1
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Ashok G, Miryala SK, Saju MT, Anbarasu A, Ramaiah S. FN1 encoding fibronectin as a pivotal signaling gene for therapeutic intervention against pancreatic cancer. Mol Genet Genomics 2022; 297:1565-1580. [PMID: 35982245 DOI: 10.1007/s00438-022-01943-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/08/2022] [Indexed: 10/15/2022]
Abstract
The delayed diagnosis of pancreatic cancer has resulted in rising mortality rate and low survival rate that can be circumvented using potent theranostics biomarkers. The treatment gets complicated with delayed detection resulting in lowered 5-year relative survival rate. In our present study, we employed systems biology approach to identify central genes that play crucial roles in tumor progression. Pancreatic cancer genes collected from various databases were used to construct a statistically significant interactome with 812 genes that was further analysed thoroughly using topological parameters and functional enrichment analysis. The significant genes in the network were then identified based on the maximum degree parameter. The overall survival analysis indicated through hazard ratio [HR] and gene expression [log Fold Change] across pancreatic adenocarcinoma revealed the critical role of FN1 [HR 1.4; log2(FC) 5.748], FGA [HR 0.78; log2(FC) 1.639] FGG [HR 0.9; log2(FC) 1.597], C3 [HR 1.1; log2(FC) 2.637], and QSOX1 [HR 1.4; log2(FC) 2.371]. The functional significance of the identified hub genes signified the enrichment of integrin cell surface interactions and proteoglycan syndecan-mediated cell signaling. The differential expression, low overall survival and functional significance of FN1 gene implied its possible role in controlling metastasis in pancreatic cancer. Furthermore, alternate splice variants of FN1 gene showed 10 protein coding transcripts with conserved cell attachment site and functional domains indicating the variants' potential role in pancreatic cancer. The strong association of the identified hub-genes can be better directed to design potential theranostics biomarkers for metastasized pancreatic tumor.
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Affiliation(s)
- Gayathri Ashok
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.,Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Sravan Kumar Miryala
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.,Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Megha Treesa Saju
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.,Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.,Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India. .,Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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2
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Ahmad S, Ashktorab H, Brim H, Housseau F. Inflammation, microbiome and colorectal cancer disparity in African-Americans: Are there bugs in the genetics? World J Gastroenterol 2022; 28:2782-2801. [PMID: 35978869 PMCID: PMC9280725 DOI: 10.3748/wjg.v28.i25.2782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/27/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Dysregulated interactions between host inflammation and gut microbiota over the course of life increase the risk of colorectal cancer (CRC). While environmental factors and socio-economic realities of race remain predominant contributors to CRC disparities in African-Americans (AAs), this review focuses on the biological mediators of CRC disparity, namely the under-appreciated influence of inherited ancestral genetic regulation on mucosal innate immunity and its interaction with the microbiome. There remains a poor understanding of mechanisms linking immune-related genetic polymorphisms and microbiome diversity that could influence chronic inflammation and exacerbate CRC disparities in AAs. A better understanding of the relationship between host genetics, bacteria, and CRC pathogenesis will improve the prediction of cancer risk across race/ethnicity groups overall.
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Affiliation(s)
- Sami Ahmad
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, DC 20060, United States
| | - Hassan Brim
- Department of Pathology, Howard University, Washington, DC 20060, United States
| | - Franck Housseau
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
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3
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Ghulam A, Lei X, Guo M, Bian C. A Review of Pathway Databases and Related Methods Analysis. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191018162505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathway analysis integrates most of the computational tools for the investigation of
high-level and complex human diseases. In the field of bioinformatics research, biological pathways
analysis is an important part of systems biology. The molecular complexities of biological
pathways are difficult to understand in human diseases, which can be explored through pathway
analysis. In this review, we describe essential information related to pathway databases and their
mechanisms, algorithms and methods. In the pathway database analysis, we present a brief introduction
on how to gain knowledge from fundamental pathway data in regard to specific human
pathways and how to use pathway databases and pathway analysis to predict diseases during an
experiment. We also provide detailed information related to computational tools that are used in
complex pathway data analysis, the roles of these tools in the bioinformatics field and how to store
the pathway data. We illustrate various methodological difficulties that are faced during pathway
analysis. The main ideas and techniques for the pathway-based examination approaches are presented.
We provide the list of pathway databases and analytical tools. This review will serve as a
helpful manual for pathway analysis databases.
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Affiliation(s)
- Ali Ghulam
- School of Computer Science, Shaanxi Normal University, Xian, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xian, China
| | - Min Guo
- School of Computer Science, Shaanxi Normal University, Xian, China
| | - Chen Bian
- School of Computer Science, Shaanxi Normal University, Xian, China
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4
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Yeyeodu ST, Kidd LR, Kimbro KS. Protective Innate Immune Variants in Racial/Ethnic Disparities of Breast and Prostate Cancer. Cancer Immunol Res 2020; 7:1384-1389. [PMID: 31481520 DOI: 10.1158/2326-6066.cir-18-0564] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Individuals of African descent are disproportionately affected by specific complex diseases, such as breast and prostate cancer, which are driven by both biological and nonbiological factors. In the case of breast cancer, there is clear evidence that psychosocial factors (environment, socioeconomic status, health behaviors, etc.) have a strong influence on racial disparities. However, even after controlling for these factors, overall phenotypic differences in breast cancer pathology remain among groups of individuals who vary by geographic ancestry. There is a growing appreciation that chronic/reoccurring inflammation, primarily driven by mechanisms of innate immunity, contributes to core functions associated with cancer progression. Germline mutations in innate immune genes that have been retained in the human genome offer enhanced protection against environmental pathogens, and protective innate immune variants against specific pathogens are enriched among populations whose ancestors were heavily exposed to those pathogens. Consequently, it is predicted that racial/ethnic differences in innate immune programs will translate into ethnic differences in both pro- and antitumor immunity, tumor progression, and prognosis, leading to the current phenomenon of racial/ethnic disparities in cancer. This review explores examples of protective innate immune genetic variants that are (i) distributed disproportionately among racial populations and (ii) associated with racial/ethnic disparities of breast and prostate cancer.
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Affiliation(s)
- Susan T Yeyeodu
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina.,Charles River Discovery Services, Morrisville, North Carolina
| | - LaCreis R Kidd
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky.,Cancer Prevention and Control Program, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky
| | - K Sean Kimbro
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina. .,Department of Biology, North Carolina Central University, Durham, North Carolina.,Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, North Carolina
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5
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Liu X, Zhang Y, Tian J, Gao F. Analyzing Genome-Wide Association Study Dataset Highlights Immune Pathways in Lip Bone Mineral Density. Front Genet 2020; 11:4. [PMID: 32211016 PMCID: PMC7077504 DOI: 10.3389/fgene.2020.00004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/06/2020] [Indexed: 12/27/2022] Open
Abstract
Osteoporosis is a common complex human disease. Until now, large-scale genome-wide association studies (GWAS) using single genetic variant have reported some novel osteoporosis susceptibility variants. However, these risk variants only explain a small proportion of osteoporosis genetic risk, and most genetic risk is largely unknown. Interestingly, the pathway analysis method has been used in investigation of osteoporosis mechanisms and reported some novel pathways. Until now, it remains unclear whether there are other risk pathways involved in BMD. Here, we selected a lip BMD GWAS with 301,019 SNPs in 5,858 Europeans, and conducted a gene-based analysis (SET SCREEN TEST) and a pathway-based analysis (WebGestalt). On the gene level, BMD susceptibility genes reported by previous GWAS were identified to be the top 10 significant signals. On the pathway level, we identified 27 significant KEGG pathways. Three immune pathways including T cell receptor signaling pathway (hsa04660), complement and coagulation cascades (hsa04610), and intestinal immune network for IgA production (hsa04672) are ranked the top three significant signals. Evidence from the PubMed and Google Scholar databases further supports our findings. In summary, our findings provide complementary information to these nine risk pathways.
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Affiliation(s)
- Xiaodong Liu
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yiwei Zhang
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jun Tian
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Feng Gao
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
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6
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Gao F, Yao Y, Zhang Y, Tian J. Integrating Genome-Wide Association Studies With Pathway Analysis and Gene Expression Analysis Highlights Novel Osteoarthritis Risk Pathways and Genes. Front Genet 2019; 10:827. [PMID: 31572443 PMCID: PMC6753977 DOI: 10.3389/fgene.2019.00827] [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: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 01/17/2023] Open
Abstract
Osteoarthritis (OA) is the most common degenerative joint disorder worldwide. To identify more genetic signals, genome-wide association study (GWAS) has been widely used and elucidated some OA susceptibility genes. However, these susceptibility genes could only explain only a small part of heritability of OA. It is suggested that the identification of disease-related pathways may contribute to understand the genomic etiology of OA. Here, we integrated the GWAS into pathway analysis to identify novel OA risk pathways. In this study, we first selected 187 independent genetic variants identified by GWAS (P < 1.00E−05) and found that most of these genetic variants are noncoding mutations. We then conducted an expression quantitative trait loci analysis and found that 165 of these 187 genetic variants could significantly regulate the expression of nearby genes. Third, we identified OA susceptibility genes corresponding to these genetic variants, conducted a pathway analysis, and identified novel OA-related KEGG pathways, GO biological processes, GO molecular functions, and GO cellular components. In KEGG database, transforming growth factor β signaling pathway is the most significant signal (P = 5.98E−05) and is the only pathway after the BH multiple-test adjustment with false discovery rate (FDR) = 0.02. In GO database, we identified 24 statistically significant GO biological processes, one statistically significant GO molecular function, and five statistically significant GO cellular components (FDR < 0.05). These signals are related with chondrocyte differentiation and development, which are all known biological pathways associated with OA. Finally, we conducted an OA case–control gene expression analysis to evaluate the differential expression of these OA risk genes. Using an OA case–control gene expression analysis, we showed that 44 risk genes were suggestively differentially expressed in OA cases compared with controls (P < 0.05). Three genes, WWP2, COG5, and MAPT, were statistically differentially expressed in OA cases compared with controls (P < 0.05/122 = 4.10E−04). Hence, our findings may contribute to understanding the genomic etiology of OA.
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Affiliation(s)
- Feng Gao
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yu Yao
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yiwei Zhang
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jun Tian
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
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7
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Liu W, Li L, Ye H, Tao H, He H. Role of COL6A3 in colorectal cancer. Oncol Rep 2018; 39:2527-2536. [PMID: 29620224 PMCID: PMC5983922 DOI: 10.3892/or.2018.6331] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/20/2018] [Indexed: 12/20/2022] Open
Abstract
Public transcriptome databases provide a valuable resource for genome-wide co-expression network analysis and investigation of the molecular mechanisms that underlie pathogenesis. To discover genes that may affect patient survival, a large-scale analysis of human colorectal cancer (CRC) datasets that were retrieved from the NCBI Gene Expression Omnibus was performed. A gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA). A total of 18 co-expressed gene modules were identified, of which two genes corresponded to cell migration and the cell cycle, two genes were involved in immune responses, two genes corresponded to mitochondrial function, and one gene corresponded to RNA splicing. A total of eight hub genes in the cell migration/extracellular matrix module were associated with poor prognosis in CRC, and the P-value for collagen type VI α3 chain (COL6A3) was the lowest. In silico analysis of cell type-specific gene expression and COL6A3 knockout experiments indicated the clinical relevance of COL6A3 in the development of CRC. In summary, the present analysis provides a basis for understanding the molecular characterization of CRC at the transcription level. COL6A3 may be a promising biomarker or target for the prognosis and treatment of CRC.
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Affiliation(s)
- Wei Liu
- Department of Bioinformatics, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Li Li
- Department of Medical Informatics, Institute of Health Service and Medical Information, Academy of Military Medical Sciences, Beijing 100850, P.R. China
| | - Hua Ye
- Department of Gastroenterology, Ningbo Medical Treatment Center Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Huan Tao
- Department of Bioinformatics, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Huaqin He
- Department of Bioinformatics, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
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8
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Gene expression analysis reveals the dysregulation of immune and metabolic pathways in Alzheimer's disease. Oncotarget 2018; 7:72469-72474. [PMID: 27732949 PMCID: PMC5341922 DOI: 10.18632/oncotarget.12505] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022] Open
Abstract
In recent years, several pathway analyses of genome-wide association studies reported the involvement of metabolic and immune pathways in Alzheimer's disease (AD). Until now, the exact mechanisms of these pathways in AD are still unclear. Here, we conducted a pathway analysis of a whole genome AD case-control expression dataset (n=41, 25 AD cases and 16 controls) from the human temporal cortex tissue. Using the differently expressed AD genes, we identified significant KEGG pathways related to metabolism and immune processes. Using the up- and down- regulated AD gene list, we further found up-regulated AD gene were significantly enriched in immune and metabolic pathways. We further compare the immune and metabolic KEGG pathways from the expression dataset with those from previous GWAS datasets, and found that most of these pathways are shared in both GWAS and expression datasets.
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9
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Meng Q, Wu S, Wang Y, Xu J, Sun H, Lu R, Gao N, Yang H, Li X, Tang B, Aschner M, Chen R. MPO Promoter Polymorphism rs2333227 Enhances Malignant Phenotypes of Colorectal Cancer by Altering the Binding Affinity of AP-2α. Cancer Res 2018. [PMID: 29540402 DOI: 10.1158/0008-5472.can-17-2538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Myeloperoxidase (MPO) promoter SNPs rs2243828 (-764T>C) and rs2333227 (G-463A) program malignant phenotypes by regulating MPO transcriptional activity. In this study, we enrolled a total of 1,175 controls and 1,078 patients with colorectal cancer with comprehensive clinical and survival information to assess whether these SNPs could affect the susceptibility and development of colorectal cancer. The MPO rs2333227 TT genotype significantly increased the risk of colorectal cancer and decreased the overall survival time of patients. Colorectal cancer cells with the rs2333227 TT genotype exhibited enhanced proliferation, migration, and invasion capacity in vitro and in vivo Mechanistically, we found that MPO SNP rs2333227 C to T mutation altered the binding affinity of the transcription factors AP-2α to the rs2333227 mutation region, sequentially enhancing expression levels of MPO and activating further IL23A-MMP9 axis-mediated oncogenic signaling. Taken together, our findings indicate that MPO SNP rs2333227 serves as a marker of enhanced risk for development of colorectal cancer.Significance: MPO polymorphisms are a guide for high risk and poor prognosis in patients colorectal cancer. Cancer Res; 78(10); 2760-9. ©2018 AACR.
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Affiliation(s)
- Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Yajie Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Jin Xu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Runze Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Na Gao
- Institute of Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
| | - Hongbao Yang
- Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, China
| | - Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China. .,Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
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10
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Han P, Liu G, Lu X, Cao M, Yan Y, Zou J, Li X, Wang G. CDH1 rs9929218 variant at 16q22.1 contributes to colorectal cancer susceptibility. Oncotarget 2018; 7:47278-47286. [PMID: 27259261 PMCID: PMC5216941 DOI: 10.18632/oncotarget.9758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/08/2016] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer. Large-scale genome-wide association studies (GWAS) have been performed and reported some novel CRC susceptibility variants in European ancestry including the CDH1 rs9929218. Following GWAS and candidate studies evaluated the association between the CDH1 rs9929218 polymorphism and CRC in European, Asian and American populations. However, these studies reported inconsistent associations. Evidence shows that rs9929218 may regulate different gene expressions in different human tissues. Here, we reevaluated this association using large-scale samples from 16 studies (n=131768) using a meta-analysis method. In heterogeneity test, we did not identify significant heterogeneity among these studies. Meta-analysis using fixed effect model showed significant association between rs9929218 and CRC (P=6.16E-21, odds ratio (OR) =0.92, 95% confidence interval (CI) 0.91-0.94). In order to validate the effect of rs9929218 variant on CDH1 expression, we further performed a functional analysis using two large-scale expression datasets. We identified significant regulation relation between rs9929218 variant and the expression of CDH1, ZFP90, RP11-354M1.2 and MCOLN2 by both cis-effect and trans-effect. In summary, our analysis highlights significant association between rs9929218 polymorphism and CRC susceptibility.
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Affiliation(s)
- Peng Han
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150040, China
| | - Guiyou Liu
- Genome Analysis Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xin Lu
- Department of Gastroenterology, The First Hospital of Harbin, Harbin, 150001, China
| | - Minmin Cao
- Department of Endocrinology, The First Hospital of Harbin, Harbin, 150001, China
| | - Youling Yan
- Department of Gastroenterology, The First Hospital of Harbin, Harbin, 150001, China
| | - Jing Zou
- Department of Hematology, The First Hospital of Harbin, Harbin, 150001, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Guangyu Wang
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150040, China
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11
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GLRB variants regulate nearby gene expression in human brain tissues. Sci Rep 2017; 7:13326. [PMID: 29042589 PMCID: PMC5645380 DOI: 10.1038/s41598-017-13702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/25/2017] [Indexed: 12/02/2022] Open
Abstract
A recent genome-wide association study (GWAS) identified four genetic variants rs78726293, rs191260602, rs17035816 and rs7688285 in GLRB gene to be associated with panic disorder (PD) risk. In fact, GWAS is an important first step to investigate the genetics of human complex diseases. In order to translate into opportunities for new diagnostics and therapies, we must identify the genes perturbed by these four variants, and understand how these variant functionally contributes to the underlying disease pathogenesis. Here, we investigated the effect of these four genetic variants and the expression of three nearby genes including PDGFC, GLRB and GRIA2 in human brain tissues using the GTEx (version 6) and Braineac eQTLs datasets. In GTEx (version 6) dataset, the results showed that both rs17035816 and rs7688285 variants could significantly regulate PDGFC and GLRB gene expression. In Braineac dataset, the results showed that rs17035816 variant could significantly regulate GLRB and GRIA2 gene expression. We believe that these findings further provide important supplementary information about the regulating mechanisms of rs17035816 and rs7688285 variants in PD risk.
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12
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Liu Y, Zhao J, Jiang T, Yu M, Jiang G, Hu Y. A pathway analysis of genome-wide association study highlights novel type 2 diabetes risk pathways. Sci Rep 2017; 7:12546. [PMID: 28970525 PMCID: PMC5624908 DOI: 10.1038/s41598-017-12873-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 09/11/2017] [Indexed: 02/04/2023] Open
Abstract
Genome-wide association studies (GWAS) have been widely used to identify common type 2 diabetes (T2D) variants. However, the known variants just explain less than 20% of the overall estimated genetic contribution to T2D. Pathway-based methods have been applied into T2D GWAS datasets to investigate the biological mechanisms and reported some novel T2D risk pathways. However, few pathways were shared in these studies. Here, we performed a pathway analysis using the summary results from a large-scale meta-analysis of T2D GWAS to investigate more genetic signals in T2D. Here, we selected PLNK and VEGAS to perform the gene-based test and WebGestalt to perform the pathway-based test. We identified 8 shared KEGG pathways after correction for multiple tests in both methods. We confirm previous findings, and highlight some new T2D risk pathways. We believe that our results may be helpful to study the genetic mechanisms of T2D.
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Affiliation(s)
- Yang Liu
- College of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Jing Zhao
- The Department of Obstetrics and Gynaecology, Heilongjiang Provincial Forestry General Hospital, Harbin, Heilongjiang, China
| | - Tao Jiang
- The 224th Hospital of Chinese People's Liberation Army, Harbin, Heilongjiang, China
| | - Mei Yu
- Research institute of Chinese Medicine in Heilongjiang province, Harbin, Heilongjiang, China
| | - Guohua Jiang
- College of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
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13
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Zhang C, Li X, Zhang W, Wang Y, Fan G, Wang W, Chen S, Qin H, Zhang X. Common genetic variant rs3802842 in 11q23 contributes to colorectal cancer risk in Chinese population. Oncotarget 2017; 8:72227-72234. [PMID: 29069782 PMCID: PMC5641125 DOI: 10.18632/oncotarget.19702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022] Open
Abstract
A genome-wide association study identified a common genetic variant rs3802842 at 11q23 to be associated with CRC risk with OR=1.1 and P = 5.80E-10 in European population. In Chinese population, several genetic association studies have investigated the association between rs3802842 variant and CRC risk. However these studies reported both positive and negative association results. It is still necessary to evaluate a specific variant in a specific population, which would be informative to reveal the disease mechanism. Until recently, there is no a systemic study to evaluate the potential association between rs3802842 and CRC risk in Chinese population by a meta-analysis method. Here, we aim to evaluate this association in Chinese population by a meta-analysis method using 12077 samples including 5816 CRC cases and 6261 controls. We identified the T allele of rs3802842 to be significantly related with an increase CRC risk (P=2.22E-05, OR=1.14, 95% CI 1.07-1.21) in Chinese population.
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Affiliation(s)
- Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xichuan Li
- Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Weihua Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Yijia Wang
- Department of Pathology, Tianjin Union Medical Center, Tianjin 300121, China
| | - Guanwei Fan
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.,State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Wenhong Wang
- Department of Imaging, Tianjin Union Medical Center, Tianjin 300121, China
| | - Shuo Chen
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Hai Qin
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
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Liu G, Zhang F, Hu Y, Jiang Y, Gong Z, Liu S, Chen X, Jiang Q, Hao J. Multiple sclerosis risk pathways differ in Caucasian and Chinese populations. J Neuroimmunol 2017; 307:63-68. [DOI: 10.1016/j.jneuroim.2017.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/05/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
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15
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Gorlova OY, Demidenko EI, Amos CI, Gorlov IP. Downstream targets of GWAS-detected genes for breast, lung, and prostate and colon cancer converge to G1/S transition pathway. Hum Mol Genet 2017; 26:1465-1471. [PMID: 28334950 DOI: 10.1093/hmg/ddx050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/06/2017] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies (GWASs) identified over 500 single nucleotide polymorphisms (SNPs) influencing cancer risk. It is logical to expect the cancer-associated genes to cluster in pathways directly involved in carcinogenesis, e.g. cell cycle. Nevertheless, analyses of the GWAS-detected cancer risk genes usually show no or weak enrichment by known cancer genes.We hypothesized that GWAS-detected cancer risk-associated genes function as upstream regulators of the genes directly involved in carcinogenesis. We have analyzed four common cancers: breast, colon, lung, and prostate. To identify downstream targets of GWAS-detected cancer risk genes we used MedScan, which is a text mining tool offered by PathwayStudio. We also used data on protein/protein interactions reported by BioGRID database. Among all identified targets we have selected common downstream targets. A gene was considered a common downstream target if it was a downstream target for at least three GWAS-detected genes for a given cancer type. Common downstream targets were identified separately for each cancer type. We found that common downstream targets for all four cancer types were enriched by cell cycle genes, more specifically, the genes involved in G1/S transition. Common downstream targets for bipolar disorder, Crohn's disease, and type 2 diabetes did not show G1/S transition enrichment.The results of this analysis suggest that many cancer risk genes function as upstream regulators of the genes directly involved in G1/S transition and exert their risk effects by reducing threshold for G1/S transition, elevating the background level of cell proliferation and cancer risk.
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Husser D, Büttner P, Ueberham L, Dinov B, Sommer P, Arya A, Hindricks G, Bollmann A. Genomic Contributors to Rhythm Outcome of Atrial Fibrillation Catheter Ablation - Pathway Enrichment Analysis of GWAS Data. PLoS One 2016; 11:e0167008. [PMID: 27870913 PMCID: PMC5117760 DOI: 10.1371/journal.pone.0167008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Left atrial enlargement and persistent atrial fibrillation (AF) are well-known predictors for arrhythmia recurrence after AF catheter ablation (LRAF). In this study, by using pathway enrichment analysis of GWAS data, we tested the hypothesis that genetic pathways associated with these phenotypes are also associated with LRAF. METHODS Samples from 660 patients with paroxysmal (n = 370) or persistent AF (n = 290) undergoing de-novo AF catheter ablation were genotyped for ~1,000,000 SNPs. SNPs found to be significantly associated with left atrial diameter (LAD) or AF type were used for gene-based association tests in a systematic biological Knowledge-based mining system for Genome-wide Genetic studies (KGG). Associated genes were tested for pathway enrichment using WEB-based Gene SeT AnaLysis Toolkit (WebGestalt), the Gene Annotation Tool to Help Explain Relationships (GATHER) and the databases provided by Kyoto Encyclopedia of Genes and Genomes (KEGG). In a second step, the association of consistently enriched pathways and LRAF was tested. RESULTS By using sequential 7-day Holter ECGs, LRAF between 3 and 12 months was observed in 48% and was associated with LAD (B = 1.801, 95% CI 0.760-2.841, p = 1.0E-3) and persistent AF (OR = 2.1; 95% CI 1.567-2.931, p = 2.0E-6). WebGestalt (adj. p = 2.7E-22) and GATHER (adj. p = 5.2E-3) identified the calcium signaling pathway (hsa04020) as the only consistently enriched pathway for LAD, while the extracellular matrix (ECM) -receptor interaction pathway (hsa04512) was the only consistently enriched pathway for AF type (adj. p = 2.1E-15 in WebGestalt; adj. p = 9.3E-4 in GATHER). Both calcium signaling (adj. p = 2.2E-17 in WebGestalt; adj. p = 2.9E-2 in GATHER) and ECM-receptor interaction (adj. p = 1.2E-10 in WebGestalt; adj. p = 2.9E-2 in GATHER) were significantly associated with LRAF. CONCLUSIONS Calcium signaling and ECM-receptor interaction pathways are associated with LAD and AF type and, in turn, with LRAF. Future and larger studies are necessary to replicate and apply these findings.
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Affiliation(s)
- Daniela Husser
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
- * E-mail:
| | - Petra Büttner
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Laura Ueberham
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Borislav Dinov
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Philipp Sommer
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Arash Arya
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Gerhard Hindricks
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Andreas Bollmann
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
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Husser D, Ueberham L, Dinov B, Kosiuk J, Kornej J, Hindricks G, Shoemaker MB, Roden DM, Bollmann A, Büttner P. Genomic contributors to atrial electroanatomical remodeling and atrial fibrillation progression: Pathway enrichment analysis of GWAS data. Sci Rep 2016; 6:36630. [PMID: 27857207 PMCID: PMC5114680 DOI: 10.1038/srep36630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/11/2016] [Indexed: 12/18/2022] Open
Abstract
In atrial fibrillation (AF), left atrial diameter (LAD) and low voltage area (LVA) are intermediate phenotypes that are associated with AF type and progression. In this study, we tested the hypothesis, that these phenotypes share common, genetically-determined pathways using pathway enrichment analysis of GWAS data. Samples from 660 patients with paroxysmal (n = 370) or persistent AF (n = 290) were genotyped for ~1,000,000 SNPs. SNPs found significantly associated with LAD, LVA or AF type were used for gene-based association tests in a systematic biological Knowledge-based mining system for Genome-wide Genetic studies (KGG). Associated genes were tested for pathway enrichment using two enrichment tools (WebGestalt and GATHER) and the databases provided by Kyoto Encyclopedia of Genes and Genomes. The calcium signaling pathway (hsa04020) was the only pathway that reached statistical significance for LAD and LVA in both enrichment tools and was also significantly associated with AF type. Within this pathway, there were 39 genes (i.e. CACNA1C, RyR2) that were associated with LAD, LVA and AF type. In conclusion, there is a genomic contribution to electroanatomical remodeling (LAD, LVA) and AF type via the calcium signaling pathway. Future and larger studies are necessary to replicate and apply these findings.
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Affiliation(s)
- Daniela Husser
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | - Laura Ueberham
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | - Borislav Dinov
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | - Jedrzej Kosiuk
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | - Jelena Kornej
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | - Gerhard Hindricks
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | | | - Dan M Roden
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Andreas Bollmann
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
| | - Petra Büttner
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Germany
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18
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Mitochondrial function controls intestinal epithelial stemness and proliferation. Nat Commun 2016; 7:13171. [PMID: 27786175 PMCID: PMC5080445 DOI: 10.1038/ncomms13171] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/09/2016] [Indexed: 02/07/2023] Open
Abstract
Control of intestinal epithelial stemness is crucial for tissue homeostasis. Disturbances in epithelial function are implicated in inflammatory and neoplastic diseases of the gastrointestinal tract. Here we report that mitochondrial function plays a critical role in maintaining intestinal stemness and homeostasis. Using intestinal epithelial cell (IEC)-specific mouse models, we show that loss of HSP60, a mitochondrial chaperone, activates the mitochondrial unfolded protein response (MT-UPR) and results in mitochondrial dysfunction. HSP60-deficient crypts display loss of stemness and cell proliferation, accompanied by epithelial release of WNT10A and RSPO1. Sporadic failure of Cre-mediated Hsp60 deletion gives rise to hyperproliferative crypt foci originating from OLFM4+ stem cells. These effects are independent of the MT-UPR-associated transcription factor CHOP. In conclusion, compensatory hyperproliferation of HSP60+ escaper stem cells suggests paracrine release of WNT-related factors from HSP60-deficient, functionally impaired IEC to be pivotal in the control of the proliferative capacity of the stem cell niche. It is unclear what role mitochondrial function plays in maintaining intestinal epithelial cell (IEC) homeostasis. Here, the authors deplete a mitochondrial chaperone, heat shock protein 60 (HSP60) in IEC and observe a loss of stemness and cell proliferation, and suggest this is accompanied by a compensatory release of WNT-related factors.
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Che J, Shi J, Gao Z, Zhang Y. Transcriptome Analysis Reveals the Genetic Basis of the Resveratrol Biosynthesis Pathway in an Endophytic Fungus (Alternaria sp. MG1) Isolated from Vitis vinifera. Front Microbiol 2016; 7:1257. [PMID: 27588016 PMCID: PMC4988973 DOI: 10.3389/fmicb.2016.01257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/29/2016] [Indexed: 12/19/2022] Open
Abstract
Alternaria sp. MG1, an endophytic fungus previously isolated from Merlot grape, produces resveratrol from glucose, showing similar metabolic flux to the phenylpropanoid biosynthesis pathway, currently found solely in plants. In order to identify the resveratrol biosynthesis pathway in this strain at the gene level, de novo transcriptome sequencing was conducted using Illumina paired-end sequencing. A total of 22,954,434 high-quality reads were assembled into contigs and 18,570 unigenes were identified. Among these unigenes, 14,153 were annotated in the NCBI non-redundant protein database and 5341 were annotated in the Swiss-Prot database. After KEGG mapping, 2701 unigenes were mapped onto 115 pathways. Eighty-four unigenes were annotated in major pathways from glucose to resveratrol, coding 20 enzymes for glycolysis, 10 for phenylalanine biosynthesis, 4 for phenylpropanoid biosynthesis, and 4 for stilbenoid biosynthesis. Chalcone synthase was identified for resveratrol biosynthesis in this strain, due to the absence of stilbene synthase. All the identified enzymes indicated a reasonable biosynthesis pathway from glucose to resveratrol via glycolysis, phenylalanine biosynthesis, phenylpropanoid biosynthesis, and stilbenoid pathways. These results provide essential evidence for the occurrence of resveratrol biosynthesis in Alternaria sp. MG1 at the gene level, facilitating further elucidation of the molecular mechanisms involved in this strain's secondary metabolism.
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Affiliation(s)
- Jinxin Che
- College of Food Science and Engineering, Northwest A & F University Yangling, China
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University Xi'an, China
| | - Zhenhong Gao
- College of Food Science and Engineering, Northwest A & F University Yangling, China
| | - Yan Zhang
- College of Food Science and Engineering, Northwest A & F University Yangling, China
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20
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Liu G, Zhang F, Jiang Y, Hu Y, Gong Z, Liu S, Chen X, Jiang Q, Hao J. Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways. Mult Scler 2016; 23:205-212. [PMID: 27207450 DOI: 10.1177/1352458516649038] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Much effort has been expended on identifying the genetic determinants of multiple sclerosis (MS). Existing large-scale genome-wide association study (GWAS) datasets provide strong support for using pathway and network-based analysis methods to investigate the mechanisms underlying MS. However, no shared genetic pathways have been identified to date. OBJECTIVE We hypothesize that shared genetic pathways may indeed exist in different MS-GWAS datasets. METHODS Here, we report results from a three-stage analysis of GWAS and expression datasets. In stage 1, we conducted multiple pathway analyses of two MS-GWAS datasets. In stage 2, we performed a candidate pathway analysis of the large-scale MS-GWAS dataset. In stage 3, we performed a pathway analysis using the dysregulated MS gene list from seven human MS case-control expression datasets. RESULTS In stage 1, we identified 15 shared pathways. In stage 2, we successfully replicated 14 of these 15 significant pathways. In stage 3, we found that dysregulated MS genes were significantly enriched in 10 of 15 MS risk pathways identified in stages 1 and 2. CONCLUSION We report shared genetic pathways in different MS-GWAS datasets and highlight some new MS risk pathways. Our findings provide new insights on the genetic determinants of MS.
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Affiliation(s)
- Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Fang Zhang
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhongying Gong
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Shoufeng Liu
- Department of Neurology, Tianjin HuanHu Hospital, Tianjin, China
| | - Xiuju Chen
- Department of Neurology, Tianjin NanKai Hospital, Tianjin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Junwei Hao
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
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Menon R, Patel AB, Joshi C. Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing. PeerJ 2016; 4:e2147. [PMID: 27441113 PMCID: PMC4941740 DOI: 10.7717/peerj.2147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/27/2016] [Indexed: 12/17/2022] Open
Abstract
River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects.
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Affiliation(s)
- Ramesh Menon
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Anand B Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Chaitanya Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
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Colorectal cancer risk genes are functionally enriched in regulatory pathways. Sci Rep 2016; 6:25347. [PMID: 27146020 PMCID: PMC4857176 DOI: 10.1038/srep25347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/12/2016] [Indexed: 02/07/2023] 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. However, the potential genetic mechanisms for newly identified CRC susceptibility variants are still unclear. Here, we selected 85 CRC susceptibility variants with suggestive association P < 1.00E-05 from the National Human Genome Research Institute GWAS catalog. To investigate the underlying genetic pathways where these newly identified CRC susceptibility genes are significantly enriched, we conducted a functional annotation. Using two kinds of SNP to gene mapping methods including the nearest upstream and downstream gene method and the ProxyGeneLD, we got 128 unique CRC susceptibility genes. We then conducted a pathway analysis in GO database using the corresponding 128 genes. We identified 44 GO categories, 17 of which are regulatory pathways. We believe that our results may provide further insight into the underlying genetic mechanisms for these newly identified CRC susceptibility variants.
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