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Investigation of UTR Variants by Computational Approaches Reveal Their Functional Significance in PRKCI Gene Regulation. Genes (Basel) 2023; 14:genes14020247. [PMID: 36833174 PMCID: PMC9956319 DOI: 10.3390/genes14020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/02/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are associated with many diseases including neurological disorders, heart diseases, diabetes, and different types of cancers. In the context of cancer, the variations within non-coding regions, including UTRs, have gained utmost importance. In gene expression, translational regulation is as important as transcriptional regulation for the normal functioning of cells; modification in normal functions can be associated with the pathophysiology of many diseases. UTR-localized SNPs in the PRKCI gene were evaluated using the PolymiRTS, miRNASNP, and MicroSNIper for association with miRNAs. Furthermore, the SNPs were subjected to analysis using GTEx, RNAfold, and PROMO. The genetic intolerance to functional variation was checked through GeneCards. Out of 713 SNPs, a total of thirty-one UTR SNPs (three in 3' UTR region and twenty-nine in 5' UTR region) were marked as ≤2b by RegulomeDB. The associations of 23 SNPs with miRNAs were found. Two SNPs, rs140672226 and rs2650220, were significantly linked with expression in the stomach and esophagus mucosa. The 3' UTR SNPs rs1447651774 and rs115170199 and the 5' UTR region variants rs778557075, rs968409340, and 750297755 were predicted to destabilize the mRNA structure with substantial change in free energy (∆G). Seventeen variants were predicted to have linkage disequilibrium with various diseases. The SNP rs542458816 in 5' UTR was predicted to put maximum influence on transcription factor binding sites. Gene damage index(GDI) and loss of function (o:e) ratio values for PRKCI suggested that the gene is not tolerant to loss of function variants. Our results highlight the effects of 3' and 5' UTR SNP on miRNA, transcription and translation of PRKCI. These analyses suggest that these SNPs can have substantial functional importance in the PRKCI gene. Future experimental validation could provide further basis for the diagnosis and therapeutics of various diseases.
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2
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Lu D, Wang M, Yang T, Wang J, Lin B, Liu G, Liang Q. Association of Interleukin-6 Polymorphisms with Schizophrenia and Depression: A Case-Control Study. Lab Med 2022; 54:250-255. [PMID: 36239635 DOI: 10.1093/labmed/lmac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
Objective
Growing evidence suggests a crossover in genetic susceptibility to schizophrenia and depression. We aimed to investigate the association of the rs1800795 and rs1800796 polymorphisms of the IL-6 gene with schizophrenia and depression in the Han Chinese population, combined with IL-6 serum levels.
Methods
Gene sequencing and enzyme-linked immunosorbent assay were performed on 113 subjects with schizophrenia, 114 subjects with depression, and 110 healthy controls.
Results
Our findings showed that IL-6 concentrations in schizophrenia and depression groups were significantly higher than in the control group. The rs1800796 CC genotype and C allele were significantly associated with depression (P = .012 and P < .05, respectively). The rs1800796 CC and CG genotype was significantly associated with chronic schizophrenia (P = .020 and P = .009, respectively). Regarding the rs1800795 polymorphism, only one case of CG genotype was detected. The remainder were of the GG genotype.
Conclusion
The IL-6 rs1800796 might serve as a protective factor for depression and schizophrenia in the Han Chinese population.
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Affiliation(s)
- Danyu Lu
- Department of Clinical Laboratory, Fifth People’s Hospital of Nanning , Nanning , China
| | - Minli Wang
- Department of Psychology, Fifth People’s Hospital of Nanning , Nanning , China
| | - Tongfei Yang
- Department of Gynecology, Fifth People’s Hospital of Nanning , Nanning , China
| | - Jianyou Wang
- Department of Psychiatry, Fifth People’s Hospital of Nanning , Nanning , China
| | - Baiquan Lin
- Department of Clinical Laboratory, Fifth People’s Hospital of Nanning , Nanning , China
| | - Guoyan Liu
- Department of Clinical Laboratory, Fifth People’s Hospital of Nanning , Nanning , China
| | - Qiaoyan Liang
- Department of Clinical Laboratory, Fifth People’s Hospital of Nanning , Nanning , China
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3
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Sargazi S, Zahedi Abghari A, Mirinejad S, Heidari Nia M, Majidpour M, Danesh H, Saravani R, Sheervalilou R, Shakiba M, Zahedi Abghari F. Long noncoding RNA HOTAIR polymorphisms and susceptibility to bipolar disorder: a preliminary case-control study. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:684-701. [PMID: 35469536 DOI: 10.1080/15257770.2022.2065017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recent studies have shown that long noncoding RNAs contribute to the pathogenesis of bipolar disorder (BD). In this study, we genotyped four HOX Transcript Antisense Intergenic RNA (HOTAIR) gene polymorphisms to investigate if these variations could affect the risk of BD and its clinical subtypes. A total of 357 subjects, comprised of 194 BD patients and 163 age-matched healthy controls, were enrolled. Genotyping was carried out using PCR-RFLP and ARMS-PCR methods. We detected significant associations between the HOTAIR gene rs1899663 G/T, rs12826786 C/T, rs4759314 A/G, and rs920778 C/T polymorphism and the risk of BD under allelic, recessive, dominant, and codominant contrasted genetic models. The CT genotype of rs920778 C/T, GT genotype of rs1899663 G/T, and CT genotype of rs12826786 C/T polymorphisms enhanced the risk of BD type II (BDII). In contrast, the GG genotype of rs4759314 A/G polymorphism significantly diminished BDII risk by 83%. A positive association was noticed between CTTA and CTCG haplotypes of rs920778/rs1899663/rs12826786/rs4759314 and BD risk. Our findings reveal an interactive effect of HOTAIR polymorphisms on the development of BD and its subtypes. Further functional studies are needed to elucidate the role of these variations on HOTAIR expression and epigenetic status.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Armin Zahedi Abghari
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdi Majidpour
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hiva Danesh
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Mansoor Shakiba
- Department of Psychiatry, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fateme Zahedi Abghari
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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4
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Alhazmi S, Alzahrani M, Farsi R, Alharbi M, Algothmi K, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan HM, Alrafiah A, Alrofaidi A. Multiple Recurrent Copy Number Variations (CNVs) in Chromosome 22 Including 22q11.2 Associated with Autism Spectrum Disorder. Pharmgenomics Pers Med 2022; 15:705-720. [PMID: 35898556 PMCID: PMC9309317 DOI: 10.2147/pgpm.s366826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a developmental disorder that can cause substantial social, communication, and behavioral challenges. Genetic factors play a significant role in ASD, where the risk of ASD has been increased for unclear reasons. Twin studies have shown important evidence of both genetic and environmental contributions in ASD, where the level of contribution of these factors has not been proven yet. It has been suggested that copy number variation (CNV) duplication and the deletion of many genes in chromosome 22 (Ch22) may have a strong association with ASD. This study screened the CNVs in Ch22 in autistic Saudi children and assessed the candidate gene in the CNVs region of Ch22 that is most associated with ASD. Methods This study included 15 autistic Saudi children as well as 4 healthy children as controls; DNA was extracted from samples and analyzed using array comparative genomic hybridization (aCGH) and DNA sequencing. Results The aCGH detected (in only 6 autistic samples) deletion and duplication in many regions of Ch22, including some critical genes. Moreover, DNA sequencing determined a genetic mutation in the TBX1 gene sequence in autistic samples. This study, carried out using aCGH, found that six autistic patients had CNVs in Ch22, and DNA sequencing revealed mutations in the TBX1 gene in autistic samples but none in the control. Conclusion CNV deletion and the duplication of the TBX1 gene could be related to ASD; therefore, this gene needs more analysis in terms of expression levels.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khloud Algothmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham M Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Correspondence: Aziza Alrafiah, Department of Medical Laboratory Science, King Abdulaziz University, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Aisha Alrofaidi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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5
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Pujar M, Vastrad B, Kavatagimath S, Vastrad C, Kotturshetti S. Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis. Sci Rep 2022; 12:9157. [PMID: 35650387 PMCID: PMC9160069 DOI: 10.1038/s41598-022-13291-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein–protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. The top hub genes such as MYC, EGFR, LNX1, YBX1, HSP90AA1, ESR1, FN1, TK1, ANLN and SMAD9 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Receiver operating characteristic curve (ROC) analysis confirmed that these genes were significantly associated with T1DM. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the advancement and progression of T1DM, and certain genes might be used as candidate target molecules to diagnose, monitor and treat T1DM.
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Affiliation(s)
- Madhu Pujar
- Department of Pediatrics, J J M Medical College, Davangere, Karnataka, 577004, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, Karnataka, 582101, India
| | - Satish Kavatagimath
- Department of Pharmacognosy, K.L.E. College of Pharmacy, Belagavi, Karnataka, 590010, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka, 580001, India.
| | - Shivakumar Kotturshetti
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka, 580001, India
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6
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HSPB1 Gene Variants and Schizophrenia: A Case-Control Study in a Polish Population. DISEASE MARKERS 2022; 2022:4933011. [PMID: 35340410 PMCID: PMC8941579 DOI: 10.1155/2022/4933011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 02/01/2022] [Accepted: 03/01/2022] [Indexed: 11/20/2022]
Abstract
Schizophrenia (SCZ) is a severe psychiatric disorder that has a significant genetic component. HSPB1 (HSP27) is known for its neuroprotective functions under stress conditions and appears to play an important role during the development of the central nervous system, which is in agreement with the neurodevelopmental hypothesis of SCZ. The aim of the present case-control study was to investigate whether HSPB1 variants contribute to the risk and clinical features (age of onset, symptoms, and suicidal behavior) of SCZ in a Polish population. To the best of our knowledge, this is the first study that investigated the association between the HSPB1 polymorphisms and SCZ. Three SNPs of HSPB1 (rs2868370, rs2868371, and rs7459185) were genotyped in a total of 1082 (403 patients and 679 controls) unrelated subjects using TaqMan assays. The results showed that the genotypes, alleles, and haplotypes of the three SNPs were not significantly different between the schizophrenic patients and healthy controls either in the overall analysis or in the gender-stratified analysis (all p > 0.05). However, we did find a significant effect of the rs2868371 genotype on the age of onset, negative symptoms, and disorganized symptoms in the five-factor model of PANSS (all p < 0.01). Post hoc comparisons showed that carriers of the rs2868371 G/G genotype had significantly higher negative and disorganized factor scores than those with the C/G and C/C genotypes, respectively. Further investigations with other larger independent samples are required to confirm our findings and to better explore the effect of the HSPB1 polymorphisms on the risk and symptomatology of SCZ.
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7
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Sargazi S, Mirani Sargazi F, Heidari Nia M, Sheervalilou R, Saravani R, Mirinejad S, Shakiba M. Functional Variants of miR-143 Are Associated with Schizophrenia Susceptibility: A Preliminary Population-Based Study and Bioinformatics Analysis. Biochem Genet 2021; 60:868-881. [PMID: 34515927 DOI: 10.1007/s10528-021-10133-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/04/2021] [Indexed: 12/19/2022]
Abstract
Single nucleotide polymorphisms within genes encoding microRNAs may alter the expression of microRNAs and their target genes, contributing to the etiology of psychiatric disorders. We aimed to investigate the link between rs4705342T/C and rs4705343T/C polymorphisms in the promoter region of miR-143 and the risk of schizophrenia (SCZ) in a sample of an Iranian population. In this experimental study, a total of 398 subjects were recruited. Genotyping carried out using allele-specific PCR (AS-PCR) method. Different bioinformatics databases and Cytoscape V3.4.0 software were used for the analysis of the gene-miRNA interaction network. The genotypic analysis of rs4705342C/T showed that CC genotype in the co-dominant model significantly decreased the risk of SCZ (p < 0.001). Also, a significantly reduced risk of SCZ was observed under allelic (p < 0.001), dominant (p = 0.007), and recessive (p = 0.001) models of this variant. As regards rs4705343T/C, significantly enhanced risk of SCZ was found under the co-dominant CC (p = 0.01) and recessive (p = 0.007) contrasted genetic models. For this variant, the C allele conferred an increased risk of SCZ by 1.41 fold. Haplotype analysis showed that the Crs4705342 Trs4705343 haplotype significantly diminished SCZ susceptibility. The result of the bioinformatics analysis showed that miR-143, as a critical miRNA, targets ERK5, ERBB3, HK2, and PKCε, the four major genes involved in SCZ development. Our findings suggest that these two polymorphisms might affect SCZ susceptibility. Elucidating the precise regulatory mechanisms of gene expression in the development of SCZ will help researchers discover a novel target for therapeutic interventions.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fariba Mirani Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Ramin Saravani
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran. .,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mansoor Shakiba
- Department of Psychiatry, Zahedan University of Medical Sciences, Zahedan, Iran
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8
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Gomes JA, Sgarioni E, Vieira IA, Fraga LR, Ashton-Prolla P, Terças-Tretell ACP, da Silva JH, Ribeiro BFR, Galera MF, de Oliveira TM, Carvalho de Andrade MDF, Carvalho IF, Schuler-Faccini L, Vianna FSL. Functional Polymorphisms in the p53 Pathway Genes on the Genetic Susceptibility to Zika Virus Teratogenesis. Front Cell Infect Microbiol 2021; 11:641413. [PMID: 34307186 PMCID: PMC8294037 DOI: 10.3389/fcimb.2021.641413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Congenital Zika Syndrome (CZS) occurs in up to 42% of individuals exposed to ZIKV prenatally. Deregulation in gene expression and protein levels of components of the p53 signaling pathway, such as p53 and MDM2, due to ZIKV infection has been reported. Here, we evaluate functional polymorphisms in genes of the p53 signaling pathway as risk factors to CZS. Forty children born with CZS and forty-eight children exposed to ZIKV, but born without congenital anomalies were included in this study. Gestational and sociodemographic information as well as the genotypic and allelic frequencies of functional polymorphisms in TP53, MDM2, MIR605 and LIF genes were compared between the two groups. We found children with CZS exposed predominantly in the first trimester and controls in the third trimester (p<0.001). Moreover, children with CZS were predominantly from families with a lower socioeconomic level (p=0.008). We did not find a statistically significant association between the investigated polymorphisms and development of CZS; however, by comparing individuals with CZS and lissencephaly or without lissencephaly, we found a significative difference in the allelic frequencies of the TP53 rs1042522, which is associated with a more potent p53-induced apoptosis (p=0.007). Our findings suggest that the TP53 rs1042522 polymorphism should be better investigate as a genetic risk factor for the development of lissencephaly in children with CZS.
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Affiliation(s)
- Julia A Gomes
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, Brazil.,Laboratório de Medicina Genômica (LMG), Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Eduarda Sgarioni
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Igor A Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratório de Medicina Genômica (LMG), Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Lucas R Fraga
- Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, Brazil.,Laboratório de Medicina Genômica (LMG), Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Patrícia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratório de Medicina Genômica (LMG), Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Juliana H da Silva
- Secretaria Municipal de Saúde de Tangará da Serra, Tangará da Serra, Brazil
| | | | - Marcial F Galera
- Departamento de Pediatria, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Thalita M de Oliveira
- Hospital Universitário Júlio Müller (HUJM), Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | | | - Isabella F Carvalho
- Curso de Odontologia, Centro Universitário Christus (UNICHRISTUS), Fortaleza, Brazil
| | - Lavínia Schuler-Faccini
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, Brazil.,Laboratório de Medicina Genômica (LMG), Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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9
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Heidari Nia M, Sargazi S, Saravani R, Mirinejad S, Jahantigh D, Shakiba M. Relationship between GABRB2 gene polymorphisms and schizophrenia susceptibility: a case-control study and in silico analyses. Int J Neurosci 2020; 132:633-642. [PMID: 32988247 DOI: 10.1080/00207454.2020.1830087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE Converging evidence has recently established the significance of γ-aminobutyric acid neurotransmitter (GABA) system in the development of schizophrenia (SCZ). We aimed to determine the association of two markers of the GABAA receptor β2 subunit gene (GABRB2), rs12187676 G/C and rs1816072 T/C, with the risk of SCZ in Iranian population. MATERIALS AND METHODS In this case-control study, 190 patients with SCZ and 200 healthy controls were recruited from December 2018 to February 2020. Genotyping was done using the Tetra-ARMS-PCR technique. In silico analyses were performed to determine the potential effects of the variants. RESULTS The C allele and genotypes of codominant CC vs.TT and CT vs.TT, dominant TT vs. TC + CC, recessive TT + TC vs. CC of rs1816072 polymorphism, as well as codominant CC vs. GG and recessive GG + GC vs. CC genetic models of rs12187676 polymorphism were significantly associated with SCZ susceptibility. Compared to the TC/GC model, we have found that the TC/CC combination significantly increased the risk of SCZ by 4.32 fold while the TT/GG combination conferred a protective role against SCZ. Haplotypes analysis indicated that GABRB2 polymorphisms are in weak linkage disequilibrium with each other (LD = 0.1). However, bioinformatics analyses predicted that these polymorphisms do not have significant effects on the secondary structure and the splicing of GABRB2-mRNA. CONCLUSIONS We found that intronic GABRB2 polymorphisms were associated with SCZ risk in a sample of the Iranian population. These findings provided proof of concept for the involvement of the GABAergic neurotransmission system in SCZ development. These observations should be validated across other ethnicities and clinical subtypes.
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Affiliation(s)
- Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Danial Jahantigh
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Mansoor Shakiba
- Department of Psychiatry, Zahedan University of Medical Sciences, Zahedan, Iran
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Sargazi S, Heidari Nia M, Sheervalilou R, Mirinejad S, Harati-Sadegh M, Moudi M, Saravani R, Shakiba M. Relationship between Single Nucleotide Polymorphisms of GRHL3 and Schizophrenia Susceptibility: A Preliminary Case-Control Study and Bioinformatics Analysis. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2020; 9:154-164. [PMID: 32934953 PMCID: PMC7489109 DOI: 10.22088/ijmcm.bums.9.2.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/28/2020] [Indexed: 12/28/2022]
Abstract
Grainyhead-like (GRHL) transcription factors were recently linked to the etiology of neural tube defects (NTDs). Overlapping patterns in the variation of schizophrenia (SCZ) incidence with that of NTDs suggests the presence of common etiological risk factors. This preliminary study was designed to examine the relationship between two missense variants of GRHL3 gene (rs2486668C/G and rs545809A/T) and SCZ susceptibility among Iranians. Three hundred ninety subjects (192 patients confirmed with SCZ, and 198 healthy controls) were enrolled and genotyped. Statistical and bioinformatics analyzes were performed to determine the effects of the variants. In silico analyzes were performed to determine the effects of the variants on the secondary structure of GRHL3 protein and prediction of silencer motifs for each variation. Statistically significant differences were observed between the studied groups under codominant AA, dominant AT+AA, and recessive AA genetic contrast models for rs545809A/T. The presence of the A allele of rs545809A/T enhanced SCZ risk by 2.33 fold. In contrast, rs2486668C/G was not linked to SCZ susceptibility (P > 0.05). Bioinformatics analysis revealed that both missense SNPs caused substantial changes in the secondary structure of GRHL3-mRNA. Screening of the flanking sequences of rs545809A/T predicted silencer motifs for this SNP. Our results demonstrated that the rs545809A/T of GRHL3 gene could affect the risk of SCZ in Iranian populations. Replication studies are warranted to confirm these results.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Roghayeh Sheervalilou
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Harati-Sadegh
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Moudi
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mansoor Shakiba
- Department of Psychiatry, Zahedan University of Medical Sciences, Zahedan, Iran.,Psychosomatic Research Center, Imam Hospital, Tehran University of Medical Sciences, Tehran, Iran
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