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Dopytalska K, Czaplicka A, Szymańska E, Walecka I. The Essential Role of microRNAs in Inflammatory and Autoimmune Skin Diseases-A Review. Int J Mol Sci 2023; 24:ijms24119130. [PMID: 37298095 DOI: 10.3390/ijms24119130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The etiopathogenesis of autoimmune skin diseases is complex and still not fully understood. The role of epigenetic factors is emphasized in the development of such diseases. MicroRNAs (miRNAs), a group of non-coding RNAs (ncRNAs-non-coding RNAs), are one of the important post-transcriptional epigenetic factors. miRNAs have a significant role in the regulation of the immune response by participating in the process of the differentiation and activation of B and T lymphocytes, macrophages, and dendritic cells. Recent advances in research on epigenetic factors have provided new insights into the pathogenesis and potential diagnostic and therapeutic targets of many pathologies. Numerous studies revealed a change in the expression of some microRNAs in inflammatory skin disorders, and the regulation of miRNA expression is a promising therapeutic goal. This review presents the state of the art regarding changes in the expression and role of miRNAs in inflammatory and autoimmune skin diseases, including psoriasis, atopic dermatitis, vitiligo, lichen planus, hidradenitis suppurativa, and autoimmune blistering diseases.
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Affiliation(s)
- Klaudia Dopytalska
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
| | - Anna Czaplicka
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
| | - Elżbieta Szymańska
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
| | - Irena Walecka
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
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2
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Okuno Y, Hattori-Kato M, Tanaka H, Tonooka A, Takeuchi T. Relationship between the Reduced Expression of Zinc Finger Protein 668 in Bladder Cancer and Its Invasiveness. Int J Mol Sci 2023; 24:ijms24108668. [PMID: 37240013 DOI: 10.3390/ijms24108668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The zinc finger protein 668 (ZNF668) gene encodes a Kruppel C2H2-type zinc-finger protein with 16 C2H2-type zinc fingers. The ZNF668 gene functions as a tumor suppressor gene in breast cancer. We histologically analyzed ZNF668 protein expression in bladder cancer and examined mutations of the ZNF668 gene in 68 cases of bladder cancer. In bladder cancer, the ZNF668 protein was expressed in the nuclei of cancer cells. In bladder cancer with submucosal and muscular infiltration, the expression of ZNF668 protein was significantly lower than that without submucosal and muscular infiltration. Eight heterozygous somatic mutations were detected in exon3 in five cases, and five of the mutations resulted in amino acid sequence mutations. Mutations resulting in amino acid sequence alterations also resulted in lower ZNF668 protein expression in bladder cancer cell nuclei, but no significant association with bladder cancer infiltration was detected. Decreased ZNF668 expression in bladder cancer was associated with submucosal and muscle invasion of cancer cells. Somatic mutations resulting in amino acid mutations in ZNF668 were found in 7.3% of the bladder cancer cases.
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Affiliation(s)
- Yumiko Okuno
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, 1-1 Kizukisumiyoshi-cho, Nakahara-ku, Kawasaki 211-8510, Japan
| | - Mami Hattori-Kato
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, 1-1 Kizukisumiyoshi-cho, Nakahara-ku, Kawasaki 211-8510, Japan
| | - Hiroki Tanaka
- Department of Pathology, JR Tokyo General Hospital, 2-1-3 Yoyogi, Sibuya-ku, Tokyo 151-8528, Japan
| | - Akiko Tonooka
- Department of Pathology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Takumi Takeuchi
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, 1-1 Kizukisumiyoshi-cho, Nakahara-ku, Kawasaki 211-8510, Japan
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3
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The critical importance of epigenetics in autoimmune-related skin diseases. Front Med 2023; 17:43-57. [PMID: 36811762 DOI: 10.1007/s11684-022-0980-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/05/2022] [Indexed: 02/24/2023]
Abstract
Autoimmune-related skin diseases are a group of disorders with diverse etiology and pathophysiology involved in autoimmunity. Genetics and environmental factors may contribute to the development of these autoimmune disorders. Although the etiology and pathogenesis of these disorders are poorly understood, environmental variables that induce aberrant epigenetic regulations may provide some insights. Epigenetics is the study of heritable mechanisms that regulate gene expression without changing DNA sequences. The most important epigenetic mechanisms are DNA methylation, histone modification, and noncoding RNAs. In this review, we discuss the most recent findings regarding the function of epigenetic mechanisms in autoimmune-related skin disorders, including systemic lupus erythematosus, bullous skin diseases, psoriasis, and systemic sclerosis. These findings will expand our understanding and highlight the possible clinical applications of precision epigenetics approaches.
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Integrated Approaches to Identify miRNA Biomarkers Associated with Cognitive Dysfunction in Multiple Sclerosis Using Text Mining, Gene Expression, Pathways, and GWAS. Diagnostics (Basel) 2022; 12:diagnostics12081914. [PMID: 36010264 PMCID: PMC9406323 DOI: 10.3390/diagnostics12081914] [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: 07/05/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple sclerosis (MS), a chronic autoimmune disorder, affects the central nervous system of many young adults. More than half of MS patients develop cognition problems. Although several genomic and transcriptomic studies are currently reported in MS cognitive impairment, a comprehensive repository dealing with all the experimental data is still underdeveloped. In this study, we combined text mining, gene regulation, pathway analysis, and genome-wide association studies (GWAS) to identify miRNA biomarkers to explore the cognitive dysfunction in MS, and to understand the genomic etiology of the disease. We first identified the dysregulated miRNAs associated with MS and cognitive dysfunction using PubTator (text mining), HMDD (experimental associations), miR2Disease, and PhenomiR database (differentially expressed miRNAs). Our results suggest that miRNAs such as hsa-mir-148b-3p, hsa-mir-7b-5p, and hsa-mir-7a-5p are commonly associated with MS and cognitive dysfunction. Next, we retrieved GWAS signals from GWAS Catalog, and analyzed the enrichment analysis of association signals in genes/miRNAs and their association networks. Then, we identified susceptible genetic loci, rs17119 (chromosome 6; p = 1 × 10−10), rs1843938 (chromosome 7; p = 1 × 10−10), and rs11637611 (chromosome 15; p = 1.00 × 10−15), associated with significant genetic risk. Lastly, we conducted a pathway analysis for the susceptible genetic variants and identified novel risk pathways. The ECM receptor signaling pathway (p = 3.98 × 10−8) and PI3K/Akt signaling pathway (p = 5.98 × 10−5) were found to be associated with differentially expressed miRNA biomarkers.
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Kneiber D, Kowalski EH, Amber KT. The Immunogenetics of Autoimmune Blistering Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:173-212. [DOI: 10.1007/978-3-030-92616-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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Sun Y, Hou Y, Meng G, Han P, Zhao Y, Wang H, Xu M, Wang Y, Qiu J, Peng J, Shao L, Sun L, Hou M. Proteomic analysis and microRNA expression profiling of plasma-derived exosomes in primary immune thrombocytopenia. Br J Haematol 2021; 194:1045-1052. [PMID: 34337736 DOI: 10.1111/bjh.17720] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 12/23/2022]
Abstract
Exosomes are released into extracellular fluids and have emerged as vital biological mediators in autoimmune diseases. Plasma-derived exosomes have been reported to take part in the pathogenesis of primary immune thrombocytopenia (ITP), but the protein and miRNA cargoes have not been entirely elucidated. Via proteomic analysis and RNA sequencing on plasma-derived exosomes from ITP patients and healthy controls, we found one upregulated exosomal protein (apolipoprotein E, ApoE), six downregulated exosomal miRNAs (miR-584-5p, miR-4433a-5p, miR-4433b-3p, miR-6842-3p, miR-130b-5p and miR-222-3p), and 10 upregulated exosomal miRNAs (miR-29a-3p, miR-142-5p, miR-16-2-3p, miR-29b-3p, miR-501-3p, miR-144-5p, miR-192-5p, miR-182-5p, miR-363-3p and miR-96-5p) in ITP patients. The elevated exosomal protein candidate ApoE in the ITP cohort was further validated using western blot. Via quantitative real-time polymerase chain reaction assays, three differentially expressed miRNAs (miR-584-5p, miR-142-5p and miR-29b-3p) were identified. This study provides direct evidence for a restricted signature of exosomal protein and miRNAs which distinguishes ITP from healthy controls. The results require further validation in larger independent ITP cohorts, which will provide insights into the potential pathophysiological significance of circulating exosomes in ITP.
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Affiliation(s)
- Yunqi Sun
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Pain, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yu Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Guiyue Meng
- Department of Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Panpan Han
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yajing Zhao
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haoyi Wang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Miao Xu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yawen Wang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jihua Qiu
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jun Peng
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Linlin Shao
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lu Sun
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Leading Research Group of Scientific Innovation, Department of Science and Technology of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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7
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Salviano-Silva A, Becker M, Augusto DG, Busch H, Adelman Cipolla G, Farias TDJ, Bumiller-Bini V, Calonga-Solís V, Munz M, Franke A, Wittig M, Camargo CM, Goebeler M, Hundt JE, Günther C, Gläser R, Hadaschik E, Pföhler C, Sárdy M, Van Beek N, Worm M, Zillikens D, Boldt ABW, Schmidt E, Petzl-Erler ML, Ibrahim S, Malheiros D. Genetic association and differential expression of HLAComplexGroup lncRNAs in pemphigus. J Autoimmun 2021; 123:102705. [PMID: 34325306 DOI: 10.1016/j.jaut.2021.102705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pemphigus is a group of bullous diseases characterized by acantholysis and skin blisters. As for other autoimmune diseases, the strongest genetic associations found so far for pemphigus foliaceus (PF) and vulgaris (PV) are with alleles of HLA genes. However, apart from protein-coding genes, the MHC region includes a set of poorly explored long non-coding RNA (lncRNA) genes, the HLA complex group (HCG). OBJECTIVES To investigate if HCG lncRNA alleles are associated with pemphigus susceptibility. METHODS AND RESULTS We analyzed SNPs in 13 HCG lncRNA genes, both in PV (Germany: 241 patients; 1,188 controls) and endemic PF (Brazil: 227 patients; 194 controls), applying multivariate logistic regression. We found 55 associations with PV (pcorr < 0.01) and nine with endemic PF (pcorr < 0.05), the majority located in TSBP1-AS1 (which includes HCG23) and HCG27 lncRNA genes, independently of HLA alleles previously associated with pemphigus. The association of TSBP1-AS1 rs3129949*A allele was further replicated in sporadic PF (p = 0.027, OR = 0.054; 75 patients and 150 controls, all from Germany). Next, we evaluated the expression levels of TSBP1-AS1, TSBP1, HCG23, and HCG27 in blood mononuclear cells of Brazilian patients and controls. HCG27 was upregulated in endemic PF (p = 0.035, log2 FC = 1.3), while TSBP1-AS1 was downregulated in PV (p = 0.029, log2 FC = -1.29). The same expression patterns were also seen in cultured keratinocytes stimulated with IgG antibodies from patients and controls from Germany. TSBP1 mRNA levels were also decreased in endemic PF blood cells (p = 0.042, log2 FC = -2.14). TSBP1-AS1 and HCG27 were also observed downregulated in CD19+ cells of endemic PF (p < 0.01, log2 FC = -0.226 and -0.46 respectively). CONCLUSIONS HCG lncRNAs are associated with susceptibility to pemphigus, being TSBP1-AS1 and HCG27 also differentially expressed in distinct cell populations. These results suggest a role for HCG lncRNAs in pemphigus autoimmunity.
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Affiliation(s)
- Amanda Salviano-Silva
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil; Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Mareike Becker
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Danillo G Augusto
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Gabriel Adelman Cipolla
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Ticiana D-J Farias
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Valéria Bumiller-Bini
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil; Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Verónica Calonga-Solís
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Matthias Munz
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Carolina M Camargo
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | | | - Claudia Günther
- Department of Dermatology, University Hospital, TU, Dresden, Germany
| | - Regine Gläser
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Claudia Pföhler
- Saarland University Medical Center, Department of Dermatology, Homburg, Germany
| | - Miklós Sárdy
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany
| | - Nina Van Beek
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Margitta Worm
- Division of Allergy and Immunology, Department of Dermatology, Venerology and Allergy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Angelica B W Boldt
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Enno Schmidt
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Maria Luiza Petzl-Erler
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Saleh Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Danielle Malheiros
- Postgraduate Program in Genetics. Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil.
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Salviano-Silva A, Farias TDJ, Bumiller-Bini V, Castro MDS, Lobo-Alves SC, Busch H, Pföhler C, Worm M, Goebeler M, van Beek N, Franke A, Wittig M, Zillikens D, de Almeida RC, Hundt JE, Boldt ABW, Ibrahim S, Augusto DG, Petzl-Erler ML, Schmidt E, Malheiros D. Genetic variability of immune-related lncRNAs: polymorphisms in LINC-PINT and LY86-AS1 are associated with pemphigus foliaceus susceptibility. Exp Dermatol 2021; 30:831-840. [PMID: 33394553 DOI: 10.1111/exd.14275] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Pemphigus foliaceus (PF) is an autoimmune blistering disease of the skin, clinically characterized by erosions and, histopathologically, by acantholysis. PF is endemic in the Brazilian Central-Western region. Numerous single nucleotide polymorphisms (SNPs) have been shown to affect the susceptibility for PF, including SNPs at long non-coding RNA (lncRNA) genes, which are known to participate in many physiological and pathogenic processes, such as autoimmunity. Here, we investigated whether the genetic variation of immune-related lncRNA genes affects the risk for endemic and sporadic forms of PF. We analysed 692 novel SNPs for PF from 135 immune-related lncRNA genes in 227 endemic PF patients and 194 controls. The SNPs were genotyped by Illumina microarray and analysed by applying logistic regression at additive model, with correction for sex and population structure. Six associated SNPs were also evaluated in an independent German cohort of 76 sporadic PF patients and 150 controls. Further, we measured the expression levels of two associated lncRNA genes (LINC-PINT and LY86-AS1) by quantitative PCR, stratified by genotypes, in peripheral blood mononuclear cells of healthy subjects. We found 27 SNPs in 11 lncRNA genes associated with endemic PF (p < .05 without overlapping with protein-coding genes). Among them, the LINC-PINT SNP rs10228040*A (OR = 1.47, p = .012) was also associated with increased susceptibility for sporadic PF (OR = 2.28, p = .002). Moreover, the A+ carriers of LY86-AS1*rs12192707 mark lowest LY86-AS1 RNA levels, which might be associated with a decreasing autoimmune response. Our results suggest a critical role of lncRNA variants in immunopathogenesis of both PF endemic and sporadic forms.
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Affiliation(s)
- Amanda Salviano-Silva
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | | | - Valéria Bumiller-Bini
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Mariana de Sousa Castro
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Sara Cristina Lobo-Alves
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Claudia Pföhler
- Department of Dermatology, Saarland University Medical Center, Homburg, Germany
| | - Margitta Worm
- Division of Allergy and Immunology, Department of Dermatology, Venerology and Allergy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Nina van Beek
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | | | | | | | - Saleh Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Danillo Gardenal Augusto
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Enno Schmidt
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Danielle Malheiros
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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9
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Calonga‐Solís V, Amorim LM, Farias TDJ, Petzl‐Erler ML, Malheiros D, Augusto DG. Variation in genes implicated in B-cell development and antibody production affects susceptibility to pemphigus. Immunology 2021; 162:58-67. [PMID: 32926429 PMCID: PMC7730027 DOI: 10.1111/imm.13259] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/23/2020] [Accepted: 08/29/2020] [Indexed: 12/12/2022] Open
Abstract
Pemphigus foliaceus (PF) is an autoimmune blistering skin disease characterized by the presence of pathogenic autoantibodies against desmoglein 1, a component of intercellular desmosome junctions. PF occurs sporadically across the globe and is endemic in some Brazilian regions. Because PF is a B-cell-mediated disease, we aimed to study the impact of variants within genes encoding molecules involved in the different steps of B-cell development and antibody production on the susceptibility of endemic PF. We analysed 3,336 single nucleotide polymorphisms (SNPs) from 167 candidate genes genotyped with Illumina microarray in a cohort of 227 PF patients and 193 controls. After quality control and exclusion of non-informative and redundant SNPs, 607 variants in 149 genes remained in the logistic regression analysis, in which sex and ancestry were included as covariates. Our results revealed 10 SNPs within or nearby 11 genes that were associated with susceptibility to endemic PF (OR >1.56; p < 0.005): rs6657275*G (TGFB2); rs1818545*A (RAG1/RAG2/IFTAP);rs10781530*A (PAXX), rs10870140*G and rs10781522*A (TRAF2); rs535068*A (TNFRSF1B); rs324011*A (STAT6);rs6432018*C (YWHAQ); rs17149161*C (YWHAG); and rs2070729*C (IRF1). Interestingly, these SNPs have been previously associated with differential gene expression, mostly in peripheral blood, in publicly available databases. For the first time, we show that polymorphisms in genes involved in B-cell development and antibody production confer differential susceptibility to endemic PF, and therefore are candidates for possible functional studies to understand immunoglobulin gene rearrangement and its impact on diseases.
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Affiliation(s)
- Verónica Calonga‐Solís
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Leonardo M. Amorim
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Ticiana D. J. Farias
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Maria Luiza Petzl‐Erler
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Danielle Malheiros
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Danillo G. Augusto
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
- Department of NeurologyUniversity of California San FranciscoSan FranciscoCAUSA
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10
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Ganguly K, Kishore U, Madan T. Interplay between C-type lectin receptors and microRNAs in cellular homeostasis and immune response. FEBS J 2020; 288:4210-4229. [PMID: 33085815 DOI: 10.1111/febs.15603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/18/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022]
Abstract
C-type lectin receptors (CLRs) belong to the family of pattern recognition receptors (PRRs). They have a critical role to play in the regulation of a range of physiological functions including development, respiration, angiogenesis, inflammation, and immunity. CLRs can recognize distinct and conserved exogenous pathogen-associated as well as endogenous damage-associated molecular patterns. These interactions set off downstream signaling cascades, leading to the production of inflammatory mediators, activation of effector immune cells as well as regulation of the developmental and physiological homeostasis. CLR signaling must be tightly controlled to circumvent the excessive inflammatory burden and to maintain the cellular homeostasis. Recently, MicroRNAs (miRNAs) have been shown to be important regulators of expression of CLRs and their downstream signaling. The delicate balance between miRNAs and CLRs seems crucial in almost all aspects of multicellular life. Any dysregulations in the miRNA-CLR axes may lead to tumorigenesis or inflammatory diseases. Here, we present an overview of the current understanding of the central role of miRNAs in the regulation of CLR expression, profoundly impacting upon homeostasis and immunity, and thus, development of therapeutics against immune disorders.
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Affiliation(s)
- Kasturi Ganguly
- Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
| | - Uday Kishore
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Taruna Madan
- Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
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11
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Wachs AS, Bohne J. Two sides of the same medal: Noncoding mutations reveal new pathological mechanisms and insights into the regulation of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1616. [PMID: 32633083 DOI: 10.1002/wrna.1616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Abstract
Noncoding sequences constitute the major part of the human genome and also of pre-mRNAs. Single nucleotide variants in these regions are often overlooked, but may be responsible for much of the variation of phenotypes observed. Mutations in the noncoding part of pre-mRNAs often reveal new and meaningful insights into the regulation of cellular gene expression. Thus, the mechanistic analysis of the pathological mechanism of such mutations will both foster a deeper understanding of the disease and the underlying cellular pathways. Even synonymous mutations can cause diseases, since the primary mRNA sequence not only encodes amino acids, but also encrypts information on RNA-binding proteins and secondary structure. In fact, the RNA sequence directs assembly of a specific mRNP complex, which in turn dictates the fate of the mRNA or regulates its biogenesis. The accumulation of genomic sequence information is increasing at a rapid pace. However, much of the diversity uncovered may not explain the phenotype of a certain syndrome or disease. For this reason, we also emphasize the value of mechanistic studies on pathological mechanisms being complementary to genome-wide studies and bioinformatic approaches. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Amelie S Wachs
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, Hanover, Germany
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12
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Petzl-Erler ML. Beyond the HLA polymorphism: A complex pattern of genetic susceptibility to pemphigus. Genet Mol Biol 2020; 43:e20190369. [PMID: 32639508 PMCID: PMC7341728 DOI: 10.1590/1678-4685-gmb-2019-0369] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Pemphigus is a group of autoimmune bullous skin diseases that result in
significant morbidity. As for other multifactorial autoimmune disorders,
environmental factors may trigger the disease in genetically susceptible
individuals. The goals of this review are to summarize the state of knowledge
about the genetic variation that may affect the susceptibility and pathogenesis
of pemphigus vulgaris and pemphigus foliaceus – both the endemic and the
sporadic forms –, to compare and discuss the possible meaning of the
associations reported, and to propose recommendations for new research
initiatives. Understanding how genetic variants translate into pathogenic
mechanisms and phenotypes remains a mystery for most of the polymorphisms that
contribute to disease susceptibility. However, genetic studies provide a strong
foundation for further developments in this field by generating testable
hypotheses. Currently, results still have limited influence on disease
prevention and prognosis, drug development, and clinical practice, although the
perspectives for future applications for the benefit of patients are
encouraging. Recommendations for the continued advancement of our understanding
as to the impact of genetic variation on pemphigus include these partially
overlapping goals: (1) Querying the functional effect of genetic variants on the
regulation of gene expression through their impact on the nucleotide sequence of
cis regulatory DNA elements such as promoters and enhancers, the splicing of
RNA, the structure of regulatory RNAs and proteins, binding of these regulatory
molecules to regulatory DNA elements, and alteration of epigenetic marks; (2)
identifying key cell types and cell states that are implicated in pemphigus
pathogenesis and explore their functional genomes; (3) integrating structural
and functional genomics data; (4) performing disease-progression longitudinal
studies to disclose the causal relationships between genetic and epigenetic
variation and intermediate disease phenotypes; (5) understanding the influence
of genetic and epigenetic variation in the response to treatment and the
severity of the disease; (6) exploring gene-gene and genotype-environment
interactions; (7) developing improved pemphigus-prone and non-prone animal
models that are appropriate for research about the mechanisms that link
genotypes to pemphigus. Achieving these goals will demand larger samples of
patients and controls and multisite collaborations.
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Affiliation(s)
- Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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13
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Song J, Hao L, Wei W, Yang R, Wang C, Geng H, Li H, Wang S, Lu G, Feng T, Sun X, Liu S, Wang G, Cheng Y. A SNP in the 3'UTR of the porcine IGF-1 gene interacts with miR-new14 to affect IGF-1 expression, proliferation and apoptosis of PK-15 cells. Domest Anim Endocrinol 2020; 72:106430. [PMID: 32171113 DOI: 10.1016/j.domaniend.2019.106430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 11/06/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023]
Abstract
The kidney of miniature pigs has been considered the most likely potential kidney source for patients needing kidney transplantation. Insulin-like growth factor 1 (IGF-1) is involved in regulating the growth of miniature pigs and inducing growth of kidneys. There are evidences showing that the SNPs in the 3'UTR of a gene may affect the gene expression by affecting the binding to a miRNA target site. In this study, one SNP (rs34142920) was screened in the IGF-1 3'UTR between 2 different body types of porcine breeds, Bama Xiang (BX) pigs, a miniature pig breed, and Large White (LW) pigs by sequencing. The secondary structure of the IGF-1 3'UTR mRNA containing the SNP in BX pigs is different from that of LW pigs. We then verified that there was a porcine miRNA (miR-new14) binding to this SNP in the 3'UTR of IGF-1 via cotransfecting the 3'UTR from the 2 breeds and miR-new14. We further found that the SNP downregulated mRNA and protein levels of IGF-1 by affecting the binding of miR-new14. To understand the function of miR-new14 in porcine kidney (PK-15) cells and its mechanism, cell proliferation and cell apoptosis assays were employed and results showed that proliferation viability of PK-15 cells was weakened and the apoptotic percentage of PK-15 cells was higher in the miR-new14 group. Porcine miRNA reduced the mRNA expression of AKT/ERK and protein levels of p-AKT/p-ERK. These results suggested that the expression of IGF-1 is influenced by this SNP and miR-new14 and that miR-new14 may suppress cell proliferation and promote cell apoptosis in PK-15 cells through regulating AKT and ERK signaling pathways, in which IGF-1 is involved.
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Affiliation(s)
- Jie Song
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Linlin Hao
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Wenzhen Wei
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Rui Yang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Chunli Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Hongwei Geng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Haoyang Li
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Siyao Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Guanhong Lu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Tianqi Feng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Xiaotong Sun
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Songcai Liu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China; Five-Star Animal Health Pharmaceutical Factory of Jilin Province, 5333 Xi'an Road, Changchun, Jilin 130062, China.
| | - Gang Wang
- Gan&Lee Pharmaceuticals, No. 8 Nanfeng West 1st Street, Huoxian, Tongzhou District, Beijing 101109, China.
| | - Yunyun Cheng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China; College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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14
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Oliveira EH, Assis AF, Speck-Hernandez CA, Duarte MJ, Passos GA. Aire Gene Influences the Length of the 3' UTR of mRNAs in Medullary Thymic Epithelial Cells. Front Immunol 2020; 11:1039. [PMID: 32547551 PMCID: PMC7270294 DOI: 10.3389/fimmu.2020.01039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Aire is a transcriptional controller in medullary thymic epithelial cells (mTECs) modulating a set of peripheral tissue antigens (PTAs) and non-PTA mRNAs as well as miRNAs. Even miRNAs exerting posttranscriptional control of mRNAs in mTECs, the composition of miRNA-mRNA networks may differ. Under reduction in Aire expression, networks exhibited greater miRNA diversity controlling mRNAs. Variations in the number of 3'UTR binding sites of Aire-dependent mRNAs may represent a crucial factor that influence the miRNA interaction. To test this hypothesis, we analyzed through bioinformatics the length of 3'UTRs of a large set of Aire-dependent mRNAs. The data were obtained from existing RNA-seq of mTECs of wild type or Aire-knockout (KO) mice. We used computational algorithms as FASTQC, STAR and HTSEQ for sequence alignment and counting reads, DESEQ2 for the differential expression, 3USS for the alternative 3'UTRs and TAPAS for the alternative polyadenylation sites. We identified 152 differentially expressed mRNAs between these samples comprising those that encode PTAs as well as transcription regulators. In Aire KO mTECs, most of these mRNAs featured an increase in the length of their 3'UTRs originating additional miRNA binding sites and new miRNA controllers. Results from the in silico analysis were statistically significant and the predicted miRNA-mRNA interactions were thermodynamically stable. Even with no in vivo or in vitro experiments, they were adequate to show that lack of Aire in mTECs might favor the downregulation of PTA mRNAs and transcription regulators via miRNA control. This could unbalance the overall transcriptional activity in mTECs and thus the self-representation.
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Affiliation(s)
- Ernna H. Oliveira
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Cesar A. Speck-Hernandez
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Max Jordan Duarte
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Geraldo A. Passos
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Laboratory of Genetics and Molecular Biology, Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, USP, Ribeirão Preto, Brazil
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15
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Curdy N, Lanvin O, Laurent C, Fournié JJ, Franchini DM. Regulatory Mechanisms of Inhibitory Immune Checkpoint Receptors Expression. Trends Cell Biol 2019; 29:777-790. [DOI: 10.1016/j.tcb.2019.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 12/31/2022]
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16
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Lobo‐Alves S, Augusto D, Magalhães W, Tarazona‐Santos E, Lima‐Costa M, Barreto M, Horta B, Almeida R, Petzl‐Erler M. Long noncoding
RNA
polymorphisms influence susceptibility to endemic pemphigus foliaceus. Br J Dermatol 2019; 181:324-331. [DOI: 10.1111/bjd.17640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2019] [Indexed: 01/21/2023]
Affiliation(s)
- S.C. Lobo‐Alves
- Laboratório de Genética Molecular Humana Departamento de Genética Universidade Federal do Paraná Curitiba Brazil
| | - D.G. Augusto
- Laboratório de Genética Molecular Humana Departamento de Genética Universidade Federal do Paraná Curitiba Brazil
- Departamento de Ciências Biológicas Universidade Estadual de Santa Cruz Ilhéus Brazil
| | - W.C.S. Magalhães
- Núcleo de Ensino e Pesquisa – NEP, Instituto Mário Penna Belo Horizonte Minas Gerais Brazil
- Instituto de Ciências Biológicas Departamento de Biologia Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - E. Tarazona‐Santos
- Instituto de Ciências Biológicas Departamento de Biologia Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - M.F. Lima‐Costa
- Instituto de Pesquisa Rene Rachou Fundação Oswaldo Cruz Belo Horizonte MG Brazil
| | - M.L. Barreto
- Instituto de Saúde Coletiva Universidade Federal da Bahia Salvador BA Brazil
| | - B.L. Horta
- Programa de Pós‐Graduação em Epidemiologia Universidade Federal de Pelotas Pelotas RS Brazil
| | - R.C. Almeida
- Department of Biomedical Data Sciences Section Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
| | - M.L. Petzl‐Erler
- Laboratório de Genética Molecular Humana Departamento de Genética Universidade Federal do Paraná Curitiba Brazil
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17
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Lobo-Alves SC, de Oliveira LA, Petzl-Erler ML. Region 1p13.2 including the RSBN1, PTPN22, AP4B1 and long non-coding RNA genes does not bear risk factors for endemic pemphigus foliaceus (fogo selvagem). Int J Immunogenet 2019; 46:139-145. [PMID: 30884100 DOI: 10.1111/iji.12423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 12/27/2022]
Abstract
Pemphigus foliaceus (PF) is an autoimmune skin disease characterized by autoantibodies directed mainly against desmoglein-1. The purpose of this study was to determine whether differential susceptibility to endemic PF in Brazil (fogo selvagem) is associated with polymorphisms at the cytogenetic location 1p13.2. Four single nucleotide polymorphisms that together tag 28 SNPs on a segment of approximately 312,000 bp encompassing the protein-coding genes MAGI3, PHTF1, RSBN1, PTPN22, BCL2L15, AP4B1, DCLRE1B, the pseudogenes MTND5P20, RPS2P14 (AL133517.1) and the long non-coding RNA genes AL137856.1, and AP4B1-AS1 were used as markers for association analysis in a case-control study. Allele, genotype and haplotype frequencies of rs33996649, rs2476601, rs3789604 and rs3195954 were compared between patient and control samples. No significant association was found. Lack of association with rs2476601 of the PTPN22 gene agrees with previous results for pemphigus vulgaris and the Tunisian form of endemic pemphigus foliaceus. The other three SNPs had never been analysed before in any form of pemphigus. We conclude that variants in structural and regulatory sites of region 1p13.2 are not susceptibility factors for fogo selvagem. We suggest careful investigation of this genomic region in diseases that had been previously associated with PTPN22, since there are several other genes relevant for immune-mediated diseases located in 1p13.2.
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Affiliation(s)
- Sara Cristina Lobo-Alves
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Liana Alves de Oliveira
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
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18
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Factors Regulating microRNA Expression and Function in Multiple Myeloma. Noncoding RNA 2019; 5:ncrna5010009. [PMID: 30654527 PMCID: PMC6468559 DOI: 10.3390/ncrna5010009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/13/2019] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Intensive research has been undertaken during the last decade to identify the implication of microRNAs (miRNAs) in the pathogenesis of multiple myeloma (MM). The expression profiling of miRNAs in MM has provided relevant information, demonstrating different patterns of miRNA expression depending on the genetic abnormalities of MM and a key role of some miRNAs regulating critical genes associated with MM pathogenesis. However, the underlying causes of abnormal expression of miRNAs in myeloma cells remain mainly elusive. The final expression of the mature miRNAs is subject to multiple regulation mechanisms, such as copy number alterations, CpG methylation or transcription factors, together with impairment in miRNA biogenesis and differences in availability of the mRNA target sequence. In this review, we summarize the available knowledge about the factors involved in the regulation of miRNA expression and functionality in MM.
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19
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Farias TDJ, Augusto DG, de Almeida RC, Malheiros D, Petzl-Erler ML. Screening the full leucocyte receptor complex genomic region revealed associations with pemphigus that might be explained by gene regulation. Immunology 2018; 156:86-93. [PMID: 30216441 DOI: 10.1111/imm.13003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 12/11/2022] Open
Abstract
Pemphigus foliaceus (PF) is a blistering autoimmune skin disease rare in most of the world but endemic in certain regions of Brazil. PF is characterized by the detachment of epidermal cells and the presence of autoantibodies against desmoglein 1. In previous studies, we have shown that genetic polymorphisms and variable expression levels of certain leucocyte receptor complex (LRC) genes were associated with PF. However, the role of the LRC on PF susceptibility remained to be investigated. Here, we analysed 527 tag single nucleotide polymorphisms (SNPs) distributed within the 1·5 Mb LRC. After quality control, a total of 176 SNPs were analysed in 229 patients with PF and 194 controls. Three SNPs were associated with differential susceptibility to PF. The intergenic variant rs465169 [odds ratio (OR) = 1·50; P = 0·004] is located in a region that might regulate several immune-related genes, including VSTM1, LILRB1/2, LAIR1/2, LILRA3/4 and LENG8. The rs35336528 (OR = 3·44; P = 0·009) and rs1865097 (OR = 0·57; P = 0·005) SNPs in LENG8 and FCAR genes, respectively, were also associated with PF. Moreover, we found four haplotypes with SNPs within the KIR3DL2/3, LAIR2 and LILRB1 genes associated with PF (P < 0·05), which corroborate previously reported associations. Thus, our results confirm the importance of the LRC for differential susceptibility to PF and reveal new markers that might influence expression levels of several LRC genes, as well as candidates for further functional studies.
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Affiliation(s)
| | - Danillo G Augusto
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil.,Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danielle Malheiros
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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20
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Zhu B, Ju S, Chu H, Shen X, Zhang Y, Luo X, Cong H. The potential function of microRNAs as biomarkers and therapeutic targets in multiple myeloma. Oncol Lett 2018; 15:6094-6106. [PMID: 29731841 PMCID: PMC5920744 DOI: 10.3892/ol.2018.8157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/10/2018] [Indexed: 12/30/2022] Open
Abstract
Multiple myeloma (MM), accounting for ~1% of all types of human cancer and 13% of all hematological malignancies, is characterized by the malignant proliferation of monoclonal plasma cells (PCs) in the bone marrow. MM leads to end stage organ impairment, including bone lesions, renal dysfunction, hypercalcemia and anemia. So far, the specific pathogenesis of MM remains unclear and no early-stage sensitive biomarker of MM has been well characterized. Furthermore, treating MM is difficult, as the majority of patients eventually relapse or become refractory following treatment using presently available methods. To date, a number of studies have demonstrated that microRNAs (miRNAs) may serve crucial functions in the progression of numerous cancers, including MM. During the tumorigenesis and pathogenesis of MM, there are multiple carcinogenic events that involve the pernicious transformation from normal to malignant PCs. miRNAs, as oncogenes or tumor suppressors, regulate MM progression-related signaling pathways. In the present review, the up-to-date preliminary basic studies and associated clinical works on the underlying mechanisms of aberrant miRNA profiling in MM have been summarized, including an evaluation of its value as a potential biomarker and a novel therapeutic strategy for MM.
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Affiliation(s)
- Bingying Zhu
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Shaoqing Ju
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Haidan Chu
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xianjuan Shen
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Yan Zhang
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xi Luo
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Hui Cong
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
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21
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de Almeida RC, Chagas VS, Castro MAA, Petzl-Erler ML. Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites. Front Genet 2018; 9:139. [PMID: 29755505 PMCID: PMC5932181 DOI: 10.3389/fgene.2018.00139] [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: 01/10/2018] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3' untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites. Yet, little is known about their effect on regulation by miRNA and the consequences for AID. Conversely, it is well known that two or more AID may share part of their genetic background. Here, we hypothesized that miRSNPs could be associated with more than one AID. To identify miRSNPs associated with AID, we integrated results from three different prediction tools (Polymirts, miRSNP, and miRSNPscore) using a naïve Bayes classifier approach to identify miRSNPs predicted to affect binding sites of miRNAs. Further, to detect miRSNPs associated with two or more AID, we integrated predictions with summary statistics from 12 AID studies. In addition, to prioritize miRSNPs, miRNAs and AID-associated target genes, we used public expression quantitative trait locus (eQTL) data and mRNA-seq and small RNA-seq data. We identified 34 miRNSPs associated with at least two AID. Furthermore, we found 86 miRNAs predicted to target 18 of the associated gene's mRNAs. Our integrative approach revealed new insights into miRNAs and AID associated target genes. Thus, it helped to prioritize AID noncoding risk SNPs that might be involved in the causal mechanisms, providing valuable information for further functional studies.
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Affiliation(s)
- Rodrigo C. de Almeida
- Human Molecular Genetics Laboratory, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Vinícius S. Chagas
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Brazil
| | - Mauro A. A. Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Brazil
| | - Maria L. Petzl-Erler
- Human Molecular Genetics Laboratory, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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22
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Bumiller-Bini V, Cipolla GA, de Almeida RC, Petzl-Erler ML, Augusto DG, Boldt ABW. Sparking Fire Under the Skin? Answers From the Association of Complement Genes With Pemphigus Foliaceus. Front Immunol 2018; 9:695. [PMID: 29686679 PMCID: PMC5900433 DOI: 10.3389/fimmu.2018.00695] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Abstract
Skin blisters of pemphigus foliaceus (PF) present concomitant deposition of autoantibodies and components of the complement system (CS), whose gene polymorphisms are associated with susceptibility to different autoimmune diseases. To investigate these in PF, we evaluated 992 single-nucleotide polymorphisms (SNPs) of 44 CS genes, genotyped through microarray hybridization in 229 PF patients and 194 controls. After excluding SNPs with minor allele frequency <1%, out of Hardy-Weinberg equilibrium in controls or in strong linkage disequilibrium (r2 ≥ 0.8), 201 SNPs remained for logistic regression. Polymorphisms of 11 genes were associated with PF. MASP1 encodes a crucial serine protease of the lectin pathway (rs13094773: OR = 0.5, p = 0.0316; rs850309: OR = 0.23, p = 0.03; rs3864098: OR = 1.53, p = 0.0383; rs698104: OR = 1.52, p = 0.0424; rs72549154: OR = 0.55, p = 0.0453). C9 (rs187875: OR = 1.46, p = 0.0189; rs700218: OR = 0.12, p = 0.0471) and C8A (rs11206934: OR = 4.02, p = 0.0323) encode proteins of the membrane attack complex (MAC) and C5AR1 (rs10404456: OR = 1.43, p = 0.0155), a potent anaphylatoxin-receptor. Two encode complement regulators: MAC-blocking CD59 (rs1047581: OR = 0.62, p = 0.0152) and alternative pathway-blocking CFH (rs34388368: OR = 2.57, p = 0.0195). One encodes opsonin: C3 (rs4807895: OR = 2.52, p = 0.0239), whereas four encode receptors for C3 fragments: CR1 (haplotype with rs6656401: OR = 1.37, p = 0.0382), CR2 (rs2182911: OR = 0.23, p = 0.0263), ITGAM (CR3, rs12928810: OR = 0.66, p = 0.0435), and ITGAX (CR4, rs11574637: OR = 0.63, p = 0.0056). Associations reinforced former findings, regarding differential gene expression, serum levels, C3, and MAC deposition on lesions. Deregulation of previously barely noticed processes, e.g., the lectin and alternative pathways and opsonization-mediated phagocytosis, also modulate PF susceptibility. The results open new crucial avenues for understanding disease etiology and may improve PF treatment through additional therapeutic targets.
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Affiliation(s)
- Valéria Bumiller-Bini
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Gabriel Adelman Cipolla
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Rodrigo Coutinho de Almeida
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo Gardenal Augusto
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratory of Molecular Immunopathology, Department of Clinical Pathology, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
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Regis S, Caliendo F, Dondero A, Bellora F, Casu B, Bottino C, Castriconi R. Main NK cell receptors and their ligands: regulation by microRNAs. AIMS ALLERGY AND IMMUNOLOGY 2018. [DOI: 10.3934/allergy.2018.2.98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Fang X, Yin Z, Li X, Xia L, Quan X, Zhao Y, Zhou B. Multiple functional SNPs in differentially expressed genes modify risk and survival of non-small cell lung cancer in Chinese female non-smokers. Oncotarget 2017; 8:18924-18934. [PMID: 28148898 PMCID: PMC5386658 DOI: 10.18632/oncotarget.14836] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022] Open
Abstract
DNA genotype can affect gene expression, and gene expression can influence the onset and progression of diseases. Here we conducted a comprehensive study, we integrated analysis of gene expression profile and single nucleotide polymorphism (SNP) microarray data in order to scan out the critical genetic changes that participate in the onset and development of non-small cell lung cancer (NSCLC). Gene expression profile datasets were downloaded from the GEO database. Firstly, differentially expressed genes (DEGs) between NSCLC samples and adjacent normal samples were identified. Next, by STRING database, protein-protein interaction (PPI) network was constructed. At the same time, hub genes in PPI network were identified. Then, some functional SNPs in hub genes that may affect gene expression have been annotated. Finally, we carried a study to explore the relationship between functional SNPs and NSCLC risk and overall survival in Chinese female non-smokers. A total of 488 DEGs were identified in our study. There are 29 proteins with a higher degree of connectivity in the PPI network, including FOS, IL6 and MMP9. By using database annotation, we got 8 candidate functional SNPs that may affect the expression level of hub proteins. In the case-control study, we found that rs4754-T allele, rs959173-C allele and rs2239144-G allele were the protective allele of NSCLC risk. In dominant model, rs4754-CT+TT genotype were associated with a shorter survival time. In general, our study provides a novel research direction in the field of multi-omic data integration, and helps us find some critical genetic changes in disease.
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Affiliation(s)
- Xue Fang
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Lingzi Xia
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xiaowei Quan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Yuxia Zhao
- Department of Radiotherapy, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
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He W, Lu M, Li G, Sun Z, Liu D, Gu L. Methylene Tetrahydrofolate Reductase (MTHFR) rs868014 Polymorphism Regulated by miR-1203 Associates with Risk and Short Term Outcome of Ischemic Stroke. Cell Physiol Biochem 2017; 41:701-710. [DOI: 10.1159/000458429] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022] Open
Abstract
Background/Aims: Genetic polymorphisms of methylene tetrahydrofolate reductase (MTHFR) were associated with ischemic stroke risk. This study analyzed MTHFR polymorphisms at the 3'-untranslated region for association with risk and outcome of ischemic stroke in a Chinese Han population. Methods: 500 patients and 600 healthy volunteers were enrolled for MTHFR rs868014 genotyping identified bioinformatically. The binding of miR-1203 to MTHFR rs868014 was determined by luciferase assay, MTHFR expression was assessed using qRT-PCR, and plasma homocysteine levels were assayed by ELISA. Results: Cigarette smoking, alcohol consumption, diabetes, hypertension (all P <0.001), low levels of serum high-density lipoprotein-C (P = 0.01), and high levels of serum low-density lipoprotein-C (P = 0.005) were associated with an increased risk of developing ischemic stroke. BMI and total serum cholesterol concentration was not associated with ischemic stroke. MTHFR rs868014 TC and CC genotypes were significantly associated with increased risk of ischemic stroke compared with the TT genotype (OR: 1.52; 95% CI: 1.01-3.39 for TC genotype, while OR: 1.99; 95% CI: 1.29-3.88 for CC genotype). Furthermore, the MTHFR rs868014 SNP was associated with a poor short-term ischemic stroke outcome. qRT-PCR confirmed that MTHFR rs868014 TC or CC genotypes could facilitate miR-1203 binding leading to low MTHFR levels in cells. In addition, patients carrying the MTHFR rs868014 TC or CC genotypes were associated with accumulation of serum tHcy and a poor ischemic stroke outcome. Linkage disequilibrium analysis indicated that the newly identified SNP rs868014 was strongly linked with the MTHFR A1298C polymorphism. Conclusion: This study demonstrates that the MTHFR rs868014 SNP is associated with increased risk in developing ischemic stroke, miR-1203 binding, low MTHFR levels in cells, and poor shot term outcome of patients.
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