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An introduction to EpiPol (Epigenetic affecting Polymorphism) concept with an in silico identification of CpG-affecting SNPs in the upstream regulatory sequences of human AHR gene. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Aftabi Y, Rafei S, Zarredar H, Amiri-Sadeghan A, Akbari-Shahpar M, Khoshkam Z, Seyedrezazadeh E, Khalili M, Mehrnejad F, Fereidouni S, Lawrence BP. Refinement of coding SNPs in the human aryl hydrocarbon receptor gene using ISNPranker: An integrative-SNP ranking web-tool. Comput Biol Chem 2020; 90:107416. [PMID: 33264727 DOI: 10.1016/j.compbiolchem.2020.107416] [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: 04/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022]
Abstract
Different bioinformatic methods apply various approaches to predict how much the effect of a SNP could be deleterious and therefore their results may differ significantly. However, variation studies often need to consider an integrated prediction result to analyze the effect of SNPs. To address this problem, we used an algorithm to map ordinal predictions to a numeral space and averaging them, and based on it we developed the ISNPranker web-tool (http://isnpranker.semilab.ir/). It takes heterogonous outputs of different predictors and generates integrated numerical predictions and ranks SNPs based on them. Afterward, we used ISNPranker to identify the most deleterious coding SNPs (cSNPs) of the human aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that governs many molecular and cellular mechanisms and cSNPs may affect its structure, interactions, and function. Forty validated cSNPs of AHR were initially analyzed using 16 publicly available SNP analyzers and the results were introduced to the ISNPranker and integrated predictions were obtained. The cSNPs were ranked in 34 levels of danger and rs200257782 in the ARNT dimerization domain (ADD121-289) of AHR was identified as the most deleterious cSNP. The rs148360742, which affect ADD40-79 and Hsp90 binding domain (HBD27-79) was in the second rank and the third and fourth ranks were occupied by ADD121-289-located variations rs571123681 and rs141667112 respectively. In conclusion, we introduced ISNPranker, which is a web-tool for integrative ranking of SNPs, and we showed that AHR structure and function may be highly sensitive to the cSNPs in the ARNT dimerization domain.
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Affiliation(s)
- Younes Aftabi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran.
| | - Saleh Rafei
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Amir Amiri-Sadeghan
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Mohsen Akbari-Shahpar
- Department of Computer Engineering, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Zahra Khoshkam
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran; Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Tehran, Tehran, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Majid Khalili
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Sasan Fereidouni
- Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - B Paige Lawrence
- Departments of Environmental Medicine and Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
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Zhang Q, Huang R, Ma X, Jiang N, Zhou W, Gao C, Zhao M, Niu P, Zhang Z, Li Q, Zhou J, Li P. Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs. Animals (Basel) 2019; 10:ani10010011. [PMID: 31861561 PMCID: PMC7023200 DOI: 10.3390/ani10010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/08/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Eastern and Southern Chinese pigs have been imported to Western countries to improve economic traits including fertility in Western pig breeds by intensive selecting Chinese advantage genes. It was reported that the selected Asian-derived non-synonymous mutations including rs339939442 (G > T) in the aryl hydrocarbon receptor (AHR) gene could increase litter size in multiple European commercial lines. The objective of this study is to identify whether rs339939442 in the AHR gene is polymorphic and has an influence on the litter size in 10 pig populations including five Chinese indigenous breeds, one cultivated breed, one lean-type breed, two North American lean-type breeds, and one European lean-type breed. We found that rs339939442 had polymorphism in all 10 populations, whereas rs339939442 was associated with litter size only in French Yorkshire (FRA-Y) and Chinese cultivated Suhuai (SH) pigs containing approximately 75% British Yorkshire pigs ancestry. Our results indicated that rs339939442 in the AHR gene was a potential marker to improve litter size in European commercial lines and the pigs containing ancestries of European commercial lines, whereas this locus maybe not a causal mutation affecting the litter size but only in linkage disequilibrium with the causal mutation for litter size.
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Affiliation(s)
- Qian Zhang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Xiang Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Nengjing Jiang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Wuduo Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Chen Gao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Moran Zhao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Zongping Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Qiang Li
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China; (Q.L.); (J.Z.)
| | - Juan Zhou
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China; (Q.L.); (J.Z.)
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
- Correspondence:
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Ren ZJ, Cao D, Ren PW, Yang B, Lu DL, Liao J, Liu SZ, Yang LC, Peng ZF, Liu LR, Dong Q. Aryl hydrocarbon receptor rs2066853 gene polymorphisms and male infertility risk: a meta-analysis. Ren Fail 2019; 41:987-994. [PMID: 31662023 PMCID: PMC6830243 DOI: 10.1080/0886022x.2019.1673775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
To evaluate the relationship between the aryl hydrocarbon receptor (AHR) rs2066853 gene polymorphism and the risk of male infertility. PubMed, Embase, Web of Science, and Chinese National Knowledge Infrastructure (CNKI) were searched for relevant case–control studies up to 31 July 2019. Odds ratio (OR) and 95% confidence interval (95% CI) were used to assess the strength of associations. Finally, seven case–control studies involving 1247 cases and 1762 controls were included in this meta-analysis. The pooled results showed that there was no significant association between AHR rs2066853 gene polymorphism and male infertility risk (A vs. G: OR = 1.08, 95% CI = 0.83–1.39; AA vs. GG: OR = 1.16, 95% CI = 0.65–2.04; AA vs. GA + GG: OR = 1.17, 95% CI = 0.66–2.07; AA + GA vs. GG: OR = 0.99, 95% CI = 0.85–1.15). Subgroup analysis by ethnicity showed the same result. However, significant association was found between AHR rs2066853 gene polymorphism and male infertility risk in oligoasthenotspermia (A vs. G: OR = 2.52, 95% CI = 1.72–3.70). In conclusion, our meta-analysis indicated that AHR rs2066853 gene polymorphism might be associated with an increased susceptibility to oligoasthenotspermia.
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Affiliation(s)
- Zheng-Ju Ren
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - DeHong Cao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peng-Wei Ren
- Department of Evidence-Based Medicine and Clinical Epidemiology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bo Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dong-Liang Lu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Liao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng-Zhuo Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lu-Cheng Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhu-Feng Peng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liang-Ren Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Dong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Roman ÁC, Carvajal-Gonzalez JM, Merino JM, Mulero-Navarro S, Fernández-Salguero PM. The aryl hydrocarbon receptor in the crossroad of signalling networks with therapeutic value. Pharmacol Ther 2017; 185:50-63. [PMID: 29258844 DOI: 10.1016/j.pharmthera.2017.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is well-known for its major contributions to the cellular responses against environmental toxins and carcinogens. Notably, AhR has also emerged as a key transcription factor controlling many physiological processes including cell proliferation and apoptosis, differentiation, adhesion and migration, pluripotency and stemness. These novel functions have broadened our understanding of the signalling pathways and molecular intermediates interacting with AhR under both homeostatic and pathological conditions. Recent discoveries link AhR with the function of essential organs such as liver, skin and gonads, and with complex organismal structures including the immune and cardiovascular systems. The identification of potential endogenous ligands able to regulate AhR activity, opens the possibility of designing ad hoc molecules with pharmacological and/or therapeutic value to treat human diseases in which AhR may have a causal role. Integration of experimental data from in vitro and in vivo studies with "omic" analyses of human patients affected with cancer, immune diseases, inflammation or neurological disorders will likely contribute to validate the clinical relevance of AhR and the possible benefits of modulating its activity by pharmacologically-driven strategies. In this review, we will highlight signalling pathways involved in human diseases that could be targetable by AhR modulators and discuss the feasibility of using such molecules in therapy. The pros and cons of AhR-aimed approaches will be also mentioned.
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Affiliation(s)
- Ángel C Roman
- Champalimaud Neuroscience Programme, Champalimoud Center for the Unknown, Lisbon, Portugal
| | - José M Carvajal-Gonzalez
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Jaime M Merino
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Sonia Mulero-Navarro
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain.
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain.
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