effects of GSTM1 present/null and CYP1A1 MspI polymorphisms with lung cancer risk: an updated meta-analysis. Biosci Rep 2021; 40:226457. [PMID: 32945337 PMCID: PMC7533282 DOI: 10.1042/bsr20202275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Many studies have been performed to explore the combined effects of glutathione-S-transferase M1 (GSTM1) present/null and cytochrome P4501A1 (CYP1A1) MspI polymorphisms with lung cancer (LC) risk, but the results are contradictory. Two previous meta-analyses have been reported on the issue in 2011 and 2014. However, several new articles since then have been published. In addition, their meta-analyses did not valuate the credibility of significantly positive results. Objectives: We performed an updated meta-analysis to solve the controversy following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Methods: False-positive report probability (FPRP), Bayesian false discovery probability (BFDP), and the Venice criteria were used to verify the credibility of meta-analyses. Results: Twenty-three publications including 5734 LC cases and 7066 controls met the inclusion criteria in the present study. A significantly increased risk of LC was found in overall analysis, Asians and Indians. However, all positive results were considered as ‘less-credible’ when we used the Venice criteria, FPRP, and BFDP test to assess the credibility of the positive results. Conclusion: These positive findings should be interpreted with caution and results indicate that significant associations may be less-credible, there are no significantly increased LC risk between the combined effects of GSTM1 present/null and CYP1A1 MspI polymorphisms.
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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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Montazeri Z, Li X, Nyiraneza C, Ma X, Timofeeva M, Svinti V, Meng X, He Y, Bo Y, Morgan S, Castellví-Bel S, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo Á, Castells A, Bishop T, Buchanan D, Jenkins MA, Keku TO, Lindblom A, van Duijnhoven FJB, Wu A, Farrington SM, Dunlop MG, Campbell H, Theodoratou E, Zheng W, Little J. Systematic meta-analyses, field synopsis and global assessment of the evidence of genetic association studies in colorectal cancer. Gut 2020; 69:1460-1471. [PMID: 31818908 PMCID: PMC7398467 DOI: 10.1136/gutjnl-2019-319313] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To provide an understanding of the role of common genetic variations in colorectal cancer (CRC) risk, we report an updated field synopsis and comprehensive assessment of evidence to catalogue all genetic markers for CRC (CRCgene2). DESIGN We included 869 publications after parallel literature review and extracted data for 1063 polymorphisms in 303 different genes. Meta-analyses were performed for 308 single nucleotide polymorphisms (SNPs) in 158 different genes with at least three independent studies available for analysis. Scottish, Canadian and Spanish data from genome-wide association studies (GWASs) were incorporated for the meta-analyses of 132 SNPs. To assess and classify the credibility of the associations, we applied the Venice criteria and Bayesian False-Discovery Probability (BFDP). Genetic associations classified as 'positive' and 'less-credible positive' were further validated in three large GWAS consortia conducted in populations of European origin. RESULTS We initially identified 18 independent variants at 16 loci that were classified as 'positive' polymorphisms for their highly credible associations with CRC risk and 59 variants at 49 loci that were classified as 'less-credible positive' SNPs; 72.2% of the 'positive' SNPs were successfully replicated in three large GWASs and the ones that were not replicated were downgraded to 'less-credible' positive (reducing the 'positive' variants to 14 at 11 loci). For the remaining 231 variants, which were previously reported, our meta-analyses found no evidence to support their associations with CRC risk. CONCLUSION The CRCgene2 database provides an updated list of genetic variants related to CRC risk by using harmonised methods to assess their credibility.
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Affiliation(s)
- Zahra Montazeri
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Xue Li
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Christine Nyiraneza
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, Chongqing, China
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Xiangrui Meng
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Yazhou He
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Yacong Bo
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Shenzhen, Hong Kong
| | - Samuel Morgan
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Ceres Fernández-Rozadilla
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Ángel Carracedo
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Daniel Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Genetic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Anna Wu
- University of Southern California, Preventative Medicine, Los Angeles, California, USA
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Julian Little
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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11
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Miao LF, Ye XH, He XF. Individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on breast cancer risk: A meta-analysis and re-analysis of systematic meta-analyses. PLoS One 2020; 15:e0216147. [PMID: 32155154 PMCID: PMC7064184 DOI: 10.1371/journal.pone.0216147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/15/2019] [Indexed: 12/14/2022] Open
Abstract
Background Fourteen previous meta-analyses have been published to analyze the polymorphisms of individual GSTM1 present/null, GSTT1 present/null, and GSTP1 IIe105Val on breast cancer (BC) risk. However, their meta-analyses did not explore the combined effects of the three genetic polymorphisms on BC risk. In addition, they did not evaluate the credibility of statistically significant associations. Furthermore, a multitude of new articles have been published on these themes, and therefore a meta-analysis and re-analysis of systematic previous meta-analyses were performed to further explore these issues. Objectives To determine the association between the individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on breast cancer risk. Methods Crude odds ratios (ORs) and their 95% confidence intervals (CIs) were applied to estimate the association between individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on BC risk. To evaluate the credibility of statistically significant associations in the current and previous meta-analyses, we applied the the false-positive report probabilities (FPRP) test and the Venice criteria. Results 101 publications were selected to evaluate the individual and combined effects of GSTM1, GSTT1 and GSTP1 polymorphisms on BC risk. Overall, statistically significant elevated BC risk was found in any individual and combined effects of GSTM1 present/null, GSTT1 present/null, and GSTP1 IIe105Val polymorphisms. However, when we restricted studies only involving with high-quality, matching, HWE, and genotyping examination performed blindly or with quality control, significantly increased BC risk was only found in overall population for GSTM1 null genotype, among all populations, Caucasians, and postmenopausal women for the combined effects of GSTM1 and GSTT1 polymorphisms, and in overall analysis for the combined effects of GSTM1, GSTT1, and GSTP1 IIe105Val polymorphisms. Further, less-credible positive results were identified when we evaluated the credibility of positive results of the current and previous meta-analyses. Conclusions This meta-analysis indicates that the individual and combined effects of GSTM1, GSTT1 and GSTP1 polymorphisms may be not associated with increased BC risk.
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Affiliation(s)
- Li-Feng Miao
- Department of Galactophore, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, China
| | - Xiang-Hua Ye
- Department of Radiotherapy, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, China
- * E-mail:
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12
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Bissahoyo AC, Xie Y, Yang L, Pearsall RS, Lee D, Elliott RW, Demant P, McMillan L, Pardo-Manuel de Villena F, Angel JM, Threadgill DW. A New Polygenic Model for Nonfamilial Colorectal Cancer Inheritance Based on the Genetic Architecture of the Azoxymethane-Induced Mouse Model. Genetics 2020; 214:691-702. [PMID: 31879319 PMCID: PMC7054011 DOI: 10.1534/genetics.119.302833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
The azoxymethane model of colorectal cancer (CRC) was used to gain insights into the genetic heterogeneity of nonfamilial CRC. We observed significant differences in susceptibility parameters across 40 mouse inbred strains, with 6 new and 18 of 24 previously identified mouse CRC modifier alleles detected using genome-wide association analysis. Tumor incidence varied in F1 as well as intercrosses and backcrosses between resistant and susceptible strains. Analysis of inheritance patterns indicates that resistance to CRC development is inherited as a dominant characteristic genome-wide, and that susceptibility appears to occur in individuals lacking a large-effect, or sufficient numbers of small-effect, polygenic resistance alleles. Our results suggest a new polygenic model for inheritance of nonfamilial CRC, and that genetic studies in humans aimed at identifying individuals with elevated susceptibility should be pursued through the lens of absence of dominant resistance alleles rather than for the presence of susceptibility alleles.
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Affiliation(s)
- Anika C Bissahoyo
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuying Xie
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lynda Yang
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - R Scott Pearsall
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Daekee Lee
- Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760 South Korea
| | - Rosemary W Elliott
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Peter Demant
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Joe M Angel
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas 77843
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas 77843
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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13
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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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14
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Jiang D, Jin M, Ye D, Li Y, Jing F, Zhang X, Li Q, Chen K. Polymorphisms of a novel long non-coding RNA RP11-108K3.2 with colorectal cancer susceptibility and their effects on its expression. Int J Biol Markers 2019; 35:3-9. [PMID: 31789575 DOI: 10.1177/1724600819888512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND RP11-108K3.2 was recently identified as a novel long non-coding RNA (lncRNA) transcript, and several single nucleotide polymorphisms (SNPs) have been identified in its coding region. This study aimed to explore the associations of tagSNPs in RP11-108K3.2 with the risk of colorectal cancer and their effects on its expression. METHODS A total of 821 colorectal cancer cases and 857 healthy controls were enrolled into this two-stage case-control study. Demographic characteristics and lifestyle information were collected by a validated questionnaire. Six tagSNPs were genotyped by using Sequenom MassARRAY platform. A total of 71 additional colorectal cancer cases were recruited, of which the genotypes of potential polymorphisms and the RP11-108K3.2 expression levels were determined. RESULTS In the discovery set, only the rs2470151 C/T polymorphism was found to have a promising association with the risk of colorectal cancer, and this polymorphism was further replicated in the validation set with a significantly decreased risk of colorectal cancer (adjusted odds ratio 0.73; 95% confidence interval 0.55, 0.97). Combined discovery set and validation set together, this negative association was found both in the heterozygote codominant model and the dominant model. Furthermore, colorectal cancer patients carrying rs2470151 CT/TT genotypes had a marginally lower RNA expression of RP11-108K3.2 than those carrying the CC genotype. Stratified analyses showed the association between rs2470151 and the risk of colorectal cancer were influenced by family history of cancer, smoking, alcohol consumption, and tea drinking. CONCLUSIONS These findings suggest that RP11-108K3.2 rs2470151 had a significant association with the risk of colorectal cancer; this may help to predict the susceptibility of colorectal cancer in Chinese populations.
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Affiliation(s)
- Danjie Jiang
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Mingjuan Jin
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Ding Ye
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China.,Department of Epidemiology and Biostatistics, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Yingjun Li
- Department of Public Health, Hangzhou Medical School, Hangzhou, Zhejiang, China
| | - Fangyuan Jing
- Department of Public Health, Hangzhou Medical School, Hangzhou, Zhejiang, China
| | - Xiaocong Zhang
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Qilong Li
- Jiashan Institute of Cancer Prevention and Treatment, Jiaxing, Zhejiang, China
| | - Kun Chen
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China.,Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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15
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Pereira C, Areia M, Dinis-Ribeiro M. Cost-utility analysis of genetic polymorphism universal screening in colorectal cancer prevention by detection of high-risk individuals. Dig Liver Dis 2019; 51:1731-1737. [PMID: 31422007 DOI: 10.1016/j.dld.2019.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/02/2019] [Accepted: 07/19/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND In the past 15 years numerous studies have been published on the involvement of low-penetrance susceptibility genes on the risk for developing colorectal cancer (CRC). AIM To perform an economic analysis of blood genetic testing in CRC screening in a population-based nationwide setting using polymorphisms in prostaglandin E2 pathway genes as proof of concept. METHODS A cost-utility analysis was performed from a societal perspective in Portugal comparing two strategies: blood genetic testing by the age of 40 versus no genetic screening under different assumptions of the cost of genetic testing (€10 and €30) and expected risk (1.5 to 5-fold). The adopted threshold was set at €44,870 (USD 50,000). The primary outcome was the incremental cost-effectiveness ratio (ICER) for a base case scenario. RESULTS Polymorphism genotyping provided cost-utility only under the assumption of a 5-fold increased risk in the general population, providing ICERs of €44,356 and €30,389 for €30 and €10 tests, respectively. CONCLUSION Blood genetic screening for colorectal cancer has cost-utility only under specific assumptions of increased CRC risk and conservative cost estimates. Future studies should focus on defining genetic profiles because single-gene approaches are very unlikely to be cost-effective considering their modest predictive value.
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Affiliation(s)
- Carina Pereira
- CINTESIS - Centre for Health Technology and Services Research, University of Porto, Rua Dr Plácido da Costa, 4200-450, Porto, Portugal; Molecular Oncology and Viral Pathology Group, IPO-Porto Research Centre, Portuguese Oncology Institute of Porto, Rua Dr Bernardino de Almeida, 4200-072, Porto, Portugal.
| | - Miguel Areia
- CINTESIS - Centre for Health Technology and Services Research, University of Porto, Rua Dr Plácido da Costa, 4200-450, Porto, Portugal; Gastroenterology Department, Portuguese Institute of Oncology, Av. Bissaya Barreto, nº 98, 3000-075, Coimbra, Portugal
| | - Mário Dinis-Ribeiro
- CINTESIS - Centre for Health Technology and Services Research, University of Porto, Rua Dr Plácido da Costa, 4200-450, Porto, Portugal; Gastroenterology Department, Portuguese Institute of Oncology, Rua Dr Bernardino de Almeida, 4200-072, Porto, Portugal
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16
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Ankathil R, Mustapha MA, Abdul Aziz AA, Mohd Shahpudin SN, Zakaria AD, Abu Hassan MR, Musa KI. Contribution of Genetic Polymorphisms of Inflammation Response Genes on Sporadic Colorectal Cancer Predisposition Risk in Malaysian Patients - A Case Control Study. Asian Pac J Cancer Prev 2019; 20:1621-1632. [PMID: 31244280 PMCID: PMC7021613 DOI: 10.31557/apjcp.2019.20.6.1621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Indexed: 02/05/2023] Open
Abstract
AIM: To investigate the frequencies and association of polymorphic genotypes of IL-8 -251 T>A, TNF-α -308 G>A, ICAM-1 K469E, ICAM-1 R241G, IL-6 -174 G>C, and PPAR-γ 34 C>G in modulating susceptibility risk in Malaysian colorectal cancer (CRC) patients. Methods: In this case-control study, peripheral blood samples of 560 study subjects (280 CRC patients and 280 controls) were collected, DNA extracted and genotyped using PCR-RFLP and Allele Specific PCR. The association between polymorphic genotype and CRC susceptibility risk was determined using Logistic Regression analysis deriving Odds ratio (OR) and 95% CI. Results: On comparing the frequencies of genotypes of all single nucleotide polymorphisms ( SNPs ) in patients and controls, the homozygous variant genotypes IL-8 -251 AA and TNF-α -308 AA and variant A alleles were significantly higher in CRC patients. Investigation on the association of the variant alleles and genotypes singly, with susceptibility risk showed the homozygous variant A alleles and genotypes IL-8 -251 AA and TNF-α -308 AA to be at higher risk for CRC predisposition. Analysis based on age, gender and smoking habits showed that the polymorphisms IL8 -251 T>A and TNF – α 308 G>A contribute to a significantly higher risk among male and female who are more than 50 years and for smokers in this population. Conclusion: We observed an association between variant allele and genotypes of IL-8-251 T>A and TNF-α-308 G>A polymorphisms and CRC susceptibility risk in Malaysian patients. These two SNPs in inflammatory response genes which undoubtedly contribute to individual risks to CRC susceptibility may be considered as potential genetic predisposition factors for CRC in Malaysian population.
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Affiliation(s)
- Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia.
| | - Mohd Aminudin Mustapha
- Center of Pre University Study, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Ahmad Aizat Abdul Aziz
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia.
| | - Siti Nurfatimah Mohd Shahpudin
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia.
| | - Andee Dzulkarnaen Zakaria
- Department of Surgery, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | | | - Kamarul Imran Musa
- Department of Community Medicine, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
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17
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Benna C, Rajendran S, Spiro G, Tropea S, Del Fiore P, Rossi CR, Mocellin S. Associations of clock genes polymorphisms with soft tissue sarcoma susceptibility and prognosis. J Transl Med 2018; 16:338. [PMID: 30518396 PMCID: PMC6280400 DOI: 10.1186/s12967-018-1715-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/30/2018] [Indexed: 12/28/2022] Open
Abstract
Background Dysfunction of the circadian clock and polymorphisms of some circadian genes have been linked to cancer development and progression. We investigated the relationship between circadian genes germline variation and susceptibility or prognosis of patients with soft tissue sarcoma. Patients and methods We considered the 14 single nucleotide polymorphisms (SNPs) of 6 core circadian genes that have a minor allele frequency > 5% and that are known to be associated with cancer risk or prognosis. Genotyping was performed by q-PCR. Peripheral blood and clinic-pathological data were available for 162 patients with liposarcoma or leiomyosarcoma and 610 healthy donors. Associations between the selected clock genes polymorphisms and sarcoma susceptibility or prognosis were tested assuming 3 models of inheritance: additive, recessive and dominant. Subgroup analysis based on sarcoma histotype was performed under the additive genetic model. Multivariate logistic regression and multivariate Cox proportional hazard regression analyses were utilized to assess the association between SNPs with patient susceptibility and survival, respectively. Pathway variation analysis was conducted employing the Adaptive Rank Truncated Product method. Results Six out of the 14 analyzed SNPs were statistically significantly associated with susceptibility or prognosis of soft tissue sarcoma (P < 0.05). The present analysis suggested that carriers of the minor allele of the CLOCK polymorphism rs1801260 (C) or of PER2 rs934945 (T) had a reduced predisposition to sarcoma (26% and 35% respectively with the additive model) and liposarcoma (33% and 41% respectively). The minor allele (A) of NPAS2 rs895520 was associated with an increased predisposition to sarcoma of 33% and leiomyosarcoma of 44%. RORA rs339972 C allele was associated with a decreased predisposition to develop sarcoma assuming an additive model (29%) and leiomyosarcoma (36%). PER1 rs3027178 was associated with a reduced predisposition only in liposarcoma subgroup (32%). rs7602358 located upstream PER2 was significantly associated with liposarcoma survival (HR: 1.98; 95% CI 1.02–3.85; P = 0.04). Germline genetic variation in the circadian pathway was associated with the risk of developing soft tissue sarcoma (P = 0.035). Conclusions Genetic variation of circadian genes appears to play a role in the determinism of patient susceptibility and prognosis. These findings prompt further studies to fully dissect the molecular mechanisms. Electronic supplementary material The online version of this article (10.1186/s12967-018-1715-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clara Benna
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy. .,Clinica Chirurgica I, Azienda Ospedaliera Padova, Padua, Italy.
| | | | - Giovanna Spiro
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Saveria Tropea
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy.,Surgical Oncology Unit, Istituto Oncologico Veneto (IOV-IRCCS), Padua, Italy
| | - Paolo Del Fiore
- Surgical Oncology Unit, Istituto Oncologico Veneto (IOV-IRCCS), Padua, Italy
| | - Carlo Riccardo Rossi
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy.,Surgical Oncology Unit, Istituto Oncologico Veneto (IOV-IRCCS), Padua, Italy
| | - Simone Mocellin
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy.,Surgical Oncology Unit, Istituto Oncologico Veneto (IOV-IRCCS), Padua, Italy
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18
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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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Wen J, Xu Q, Yuan Y. Single nucleotide polymorphisms and sporadic colorectal cancer susceptibility: a field synopsis and meta-analysis. Cancer Cell Int 2018; 18:155. [PMID: 30337837 PMCID: PMC6180373 DOI: 10.1186/s12935-018-0656-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 01/05/2023] Open
Abstract
Background Although mounting non-hereditary colorectal cancer (NHCRC) associated single nucleotide polymorphisms (SNPs) have been observed, no field synopsis and meta-analysis has been conducted through systematically assessing cumulative evidence, during the past 5 years. Methods We retrieved the database via the PubMed, Web of Science and Embase gateways to identify publications concerning the associations between SNPs and risk of NHCRC, up to May 1st, 2017. To assess the finding credibility, cumulative evidence was graded based on the Venice criteria. Meta-analysis was also performed for three subgroups including ethnicity (Asian vs Caucasian), primary cancer site (colon vs rectum) and TNM stage (I II vs III IV). Then, we arranged those high quality SNPs into different regions according to their locations on genes to evaluate their functional roles on CRC development. Results 5114 publications were collected and 1001 of them met our inclusion criteria, which totally included 1788 SNPs in 793 genes or distinct chromosomal loci. Totally, we performed 359 primary and subgroup meta-analyses for 160 SNPs in 96 distinct genes. By utilizing the Venice criteria, we identified 15 high quality SNPs with 25 high credibility significant associations. Furthermore, we artificially divided the high quality SNPs into different groups, based on their SNP loci (exon region, intron region, promoter region, downstream region, non-coding region and intergenic region). Conclusion We have identified 15 high quality SNPs which may act as promising genetic biomarkers for clinical NHCRC susceptibility screening and explored their functional roles on the NHCRC development based on their locations on genes.
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Affiliation(s)
- Jing Wen
- 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001 Liaoning China.,2Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,3Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
| | - Qian Xu
- 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001 Liaoning China.,2Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,3Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
| | - Yuan Yuan
- 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001 Liaoning China.,2Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,3Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
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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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Xu K, Dai H, Wang S, Zhang J, Liu T. The CXCL12 rs1801157 polymorphism and risk of colorectal cancer: a meta-analysis. Onco Targets Ther 2018; 11:2445-2452. [PMID: 29760554 PMCID: PMC5937488 DOI: 10.2147/ott.s151514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background The CXCL12 rs1801157 polymorphism is putatively associated with the risk of malignancy. However, research results are inconsistent regarding particular cancers, especially colorectal cancer (CRC). Methods We conducted a meta-analysis via a comprehensive literature search of the databases PubMed and Embase. Odds ratios and their corresponding 95% confidence intervals were extracted to assess comprehensively the association between the CXCL12 rs1801157 polymorphism and the risk of CRC. Results According to the following models, the correlation between the presence of the CXCL12 rs1801157 polymorphism and the risk of CRC was not statistically significant: allelic (G cf. A), heterozygous (GG cf. GA), homozygous (GG cf. AA), dominant (GG cf. GA+AA), or recessive (AA cf. GA+GG) for pooled calculating. However, in subgroup analysis, elevated risk of CRC was found in the non-Caucasian group in four genetic models, while no connection was found in the Caucasian group. The sensitivity analysis confirmed that the result of the Caucasian group was stable and analyzed the heterogeneity of the non-Caucasian group. Conclusion This meta-analysis suggested that the CXCL12 rs1801157 polymorphism did not significantly confer a risk of CRC among Caucasians but may among non-Caucasians. These results warrant confirmation and further studies of different ethnic populations.
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Affiliation(s)
- Ke Xu
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, People's Republic of China
| | - Hong Dai
- Department of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Shaolong Wang
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, People's Republic of China
| | - Jie Zhang
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, People's Republic of China
| | - Tao Liu
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, People's Republic of China
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22
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Genetic susceptibility to bone and soft tissue sarcomas: a field synopsis and meta-analysis. Oncotarget 2018; 9:18607-18626. [PMID: 29719630 PMCID: PMC5915097 DOI: 10.18632/oncotarget.24719] [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: 01/24/2018] [Accepted: 03/07/2018] [Indexed: 12/18/2022] Open
Abstract
Background The genetic architecture of bone and soft tissue sarcomas susceptibility is yet to be elucidated. We aimed to comprehensively collect and meta-analyze the current knowledge on genetic susceptibility in these rare tumors. Methods We conducted a systematic review and meta-analysis of the evidence on the association between DNA variation and risk of developing sarcomas through searching PubMed, The Cochrane Library, Scopus and Web of Science databases. To evaluate result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Integrative analysis of genetic and eQTL (expression quantitative trait locus) data was coupled with network and pathway analysis to explore the hypothesis that specific cell functions are involved in sarcoma predisposition. Results We retrieved 90 eligible studies comprising 47,796 subjects (cases: 14,358, 30%) and investigating 1,126 polymorphisms involving 320 distinct genes. Meta-analysis identified 55 single nucleotide polymorphisms (SNPs) significantly associated with disease risk with a high (N=9), moderate (N=38) and low (N=8) level of evidence, findings being classified as noteworthy basically only when the level of evidence was high. The estimated joint population attributable risk for three independent SNPs (rs11599754 of ZNF365/EGR2, rs231775 of CTLA4, and rs454006 of PRKCG) was 37.2%. We also identified 53 SNPs significantly associated with sarcoma risk based on single studies.Pathway analysis enabled us to propose that sarcoma predisposition might be linked especially to germline variation of genes whose products are involved in the function of the DNA repair machinery. Conclusions We built the first knowledgebase on the evidence linking DNA variation to sarcomas susceptibility, which can be used to generate mechanistic hypotheses and inform future studies in this field of oncology.
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23
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Association of genetic variants in lncRNA H19 with risk of colorectal cancer in a Chinese population. Oncotarget 2018; 7:25470-7. [PMID: 27027436 PMCID: PMC5041918 DOI: 10.18632/oncotarget.8330] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/10/2016] [Indexed: 02/06/2023] Open
Abstract
Objective The long non-coding RNA (lncRNA) gene, H19, has been involving in multiple biological functions, which also plays a vital role in colorectal cancer carcinogenesis. However, the association between genetic variants in H19 and colorectal cancer susceptibility has not been reported. In this study, we aim to explore whether H19 polymorphisms are related to the susceptibility of colorectal cancer. Methods We conducted a case-control study to evaluate the association between four selected single nucleotide polymorphisms (SNPs) (rs2839698, rs3024270, rs217727, and rs2735971) in H19 and the risk of colorectal cancer in a Chinese population. Results We found that individuals with rs2839698 A allele had a significantly increased risk of colorectal cancer, compared to those carrying G allele [odds ratio (OR) = 1.20, 95% confidence interval (CI) = 1.05–1.36 in additive model]. Further stratified analyses revealed that colon tumor site, well differentiated grade and Duke's stage of C/D were significantly associated with colorectal cancer risk (P < 0.05). Additionally, bioinformatic analysis showed that rs2839698 may change the crucial folding structures and alter the target microRNAs of H19. Conclusions Our results provided the evidence that rs2839698 in H19 was associated with elevated risk of colorectal cancer, which may be a potential biomarker for predicting colorectal cancer susceptibility.
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24
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Farhana L, Banerjee HN, Verma M, Majumdar APN. Role of Microbiome in Carcinogenesis Process and Epigenetic Regulation of Colorectal Cancer. Methods Mol Biol 2018; 1856:35-55. [PMID: 30178245 DOI: 10.1007/978-1-4939-8751-1_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic changes during the development of colorectal cancer (CRC) play a significant role. Along with factors such as diet, lifestyle, and genetics, oncogenic infection, bacteria alone or whole microbiome, has been associated with this tumor type. How gut microbiome contributes to CRC pathogenesis in the host is not fully understood. Most of the epigenetic studies in CRC have been conducted in populations infected with Helicobacter pylori. In the current review, we summarize how the gut microbiota contributes in colon carcinogenesis and the potential role of epigenetic mechanism in gene regulation. We discuss microbiota-mediated initiation and progression of colon tumorigenesis and have also touched upon the role of microbial metabolites as an initiator or an inhibitor for procarcinogenic or antioncogenic activities. The hypothesis of gut microbiota associated CRC revealed the dynamic and complexity of microbial interaction in initiating the development of CRC. In the multifaceted processes of colonic carcinogenesis, gradual alteration of microbiota along with their microenvironment and the potential oncopathogenic microbes mediated modulation of cancer therapy and other factors involved in microbiome dysbiosis leading to the CRC have also been discussed. This review provides a comprehensive summary of the mechanisms of CRC development, the role of microbiome or single bacterial infection in regulating the processes of carcinogenesis, and the intervention by novel therapeutics. Epigenetic mechanism involved in CRC is also discussed.
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Affiliation(s)
- Lulu Farhana
- Veterans Affairs Medical Center, Research Service, Detroit, MI, USA
- Department of Internal Medicine, Wayne State University, Detroit, MI, USA
| | | | - Mukesh Verma
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, MD, USA
| | - Adhip P N Majumdar
- Veterans Affairs Medical Center, Research Service, Detroit, MI, USA.
- Department of Internal Medicine, Wayne State University, Detroit, MI, USA.
- Karmanos Cancer Institute, Wayne State University-School of Medicine, Detroit, MI, USA.
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25
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Benna C, Helfrich-Förster C, Rajendran S, Monticelli H, Pilati P, Nitti D, Mocellin S. Genetic variation of clock genes and cancer risk: a field synopsis and meta-analysis. Oncotarget 2017; 8:23978-23995. [PMID: 28177907 PMCID: PMC5410358 DOI: 10.18632/oncotarget.15074] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/27/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The number of studies on the association between clock genes’ polymorphisms and cancer susceptibility has increased over the last years but the results are often conflicting and no comprehensive overview and quantitative summary of the evidence in this field is available. RESULTS Literature search identified 27 eligible studies comprising 96756 subjects (cases: 38231) and investigating 687 polymorphisms involving 14 clock genes. Overall, 1025 primary and subgroup meta-analyses on 366 gene variants were performed. Study distribution by tumor was as follows: breast cancer (n=15), prostate cancer (n=3), pancreatic cancer (n=2), non-Hodgkin's lymphoma (n=2), glioma (n=1), chronic lymphocytic leukemia (n=1), colorectal cancer (n=1), non-small cell lung cancer (n=1) and ovarian cancer (n=1). We identified 10 single nucleotide polymorphisms (SNPs) significantly associated with cancer risk: NPAS2 rs10165970 (mixed and breast cancer shiftworkers), rs895520 (mixed), rs17024869 (breast) and rs7581886 (breast); CLOCK rs3749474 (breast) and rs11943456 (breast); RORA rs7164773 (breast and breast cancer postmenopausal), rs10519097 (breast); RORB rs7867494 (breast cancer postmenopausal), PER3 rs1012477 (breast cancer subgroups) and assessed the level of quality evidence to be intermediate. We also identified polymorphisms with lower quality statistically significant associations (n=30). CONCLUSIONS Our work supports the hypothesis that genetic variation of clock genes might affect cancer risk. These findings also highlight the need for more efforts in this research field in order to fully establish the contribution of clock gene variants to the risk of developing cancer. METHODS We conducted a systematic review and meta-analysis of the evidence on the association between clock genes’ germline variants and the risk of developing cancer. To assess result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Subgroup meta-analysis was also performed based on participant features and tumor type. The breast cancer subgroup was further stratified by work conditions, estrogen receptor/progesterone receptor status and menopausal status, conditions associated with the risk of breast cancer in different studies.
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Affiliation(s)
- Clara Benna
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Charlotte Helfrich-Förster
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Senthilkumar Rajendran
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | | | | | - Donato Nitti
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy.,Clinica Chirurgica I, Azienda Ospedaliera Padova, Padova, Italy
| | - Simone Mocellin
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy.,Istituto Oncologico Veneto, IOV-IRCSS, Padova, Italy
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Schubert SA, Ruano D, Elsayed FA, Boot A, Crobach S, Sarasqueta AF, Wolffenbuttel B, van der Klauw MM, Oosting J, Tops CM, van Eijk R, Vasen HFA, Vossen RHAM, Nielsen M, Castellví-Bel S, Ruiz-Ponte C, Tomlinson I, Dunlop MG, Vodicka P, Wijnen JT, Hes FJ, Morreau H, de Miranda NFCC, Sijmons RH, van Wezel T. Evidence for genetic association between chromosome 1q loci and predisposition to colorectal neoplasia. Br J Cancer 2017; 117:1215-1223. [PMID: 28742792 PMCID: PMC5589990 DOI: 10.1038/bjc.2017.240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/31/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A substantial fraction of familial colorectal cancer (CRC) and polyposis heritability remains unexplained. This study aimed to identify predisposing loci in patients with these disorders. METHODS Homozygosity mapping was performed using 222 563 SNPs in 302 index patients with various colorectal neoplasms and 3367 controls. Linkage analysis, exome and whole-genome sequencing were performed in a family affected by microsatellite stable CRCs. Candidate variants were genotyped in 10 554 cases and 21 480 controls. Gene expression was assessed at the mRNA and protein level. RESULTS Homozygosity mapping revealed a disease-associated region at 1q32.3 which was part of the linkage region 1q32.2-42.2 identified in the CRC family. This includes a region previously associated with risk of CRC. Sequencing identified the p.Asp1432Glu variant in the MIA3 gene (known as TANGO1 or TANGO) and 472 additional rare, shared variants within the linkage region. In both cases and controls the population frequency was 0.02% for this MIA3 variant. The MIA3 mutant allele showed predominant mRNA expression in normal, cancer and precancerous tissues. Furthermore, immunohistochemistry revealed increased expression of MIA3 in adenomatous tissues. CONCLUSIONS Taken together, our two independent strategies associate genetic variations in chromosome 1q loci and predisposition to familial CRC and polyps, which warrants further investigation.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Fadwa A Elsayed
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Arantza Farina Sarasqueta
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Bruce Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands
| | - Melanie M van der Klauw
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Hans FA Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Rolf HAM Vossen
- Department of Human Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia 08036, Spain
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela 15706, Spain
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, MRC Human Genetics Unit, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Pavel Vodicka
- Institute of Experimental Medicine, Institute of Biology and Medical Genetics, Prague 142 00, Czech Republic
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Noel FCC de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen 9700 RB, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
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Rey JM, Ducros V, Pujol P, Wang Q, Buisine MP, Aissaoui H, Maudelonde T, Olschwang S. Improving Mutation Screening in Patients with Colorectal Cancer Predisposition Using Next-Generation Sequencing. J Mol Diagn 2017; 19:589-601. [PMID: 28502729 DOI: 10.1016/j.jmoldx.2017.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/03/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of genetic alterations is important for family risk assessment in colorectal cancers. Next-generation sequencing (NGS) technologies provide useful tools for single-nucleotide and copy number variation (CNV) identification in many genes and samples simultaneously. Herein, we present the validation of current Multiplicom MASTR designs of mismatch repair combined to familial adenomatous polyposis genes in a single PCR reamplification test for eight DNA samples simultaneously on a MiSeq apparatus. Blood samples obtained from 224 patients were analyzed. We correctly identified the 97 mutations selected among 48 samples tested in a validation cohort. PMS2 NGS analysis of the eight positive controls identified single-nucleotide variations not detected with targeted referent methods. As NGS method could not discriminate if some of them were assigned to PMS2 or pseudogenes, only CNV analysis with multiplex ligand probe-dependent amplification confirmation was retained for clinical use. Twenty-seven new variants of unknown significance, 21 disease-causing variants, and two CNVs were detected among the 176 patient samples analyzed in diagnosis routine. MUTYH disease-causing mutations were identified in two patient samples assessed for mismatch repair testing, confirming that this method facilitates accurate and rapid individual risk assessments. In one sample, the MUTYH mutation was associated with a MSH6 disease-causing mutation, suggesting that this method is helpful to identify additional cancer risk modifiers and provides a useful tool to optimize clinical issues.
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Affiliation(s)
- Jean-Marc Rey
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France.
| | - Vincent Ducros
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Pascal Pujol
- Oncogenetic Department, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Qing Wang
- Laboratoire de Génétique Constitutionnelle des Cancers Fréquents, Léon Bérard Center, Lyon, France
| | - Marie-Pierre Buisine
- Laboratoire de Biochimie et Biologie Moléculaire, Oncologie et Génétique Moléculaire, Center de Biologie Pathologie, CHRU Lille, Lille, France
| | | | - Thierry Maudelonde
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France; Montpellier University, EA2415, Institut Universitaire de Recherche Clinique, Montpellier, France
| | - Sylviane Olschwang
- INSERM UMR_S910, Aix-Marseille University, Ramsay Générale de Santé Clairval Hospital, Marseille, France
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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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29
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Haerian MS, Haerian BS, Molanaei S, Kosari F, Sabeti S, Bidari-Zerehpoosh F, Abdolali E, Zali MR. MTHFR rs1801133 polymorphism and susceptibility to colorectal cancer in Iranian population: evidence of a case-control study and meta-analysis. Pharmacogenomics 2016; 17:1957-1965. [PMID: 27790938 DOI: 10.2217/pgs-2016-0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Several studies have investigated whether MTHFR rs1801133 polymorphism contributes to risk of colorectal cancer (CRC), however the results are inconclusive. AIM The purpose of this study was to investigate this hypothesis in a case-control study and meta-analysis in Iranian population. MATERIALS & METHODS This polymorphism was genotyped in the 2421 subjects (46% CRC patients) from Tehran. Meta-analysis was performed for determining the risk effect size of this polymorphism on CRC. RESULTS Both case-control study and meta-analysis showed no association between rs1801133 and CRC risk or its features. CONCLUSION This study failed to identify an association between the rs1801133 and susceptibility to CRC in Iranian population.
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Affiliation(s)
- Monir Sadat Haerian
- Bone and Joint Reconstruction Research Center, Shafa Yahyaeian Orthopedics Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Batoul Sadat Haerian
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Farid Kosari
- Department of Pathology, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahram Sabeti
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farahnaz Bidari-Zerehpoosh
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Abdolali
- Department of Pathology, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology & Liver Diseases Research Center (GLDRC), Shahid Beheshti University of Medical Science, Tehran, Iran
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Banday MZ, Balkhi HM, Hamid Z, Sameer AS, Chowdri NA, Haq E. Tumor necrosis factor-α (TNF-α)-308G/A promoter polymorphism in colorectal cancer in ethnic Kashmiri population - A case control study in a detailed perspective. Meta Gene 2016; 9:128-36. [PMID: 27331018 PMCID: PMC4908285 DOI: 10.1016/j.mgene.2016.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/01/2016] [Indexed: 12/31/2022] Open
Abstract
Background Inflammation constitutes one of the important components of colorectal cancer (CRC) pathogenesis. Tumor necrosis factor-α (TNF-α), a cytokine and an important inflammatory mediator plays a pivotal role in the malignant cellular proliferation, angiogenesis, tissue invasion and metastasis in CRC. The studies on association of various polymorphisms in human TNF-α gene including TNF-α-308G/A single nucleotide polymorphism (SNP) are limited, mixed and inconclusive. Materials and methods The aim of this study was to analyze the association of TNF-α-308G/A promoter SNP with colorectal cancer (CRC) susceptibility and development risk and also to evaluate the modifying effects of possible TNF-α-308G/A genotypes on different risk factors of CRC in ethnic population of Kashmir, India through a case–control setup. The genotype frequencies of TNF-α-308G/A promoter SNP were compared between 142 CRC patients and 184 individually matched healthy controls by using polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method. The associations between the TNF-α-308G/A SNP and CRC risk were examined through conditional logistic regression models adjusted for multiple possible confounding (third) variables. Further, the associations between this SNP and various clinico-pathological parameters, demographic variables and environmental factors within the case group subjects with regard to CRC risk were also evaluated. Results The association between the TNF-α-308G/A SNP and the modulation of risk of CRC was not found to be significant (p value = 0.156). The effect of less common TNF-α-308A allele on the risk of colorectal cancer was also not found to be significant (p value = 0.175). The variant genotype (AA) was nonexistent in the study population. Further, we found no significant effect modulation of CRC risk by wild and heterozygous TNF-α-308G/A SNP genotypes in presence of different possible risk factors (p > 0.05). We also found no significant association of TNF-α-308G/A SNP with the subsets of various characteristics of the case group subjects under study (p > 0.05). Conclusions This study indicates that there is no significant association between the TNF-α-308G/A promoter SNP and the risk of developing CRC in ethnic Kashmiri population. However, in order to substantiate our findings, this study needs to be replicated with bigger sample size and should involve other ethnically defined populations with high CRC risk.
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Affiliation(s)
- Mujeeb Zafar Banday
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, Kashmir, India
| | - Henah Mehraj Balkhi
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, Kashmir, India
| | - Zeenat Hamid
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, Kashmir, India
| | - Aga Syed Sameer
- Department of Basic Medical Sciences, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Nissar A. Chowdri
- Department of Surgery, Sher-I-Kashmir Institute of Medical Sciences, Soura, Srinagar, Kashmir, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, Kashmir, India
- Corresponding author.
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Agarwal R, Kumar B, Jayadev M, Raghav D, Singh A. CoReCG: a comprehensive database of genes associated with colon-rectal cancer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw059. [PMID: 27114494 PMCID: PMC4843536 DOI: 10.1093/database/baw059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 03/23/2016] [Indexed: 12/19/2022]
Abstract
Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. Database URL: lms.snu.edu.in/corecg
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Affiliation(s)
- Rahul Agarwal
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Binayak Kumar
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Msk Jayadev
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Dhwani Raghav
- Department of Health Research (Ministry of Health & Family Welfare), Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Ashutosh Singh
- Department of Life Science, Shiv Nadar University, Greater Noida, India
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Identification of Novel Candidate Genes for Early-Onset Colorectal Cancer Susceptibility. PLoS Genet 2016; 12:e1005880. [PMID: 26901136 PMCID: PMC4764646 DOI: 10.1371/journal.pgen.1005880] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Approximately 25-30% of colorectal cancer (CRC) cases are expected to result from a genetic predisposition, but in only 5-10% of these cases highly penetrant germline mutations are found. The remaining CRC heritability is still unexplained, and may be caused by a hitherto-undefined set of rare variants with a moderately penetrant risk. Here we aimed to identify novel risk factors for early-onset CRC using whole-exome sequencing, which was performed on a cohort of CRC individuals (n = 55) with a disease onset before 45 years of age. We searched for genes that were recurrently affected by rare variants (minor allele frequency ≤ 0.001) with potentially damaging effects and, subsequently, re-sequenced the candidate genes in a replication cohort of 174 early-onset or familial CRC individuals. Two functionally relevant genes with low frequency variants with potentially damaging effects, PTPN12 and LRP6, were found in at least three individuals. The protein tyrosine phosphatase PTP-PEST, encoded by PTPN12, is a regulator of cell motility and LRP6 is a component of the WNT-FZD-LRP5-LRP6 complex that triggers WNT signaling. All variants in LRP6 were identified in individuals with an extremely early-onset of the disease (≤30 years of age), and two of the three variants showed increased WNT signaling activity in vitro. In conclusion, we present PTPN12 and LRP6 as novel candidates contributing to the heterogeneous susceptibility to CRC.
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Montazeri Z, Theodoratou E, Nyiraneza C, Timofeeva M, Chen W, Svinti V, Sivakumaran S, Gresham G, Cubitt L, Carvajal-Carmona L, Bertagnolli MM, Zauber AG, Tomlinson I, Farrington SM, Dunlop MG, Campbell H, Little J. Systematic meta-analyses and field synopsis of genetic association studies in colorectal adenomas. Int J Epidemiol 2016; 45:186-205. [PMID: 26451011 PMCID: PMC5860727 DOI: 10.1093/ije/dyv185] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Low penetrance genetic variants, primarily single nucleotide polymorphisms, have substantial influence on colorectal cancer (CRC) susceptibility. Most CRCs develop from colorectal adenomas (CRA). Here we report the first comprehensive field synopsis that catalogues all genetic association studies on CRA, with a parallel online database [http://www.chs.med.ed.ac.uk/CRAgene/]. METHODS We performed a systematic review, reviewing 9750 titles, and then extracted data from 130 publications reporting on 181 polymorphisms in 74 genes. We conducted meta-analyses to derive summary effect estimates for 37 polymorphisms in 26 genes. We applied the Venice criteria and Bayesian False Discovery Probability (BFDP) to assess the levels of the credibility of associations. RESULTS We considered the association with the rs6983267 variant at 8q24 as 'highly credible', reaching genome-wide statistical significance in at least one meta-analysis model. We identified 'less credible' associations (higher heterogeneity, lower statistical power, BFDP > 0.02) with a further four variants of four independent genes: MTHFR c.677C>T p.A222V (rs1801133), TP53 c.215C>G p.R72P (rs1042522), NQO1 c.559C>T p.P187S (rs1800566), and NAT1 alleles imputed as fast acetylator genotypes. For the remaining 32 variants of 22 genes for which positive associations with CRA risk have been previously reported, the meta-analyses revealed no credible evidence to support these as true associations. CONCLUSIONS The limited number of credible associations between low penetrance genetic variants and CRA reflects the lower volume of evidence and associated lack of statistical power to detect associations of the magnitude typically observed for genetic variants and chronic diseases. The CRA gene database provides context for CRA genetic association data and will help inform future research directions.
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Affiliation(s)
- Zahra Montazeri
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada
| | - Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Christine Nyiraneza
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital, Edinburgh, UK
| | - Wanjing Chen
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital, Edinburgh, UK
| | - Shanya Sivakumaran
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Gillian Gresham
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada
| | - Laura Cubitt
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Luis Carvajal-Carmona
- Biochemistry and Molecular Medicine, Genome and Biomedical Sciences Facility, UC Davis School of Medicine, University of California Davis, Davis, CA, USA
| | | | - Ann G Zauber
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA and
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital, Edinburgh, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital, Edinburgh, UK
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK, Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital, Edinburgh, UK
| | - Julian Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada,
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Haerian BS, Haerian MS. Evaluation of association studies and meta-analyses of MTHFR gene polymorphisms in colorectal cancer. Pharmacogenomics 2016; 16:413-25. [PMID: 25823789 DOI: 10.2217/pgs.14.177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is a discrepancy between the results of 89 original studies and 15 meta-analyses investigating the association of MTHFR rs1801133 and rs1801131 polymorphisms with colorectal cancer (CRC) risk. We examined this hypothesis through meta-analyses of both loci and their diplotypes as well as evaluation of previous meta-analyses. The present meta-analysis showed that rs1801133 and rs1801131 might be CRC susceptibility variants in Americans and Australians and rs1801133 in Brazilians and Japanese. A strong linkage disequilibrium was observed between both loci and their diplotypes were associated with CRC risk. Evaluation of 15 meta-analyses showed a high discrepancy among their findings, mainly caused by population stratification of original studies and data analysis strategies in meta-analysis. Population stratification was more dominant in the studies from Australia, America and Brazil leading to false positive or negative results. In conclusion, these loci alone might modify the development of CRC in some ethnicities.
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Affiliation(s)
- Batoul Sadat Haerian
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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35
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Yang T, Chen BZ, Li DF, Wang HM, Lin XS, Wei HF, Zeng YM. Reduced NM23 Protein Level Correlates With Worse Clinicopathologic Features in Colorectal Cancers: A Meta-Analysis of Pooled Data. Medicine (Baltimore) 2016; 95:e2589. [PMID: 26825905 PMCID: PMC5291575 DOI: 10.1097/md.0000000000002589] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/04/2015] [Accepted: 12/29/2015] [Indexed: 02/05/2023] Open
Abstract
The clinical value of a prominent metastasis suppressor, nonmetastatic protein 23 (NM23), remains controversial. In this study, we examined the correlation between NM23 protein levels and the clinicopathologic features of colorectal cancers (CRC), and assessed the overall prognostic value of NM23 for CRC. Embase, PubMed, Web of Science, and other scientific literature databases were exhaustively searched to identify relevant studies published prior to June 31, 2015. The methodological qualities of selected studies were scored based on the critical appraisal skills program (CASP) criteria, as independently assessed by 2 reviewers. NM23 protein levels in tumor tissues of CRC patients were examined in relation to Dukes stage, differentiation grade, T-stage, lymph node metastasis status, and overall survival (OS). STATA software version 12.0 (Stata Corp, College Station, TX) was used for statistical analysis of data pooled from selected studies. Nineteen cohort studies met the inclusion criteria for present study and contained a combined total of 2148 study subjects. Pooled odd ratios (ORs) for NM23 expression revealed that reduced NM23 protein levels in CRC tumor tissues correlated with Dukes stage C and D (OR = 1.89, 95% CI: 1.06-3.39, P = 0.032), poor differentiation grades (OR = 1.41, 95% CI: 1.03-1.94, P = 0.032), and positive lymph node metastasis status (OR = 3.21, 95% CI: 1.95-5.29, P < 0.001). On the other hand, no such correlations were evident with T-stage T3-4 (OR = 1.56, 95% CI: 0.60-4.06, P = 0.367) or OS (OR = 0.79, 95% CI: 0.58-1.08, P = 0.138). Our analysis of pooled data found that NM23 expression is reduced in CRC tissues and low NM23 levels tightly correlate with higher Dukes stages, poorer differentiation grade, and positive lymph node metastases. However, NM23 levels did not influence the OS in CRC patients.
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Affiliation(s)
- Tian Yang
- From the Department of Gastrointestinal Surgery, The First Affiliated Hospital, Shantou University Medical College, Shantou, China
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Dai Q, Wei HL, Huang J, Zhou TJ, Chai L, Yang ZH. KRAS polymorphisms are associated with survival of CRC in Chinese population. Tumour Biol 2015; 37:4727-34. [PMID: 26515332 DOI: 10.1007/s13277-015-4314-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023] Open
Abstract
rs12245, rs12587, rs9266, rs1137282, rs61764370, and rs712 of KRAS oncogene are characterized in the 3'UTR. The study highlights the important role of these polymorphisms playing in the susceptibility, oxaliplatin-based chemotherapy sensitivity, progression, and prognosis of CRC. Improved multiplex ligation detection reaction (iMLDR) technique is used for genotyping. An unconditional logistic regression model was used to estimate the association of certain polymorphism and CRC risk. The Kaplan-Meier method, log-rank test, and Cox regression model were used to evaluate the effects of polymorphisms on survival analysis. Results demonstrated that TT genotype and T allele of rs712 were associated with the increased risk of CRC; the patients with GG genotype and G allele of rs61764370 had a shorter survival and a higher risk of relapse or metastasis of CRC. Our studies supported the conclusions that rs61764370 and rs712 polymorphisms of the KRAS are functional and it may play an important role in the development of CRC and oxaliplatin-based chemotherapy efficiency and prognosis of CRC.
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Affiliation(s)
- Qiong Dai
- Department of Human Anatomy, Luzhou Medical College, Luzhou, 646000, Sichuan, People's Republic of China
| | - Hui Lian Wei
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou, 646000, Sichuan, People's Republic of China
| | - Juan Huang
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou, 646000, Sichuan, People's Republic of China
| | - Tie Jun Zhou
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou, 646000, Sichuan, People's Republic of China
| | - Li Chai
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zhi-Hui Yang
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou, 646000, Sichuan, People's Republic of China.
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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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Zhou Q, Li K, Lin GZ, Shen JC, Dong H, Gu YT, Liu HZ. Incidence trends and age distribution of colorectal cancer by subsite in Guangzhou, 2000-2011. CHINESE JOURNAL OF CANCER 2015; 34:358-64. [PMID: 26245843 PMCID: PMC4593365 DOI: 10.1186/s40880-015-0026-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/28/2015] [Indexed: 02/07/2023]
Abstract
Introduction Colorectal cancer (CRC) is the third most common cancer in China. The incidence of CRC has been increasing in recent years. The aim of this study was to explore the incidence trends and the age distribution of CRC by subsite in Guangzhou between 2000 and 2011. Methods A total of 22,432 incident cases of CRC between 2000 and 2011 from Guangzhou Cancer Registry were identified. Crude incidence and age-standardized rates (ASRs), using the Segi’s world standard population, were calculated for CRC and CRC subsites. The incidence trend was analyzed and the annual percentage change (APC) in incidence was calculated by using JoinPoint software. Results The crude incidence increased significantly from 23.4/105 in 2000 to 37.4/105 in 2011 for males and from 20.9/105 to 30.5/105 for females. The ASRs of CRC incidence stabilized during the period of 2000–2011 for both males and females. The ages at the onset of CRC for both males and females during 2010–2011 were significantly higher compared with those during 2000–2002 (males: t = 1.95, P = 0.05; females: t = 6.03, P < 0.01). For males aged 50–64 years, the CRC incidence increased by 8.50% annually (P = 0.04) during 2000–2004 and by 1.68% annually (P = 0.03) during 2005–2011. For females aged 65 years and older, the CRC incidence increased by 5.77% annually (P = 0.03) during 2000–2004. There were no significant changes for the CRC incidences in males aged 49 and younger and 65 years and older and females aged 64 years and younger during 2000–2004, or for those in all females as well as males aged 49 years and younger and 65 years and older during 2005–2011. The percentage of colon cancer in all CRCs increased significantly for both males and females between the periods of 2000–2002 and 2010–2011. The ASRs of descending colon and sigmoid colon cancer incidences increased significantly for females during 2005–2011 (APC, 5.51% and 1.08%, respectively, both P < 0.05). Conclusions The crude incidence of CRC increased significantly between 2000 and 2011 because of the aging, whereas the ASRs kept stable. The percentage of colon cancer in all CRCs increased significantly. Further surveillance, research, and intervention are needed to identify the causes of these changes and to reduce the incidence and mortality of CRC.
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Affiliation(s)
- Qin Zhou
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
| | - Ke Li
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
| | - Guo-Zhen Lin
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
| | - Ji-Chuan Shen
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
| | - Hang Dong
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
| | - Yu-Ting Gu
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
| | - Hua-Zhang Liu
- Department of Biostatistics and Cancer Registration, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510060, P.R. China.
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Mocellin S, Verdi D, Pooley KA, Nitti D. Genetic variation and gastric cancer risk: a field synopsis and meta-analysis. Gut 2015; 64:1209-19. [PMID: 25731870 DOI: 10.1136/gutjnl-2015-309168] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/06/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND Data on genetic susceptibility to sporadic gastric carcinoma have been published at a growing pace, but to date no comprehensive overview and quantitative summary has been available. METHODS We conducted a systematic review and meta-analysis of the evidence on the association between DNA variation and risk of developing stomach cancer. To assess result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Meta-analysis was also conducted for subgroups, which were defined by ethnicity (Asian vs Caucasian), tumour histology (intestinal vs diffuse), tumour site (cardia vs non-cardia) and Helicobacter pylori infection status (positive vs negative). RESULTS Literature search identified 824 eligible studies comprising 2 530 706 subjects (cases: 261 386 (10.3%)) and investigating 2841 polymorphisms involving 952 distinct genes. Overall, we performed 456 primary and subgroup meta-analyses on 156 variants involving 101 genes. We identified 11 variants significantly associated with disease risk and assessed to have a high level of summary evidence: MUC1 rs2070803 at 1q22 (diffuse carcinoma subgroup), MTX1 rs2075570 at 1q22 (diffuse), PSCA rs2294008 at 8q24.2 (non-cardia), PRKAA1 rs13361707 5p13 (non-cardia), PLCE1 rs2274223 10q23 (cardia), TGFBR2 rs3087465 3p22 (Asian), PKLR rs3762272 1q22 (diffuse), PSCA rs2976392 (intestinal), GSTP1 rs1695 11q13 (Asian), CASP8 rs3834129 2q33 (mixed) and TNF rs1799724 6p21.3 (mixed), with the first nine variants characterised by a low FPRP. We also identified polymorphisms with lower quality significant associations (n=110). CONCLUSIONS We have identified several high-quality biomarkers of gastric cancer susceptibility. These data will form the backbone of an annually updated online resource that will be integral to the study of gastric carcinoma genetics and may inform future screening programmes.
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Affiliation(s)
- Simone Mocellin
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Daunia Verdi
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Karen A Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Donato Nitti
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
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Erstad DJ, Tumusiime G, Cusack JC. Prognostic and Predictive Biomarkers in Colorectal Cancer: Implications for the Clinical Surgeon. Ann Surg Oncol 2015. [DOI: 10.1245/s10434-015-4706-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Chen P, Wang BL, Pan BS, Guo W. MiR-1297 regulates the growth, migration and invasion of colorectal cancer cells by targeting cyclo-oxygenase-2. Asian Pac J Cancer Prev 2015; 15:9185-90. [PMID: 25422199 DOI: 10.7314/apjcp.2014.15.21.9185] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cyclo-oxygenase-2(Cox-2), a key regulator of inflammation-producing prostaglandins, promotes cell proliferation and growth. Therefore, a better understanding of the regulatory mechanisms of Cox-2 could lead to novel targeted cancer therapies. MicroRNAs are strongly implicated in colorectal cancer but their specific roles and functions have yet to be fully elucidated. MiR-1297 plays an important role in lung adenocarcinoma and laryngeal squamous cell carcinoma, but its significance in colorectal cancer (CRC) has yet to be reported. In our present study, we found miR-1297 to be down regulated in both CRC-derived cell lines and clinical CRC samples, when compared with normal tissues. Furthermore, miR-1297 could inhibit human colorectal cancer LOVO and HCT116 cell proliferation, migration, and invasion in vitro and tumorigenesis in vivo by targeting Cox-2. Moreover, miR-1297 directly binds to the 3`-UTR of Cox-2, and the expression level was drastically decreased in LOVO and HCT116 cells following overexpression of miR-1297. Additionally, Cox-2 expression levels are inversely correlated with miR-1297 expression in human colorectal cancer xenograft tissues. These results imply that miR-1297 has the potential to provide a new approach to colorectal cancer therapy by directly inhibiting Cox-2 expression.
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Affiliation(s)
- Pu Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China E-mail :
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Identification of a DNA methylation signature to predict disease-free survival in locally advanced rectal cancer. Oncotarget 2015; 5:8123-35. [PMID: 25261372 PMCID: PMC4226671 DOI: 10.18632/oncotarget.2347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In locally advanced rectal cancer a preoperative predictive biomarker is necessary to adjust treatment specifically for those patients expected to suffer relapse. We applied whole genome methylation CpG island array analyses to an initial set of patients (n=11) to identify differentially methylated regions (DMRs) that separate a good from a bad prognosis group. Using a quantitative high-resolution approach, candidate DMRs were first validated in a set of 61 patients (test set) and then confirmed DMRs were further validated in additional independent patient cohorts (n=71, n=42). We identified twenty highly discriminative DMRs and validated them in the test set using the MassARRAY technique. Ten DMRs could be confirmed which allowed separation into prognosis groups (p=0.0207, HR=4.09). The classifier was validated in two additional cohorts (n=71, p=0.0345, HR=3.57 and n=42, p=0.0113, HR=3.78). Interestingly, six of the ten DMRs represented regions close to the transcriptional start sites of genes which are also marked by the Polycomb Repressor Complex component EZH2. In conclusion we present a classifier comprising 10 DMRs which predicts patient prognosis with a high degree of accuracy. These data may now help to discriminate between patients that may respond better to standard treatments from those that may require alternative modalities.
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Dai Q, Luo H, Li XP, Huang J, Zhou TJ, Yang ZH. XRCC1 and ERCC1 polymorphisms are related to susceptibility and survival of colorectal cancer in the Chinese population. Mutagenesis 2015; 30:441-9. [PMID: 25690281 DOI: 10.1093/mutage/geu088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Excision repair cross complementing group 1 (ERCC1) and X-ray repair cross-complementing groups 1 (XRCC1) are DNA repair enzymes. Polymorphisms in DNA repair genes may be important factors affecting cancer susceptibility, prognosis and therapy outcome. The purpose of this study was to investigate the correlation of ERCC1 and XRCC1 polymorphisms with colorectal cancer (CRC) risk, and explore the effect of polymorphisms on event-free, overall survival and oxaliplatin-based therapy in CRC patients. Genotyping was examined with the iMLDR technique. An unconditional logistic regression model was used to estimate the association of certain polymorphisms with CRC risk. The Kaplan-Meier method, log-rank test and Cox regression model were employed to evaluate the effects of polymorphisms on survival analysis. Results showed that Trp/Trp genotype of XRCC1 Arg194Trp and AA genotype of ERCC1 rs2336219 have a significantly increased risk of CRC; Trp allele of XRCC1 Arg194Trp and CC genotype of ERCC1 rs735482 were associated with lower response to oxaliplatin-based chemotherapy, a shorter survival and a higher risk of relapse or metastasis. 194Trp/280Arg/399Arg haplotype was associated with a significant resistance, and the ERCC1 protein expression was statistically higher in tumours with rs735482 CC genotype than with AA genotype. Our studies indicate that XRCC1 and ERCC1 polymorphisms probably affect susceptibility, chemotherapy response and survival of CRC patients.
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Affiliation(s)
- Qiong Dai
- Department of Human Anatomy, Luzhou Medical College, Luzhou 646000, Sichuan, China and
| | - Hua Luo
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou 646000, Sichuan, China
| | - Xing Pu Li
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou 646000, Sichuan, China
| | - Juan Huang
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou 646000, Sichuan, China
| | - Tie Jun Zhou
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou 646000, Sichuan, China
| | - Zhi-Hui Yang
- Department of Pathology, The First Affiliated Hospital of Luzhou Medical College, Luzhou 646000, Sichuan, China
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Analyzing large-scale samples confirms the association between rs16892766 polymorphism and colorectal cancer susceptibility. Sci Rep 2015; 5:7957. [PMID: 25609216 PMCID: PMC4302297 DOI: 10.1038/srep07957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/24/2014] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) is a common complex disease caused by the combination of genetic variants and environmental factors. Genome-wide association studies (GWAS) have been performed and reported some novel CRC susceptibility variants. The rs16892766 (8q23.3) polymorphism was first identified to be significantly associated with CRC in European ancestry. The following studies investigated this association in Chinese, Japanese, Romanian, Swedish, African American, European American, and Croatian populations. These studies reported consistent and inconsistent results. Here, we reevaluated this association using the relatively large-scale samples from 13 studies (N = 59737, 26237 cases and 33500 controls) using a meta-analysis by searching the PubMed, Google Scholar and CRCgene databases. We observed no significant heterogeneity among the included studies. Our results showed significant association between rs16892766 polymorphism and CRC (P = 1.33E-35, OR = 1.23, 95% CI 1.20-1.27). Collectively, our analysis further supports previous findings that the rs16892766 polymorphism is significantly associated with CRC susceptibility. We believe that our findings will be very useful for future genetic studies on CRC.
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Ananthakrishnan AN, Du M, Berndt SI, Brenner H, Caan BJ, Casey G, Chang-Claude J, Duggan D, Fuchs CS, Gallinger S, Giovannucci EL, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hou L, Hsu L, Jenkins MA, Kraft P, Ma J, Nan H, Newcomb PA, Ogino S, Potter JD, Seminara D, Slattery ML, Thornquist M, White E, Wu K, Peters U, Chan AT. Red meat intake, NAT2, and risk of colorectal cancer: a pooled analysis of 11 studies. Cancer Epidemiol Biomarkers Prev 2015; 24:198-205. [PMID: 25342387 PMCID: PMC4294960 DOI: 10.1158/1055-9965.epi-14-0897] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Red meat intake has been associated with risk of colorectal cancer, potentially mediated through heterocyclic amines. The metabolic efficiency of N-acetyltransferase 2 (NAT2) required for the metabolic activation of such amines is influenced by genetic variation. The interaction between red meat intake, NAT2 genotype, and colorectal cancer has been inconsistently reported. METHODS We used pooled individual-level data from the Colon Cancer Family Registry and the Genetics and Epidemiology of Colorectal Cancer Consortium. Red meat intake was collected by each study. We inferred NAT2 phenotype based on polymorphism at rs1495741, highly predictive of enzyme activity. Interaction was assessed using multiplicative interaction terms in multivariate-adjusted models. RESULTS From 11 studies, 8,290 colorectal cancer cases and 9,115 controls were included. The highest quartile of red meat intake was associated with increased risk of colorectal cancer compared with the lowest quartile [OR, 1.41; 95% confidence interval (CI), 1.29-1.55]. However, a significant association was observed only for studies with retrospective diet data, not for studies with diet prospectively assessed before cancer diagnosis. Combining all studies, high red meat intake was similarly associated with colorectal cancer in those with a rapid/intermediate NAT2 genotype (OR, 1.38; 95% CI, 1.20-1.59) as with a slow genotype (OR, 1.43; 95% CI, 1.28-1.61; P interaction = 0.9). CONCLUSION We found that high red meat intake was associated with increased risk of colorectal cancer only from retrospective case-control studies and not modified by NAT2 enzyme activity. IMPACT Our results suggest no interaction between NAT2 genotype and red meat intake in mediating risk of colorectal cancer.
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Affiliation(s)
| | - Mengmeng Du
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sonja I Berndt
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. German Cancer Consortium, Heidelberg, Germany
| | | | - Graham Casey
- University of Southern California, Los Angeles, California
| | - Jenny Chang-Claude
- German Cancer Consortium, Heidelberg, Germany. Division of Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona
| | - Charles S Fuchs
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts. Channing Division of Network Medicine, Boston, Massachusetts
| | - Steven Gallinger
- Mount Sinai Hospital and University Health Network Toronto General Hospital, Toronto, Canada
| | - Edward L Giovannucci
- Channing Division of Network Medicine, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts
| | | | | | | | - John L Hopper
- Melbourne School of Population Health, The University of Melbourne, Australia
| | - Lifang Hou
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Evanston, Illinois
| | - Li Hsu
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Melbourne School of Population Health, The University of Melbourne, Australia
| | - Peter Kraft
- Harvard School of Public Health, Boston, Massachusetts
| | - Jing Ma
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts. Channing Division of Network Medicine, Boston, Massachusetts
| | - Hongmei Nan
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Simon Cancer Center, Indiana University, Indianapolis, Indiana
| | | | - Shuji Ogino
- Channing Division of Network Medicine, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - John D Potter
- Fred Hutchinson Cancer Research Center, Seattle, Washington. University of Washington School of Public Health, Seattle, Washington. Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Daniela Seminara
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kana Wu
- Channing Division of Network Medicine, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, Washington. University of Washington School of Public Health, Seattle, Washington.
| | - Andrew T Chan
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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Belbasis L, Panagiotou OA, Dosis V, Evangelou E. A systematic appraisal of field synopses in genetic epidemiology: a HuGE review. Am J Epidemiol 2015; 181:1-16. [PMID: 25504025 DOI: 10.1093/aje/kwu249] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Evidence from genetic association studies is accumulating rapidly. Field synopses have recently arisen as an unbiased way of systematically synthesizing this evidence. We performed a systematic review and appraisal of published field synopses in genetic epidemiology and assessed their main findings and methodological characteristics. We identified 61 eligible field synopses, published between January 1, 2007, and October 31, 2013, on 52 outcomes reporting 734 significant associations at the P < 0.05 level. The median odds ratio for these associations was 1.25 (interquartile range, 1.15-1.43). Egger's test was the most common method (n = 30 synopses) of assessing publication bias. Only 12 synopses (20%) used the Venice criteria to evaluate the epidemiologic credibility of their findings (n = 449 variants). Eleven synopses (18%) were accompanied by an online database that has been regularly updated. These synopses received more citations (P = 0.01) and needed a larger research team (P = 0.02) than synopses without an online database. Overall, field synopses are becoming a valuable tool for the identification of common genetic variants, especially when researchers follow relevant methodological guidelines. Our work provides a summary of the current status of the field synopses published to date and may help interested readers efficiently identify the online resources containing the relevant genetic evidence.
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Park SJ, Kim SM, Hong YS, Lee JL, Kim JE, Kim KP, Hong SM, Jin DH, Kim CW, Yoon YS, Park IJ, Lim SB, Yu CS, Kim JC, Kim TW. TFAP2E methylation status and prognosis of patients with radically resected colorectal cancer. Oncology 2014; 88:122-32. [PMID: 25341849 DOI: 10.1159/000362820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/10/2014] [Indexed: 11/19/2022]
Abstract
OBJECTIVES This study investigates the clinical significance of the gene encoding AP-2ε (TFAP2E) in colorectal cancer (CRC) patients undergoing curative resection. METHODS A single-institution cohort of 248 patients who underwent curative resection of stage I/II/III CRCs between March and December 2004 was enrolled, and 193 patients whose tumors were available for the determination of the TFAP2E methylation status were included in the analysis. RESULTS TFAP2E hypermethylation was detected in 112 patients (58%) and was significantly associated with distally located CRCs, low pathologic T stage (T1/T2), and stage I tumors. After a median follow-up of 86.3 months, the patients with TFAP2E hypermethylation tended to show better relapse-free survival (RFS) and overall survival (OS) than the patients with TFAP2E hypomethylation (5-year RFS rate: 90 vs. 80%, p = 0.063; 6-year OS rate: 88 vs. 80%, p = 0.083). Multivariate analysis showed that the pathologic nodal stage and TFAP2E methylation status were independent prognostic factors for RFS and OS, and they remained significant factors in the subgroup analysis that included 154 patients with stage II/III CRCs who had received adjuvant chemotherapy. CONCLUSIONS TFAP2E hypermethylation is associated with good clinical outcomes and may be considered as an independent prognostic factor in patients with curatively resected CRCs.
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Affiliation(s)
- Seong Joon Park
- Department of Oncology, Asan Institute for Life Science, University of Ulsan College of Medicine, Seoul, Korea
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Horpaopan S, Spier I, Zink AM, Altmüller J, Holzapfel S, Laner A, Vogt S, Uhlhaas S, Heilmann S, Stienen D, Pasternack SM, Keppler K, Adam R, Kayser K, Moebus S, Draaken M, Degenhardt F, Engels H, Hofmann A, Nöthen MM, Steinke V, Perez-Bouza A, Herms S, Holinski-Feder E, Fröhlich H, Thiele H, Hoffmann P, Aretz S. Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis. Int J Cancer 2014; 136:E578-89. [PMID: 25219767 DOI: 10.1002/ijc.29215] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022]
Abstract
To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mutation negative patient cohort followed by a targeted next generation sequencing (NGS) approach. Genomic DNA from 221 unrelated German patients was genotyped on high-resolution SNP arrays. Putative CNVs were filtered according to stringent criteria, compared with those of 531 population-based German controls, and validated by qPCR. Candidate genes were prioritized using in silico, expression, and segregation analyses, data mining and enrichment analyses of genes and pathways. In 27% of the 221 unrelated patients, a total of 77 protein coding genes displayed rare, nonrecurrent, germline CNVs. The set included 26 candidates with molecular and cellular functions related to tumorigenesis. Targeted high-throughput sequencing found truncating point mutations in 12% (10/77) of the prioritized genes. No clear evidence was found for autosomal recessive subtypes. Six patients had potentially causative mutations in more than one of the 26 genes. Combined with data from recent studies of early-onset colorectal and breast cancer, recurrent potential loss-of-function alterations were detected in CNTN6, FOCAD (KIAA1797), HSPH1, KIF26B, MCM3AP, YBEY and in three genes from the ARHGAP family. In the canonical Wnt pathway oncogene CTNNB1 (β-catenin), two potential gain-of-function mutations were found. In conclusion, the present study identified a group of rarely affected genes which are likely to predispose to colorectal adenoma formation and confirmed previously published candidates for tumor predisposition as etiologically relevant.
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Gwinn M, Ioannidis JP, Little J, Khoury MJ. Editorial: Updated guidance on human genome epidemiology (HuGE) reviews and meta-analyses of genetic associations. Am J Epidemiol 2014; 180:559-61. [PMID: 25164421 DOI: 10.1093/aje/kwu196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Inamura K, Yamauchi M, Nishihara R, Lochhead P, Qian ZR, Kuchiba A, Kim SA, Mima K, Sukawa Y, Jung S, Zhang X, Wu K, Cho E, Chan AT, Meyerhardt JA, Harris CC, Fuchs CS, Ogino S. Tumor LINE-1 methylation level and microsatellite instability in relation to colorectal cancer prognosis. J Natl Cancer Inst 2014; 106:dju195. [PMID: 25190725 DOI: 10.1093/jnci/dju195] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Hypomethylation in long interspersed nucleotide element-1 (LINE-1) and high-degree microsatellite instability (MSI-high) in colorectal cancer (CRC) have been associated with inferior and superior survival, respectively; however, it remains uncertain whether the prognostic association of LINE-1 hypomethylation differs by MSI status. We hypothesized that the adverse prognostic association of LINE-1 hypomethylation might be stronger in MSI-high CRCs than in microsatellite stable (MSS) CRCs. METHODS Utilizing 1211 CRCs in the Nurses' Health Study and the Health Professionals Follow-up Study, we examined patient survival according to LINE-1 hypomethylation status in strata of MSI status. A Cox proportional hazards model was used to compute multivariable CRC-specific mortality hazard ratios (HRs) for a 10% decrease in LINE-1 methylation level (range = 23.1-93.1%), adjusting for potential confounders, including CpG island methylator phenotype, and KRAS, BRAF, and PIK3CA mutations. Statistical tests (log-rank test, chi-square test, and likelihood ratio test) were two-sided. RESULTS In MSI-high cancers, the association of LINE-1 hypomethylation with higher mortality (HR = 2.45, 95% confidence interval [CI] = 1.64 to 3.66, P < .001) was stronger than that in MSS cancers (HR = 1.10, 95% CI = 0.98 to 1.24, P = .11) (P interaction < .001, between LINE-1 and MSI statuses). In MSI-high cases with CRC family history, the association of LINE-1 hypomethylation with higher mortality (HR = 5.13, 95% CI = 1.99 to 13.2; P < .001) was stronger than that in MSI-high cases without CRC family history (HR = 1.62, 95% CI = 0.89 to 2.94, P = .11) (P interaction = .02, between LINE-1 and CRC family history statuses). CONCLUSIONS The association of LINE-1 hypomethylation with inferior survival is stronger in MSI-high CRCs than in MSS CRCs. Tumor LINE-1 methylation level may be a useful prognostic biomarker to identify aggressive carcinomas among MSI-high CRCs.
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Affiliation(s)
- Kentaro Inamura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Mai Yamauchi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Reiko Nishihara
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Paul Lochhead
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Zhi Rong Qian
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Aya Kuchiba
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Sun A Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Kosuke Mima
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Yasutaka Sukawa
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Seungyoun Jung
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Xuehong Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Kana Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Eunyoung Cho
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Andrew T Chan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Curtis C Harris
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (KI, MY, RN, PL, ZRQ, AK, SAK, KM, YS, JAM, CSF, SO); Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD (KI, CCH); Department of Nutrition, Harvard School of Public Health, Boston, MA (RN, AK, KW); Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK (PL); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SJ, XZ, EC, ATC, CSF); Department of Dermatology, The Warren Alpert Medical School of Brown University, Province, RI (EC); Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); Department of Epidemiology, Harvard School of Public Health, Boston, MA (SO); Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA (SO)
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