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Ren N, Dai S, Ma S, Yang F. Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases. Clin Genet 2023; 103:392-400. [PMID: 36527336 DOI: 10.1111/cge.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Genome-wide association studies (GWAS) have identified a large number of single nucleotide polymorphism (SNP) sites associated with human diseases. In the annotation of human diseases, especially cancers, SNPs, as an important component of genetic factors, have gained increasing attention. Given that most of the SNPs are located in non-coding regions, the functional verification of these SNPs is a great challenge. The key to functional annotation for risk SNPs is to screen SNPs with regulatory activity from thousands of disease associated-SNPs. In this review, we systematically recapitulate the characteristics and functional roles of SNP sites, discuss three parallel reporter screening strategies in detail based on barcode tag classification, and recommend the common in silico strategies to help supplement the annotation of SNP sites with epigenetic activity analysis, prediction of target genes and trans-acting factors. We hope that this review will contribute to this exuberant research field by providing robust activity analysis strategies that can facilitate the translation of GWAS results into personalized diagnosis and prevention measures for human diseases.
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Affiliation(s)
- Naixia Ren
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shangkun Dai
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shumin Ma
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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Zhu C, Liu C, Chai Z. Role of the PADI family in inflammatory autoimmune diseases and cancers: A systematic review. Front Immunol 2023; 14:1115794. [PMID: 37020554 PMCID: PMC10067674 DOI: 10.3389/fimmu.2023.1115794] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/08/2023] [Indexed: 04/07/2023] Open
Abstract
The peptidyl arginine deiminase (PADI) family is a calcium ion-dependent group of isozymes with sequence similarity that catalyze the citrullination of proteins. Histones can serve as the target substrate of PADI family isozymes, and therefore, the PADI family is involved in NETosis and the secretion of inflammatory cytokines. Thus, the PADI family is associated with the development of inflammatory autoimmune diseases and cancer, reproductive development, and other related diseases. In this review, we systematically discuss the role of the PADI family in the pathogenesis of various diseases based on studies from the past decade to provide a reference for future research.
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Affiliation(s)
- Changhui Zhu
- Department of Plastic Surgery, Shandong Provincial Qianfoshan Hospital, School of Basic Medical Sciences, Weifang Medical University, Weifang, Shandong, China
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Chunyan Liu
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- *Correspondence: Chunyan Liu, ; Zhengbin Chai,
| | - Zhengbin Chai
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
- *Correspondence: Chunyan Liu, ; Zhengbin Chai,
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TLR-8, TNF-α, and ESR-1α Gene Polymorphism Susceptibility in Onset of Arthritis. Genet Res (Camb) 2022; 2022:9208765. [PMID: 36262248 PMCID: PMC9553836 DOI: 10.1155/2022/9208765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
Arthritis is a genetic disorder characterized by bones and joint degradation assisted by severe pain and inflammation. It is evident by the studies that 0 candidate genes variations play vital role in its development and progression. Therefore, we investigated the genetic variation of TLR-8, TNF, and ESR-1α genes in the Pakistani population. A case-control study comprising 300 RA, 316 OA, and 412 control subjects was conducted. PCR-RFLP and direct sequencing methods were used for determining genetic variations. Analysis was performed by using PLINK and MEGA 6.0 software. Allelic and genetic frequencies of polymorphisms identified on rs3764879 (TLR-8), rs3764880 (TLR-8), rs5744080 (TLR-8), rs1800629 (TNF), rs2228480 (ESR-1α), and rs1451501590 (ESR-1α) were significantly varied among RA, OA, and controls. Novel functional mutations SCV000844945 and SCV000844946 on TLR-8 as well as a non-functional SCV000804801 and functional variation SCV000804802 on ESR-1α were also identified and reported for the first time in the studied population. Multiple site analyses indicated that polymorphisms on TLR-8 and ESR-1α genes were significant risk factors in disease onset to the next generation. In conclusion, TLR-08 and ESR-1α were significant in the onset of arthritis whereas the TNF was not found as a significant risk factor in the onset of RA and OA.
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Mikhaylenko DS, Kuznetsova EB, Musatova VV, Bure IV, Deryagina TA, Alekseeva EA, Tarasov VV, Zamyatnin AA, Nemtsova MV. Genetic and Clinical Factors Associated with Olokizumab Treatment in Russian Patients with Rheumatoid Arthritis. J Pers Med 2022; 12:jpm12040641. [PMID: 35455757 PMCID: PMC9024465 DOI: 10.3390/jpm12040641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease and its treatment is an urgent problem of rheumatology. Olokizumab (OKZ) is a new humanized monoclonal antibody targeting IL-6 and is one of the few promising drugs for RA therapy. One-hundred-and-twenty-five DNA samples from Russian patients with RA, treated with olokizumab, were genotyped with an NGS panel containing 60 single nucleotide polymorphisms (SNPs) and the whole coding sequences of IL6, IL6R, TNFRSF1A, CTLA4, IL10, IL23R, and PADI4; and by RT-PCR for HLA-DRB1 and HLA-B. Associations of polymorphic variants with olokizumab efficacy according to the scores ACR20, ACR50, and DAS28-CRP were determined. We analyzed the obtained data by using logistic regression, ROC curves, and multivariate ANOVA. A high predictive value of the response to olokizumab therapy at 24 weeks was found for the combination of HLA-DRB1*04 and HLA-B*27 alleles with SNPs located in non-HLA genes (IL1B, IL17A, PADI4, DHODH, GLCCI1, IL23R, and TNFAIP3), and clinical characteristics (age, RA duration, and intensity) according to ACR20. Thus, the comprehensive assessment of polymorphic variants of HLA and non-HLA genes considering population characteristics in combination with clinical parameters allows for the elaboration of an RA prognostic panel.
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Affiliation(s)
- Dmitry S. Mikhaylenko
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.M.); (E.B.K.); (I.V.B.); (E.A.A.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.V.M.); (T.A.D.)
| | - Ekaterina B. Kuznetsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.M.); (E.B.K.); (I.V.B.); (E.A.A.); (M.V.N.)
| | - Viktoria V. Musatova
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.V.M.); (T.A.D.)
| | - Irina V. Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.M.); (E.B.K.); (I.V.B.); (E.A.A.); (M.V.N.)
| | - Tatiana A. Deryagina
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.V.M.); (T.A.D.)
| | - Ekaterina A. Alekseeva
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.M.); (E.B.K.); (I.V.B.); (E.A.A.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.V.M.); (T.A.D.)
| | - Vadim V. Tarasov
- Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.M.); (E.B.K.); (I.V.B.); (E.A.A.); (M.V.N.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7X, UK
- Correspondence: ; Tel.: +7-9261180220
| | - Marina V. Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.M.); (E.B.K.); (I.V.B.); (E.A.A.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.V.M.); (T.A.D.)
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