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Jibon MDK, Islam MA, Hosen ME, Faruqe MO, Zaman R, Acharjee UK, Sikdar B, Tiruneh YK, Khalekuzzaman M, Jawi M, Zaki MEA. In-silico analysis of deleterious non-synonymous SNPs in the human AVPR1a gene linked to autism. BMC Genomics 2025; 26:492. [PMID: 40375167 PMCID: PMC12083178 DOI: 10.1186/s12864-025-11655-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2025] [Accepted: 04/29/2025] [Indexed: 05/18/2025] Open
Abstract
Single nucleotide polymorphisms are the most prevalent type of DNA variation occurring at a single nucleotide within the genomic sequence. The AVPR1a gene exhibits genetic polymorphism and is linked to neurological and developmental problems, including autism spectrum disorder. Due to the difficulties of studying all non-synonymous single nucleotide polymorphisms (nsSNPs) of the AVPR1a gene in the general population, our goal is to use a computational approach to identify the most detrimental nsSNPs of the AVPR1a gene. We employed several bioinformatics tools, such as SNPnexus, PROVEAN, PANTHER, PhD-SNP, SNP & GO, and I-Mutant2.0, to detect the 23 most detrimental mutants (R85H, D202N, E54G, H92P, D148Y, C203G, V297M, D148V, S182N, Q108L, R149C, G212V, M145T, G212S, Y140S, F207V, Q108H, W219G, R284W, L93F, P156R, F136C, P107L). Later, we used other bioinformatics tools to perform domain and conservation analysis. We analyzed the consequences of high‑risk nsSNPs on active sites, post-translational modification (PTM) sites, and their functional effects on protein stability. 3D modeling, structure validation, protein-ligand binding affinity prediction, and Protein-protein docking were conducted to verify the presence of five significant substitutions (R284W, Y140S, P107L, R149C, and F207V) and explore the modifications induced due to these mutants. These non-synonymous single nucleotide polymorphisms can potentially be the focus of future investigations into various illnesses caused by AVPR1a malfunction. Employing in-silico methodologies to evaluate AVPR1a gene variants will facilitate the coordination of extensive investigations and the formulation of specific therapeutic approaches for diseases associated with these variations.
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Affiliation(s)
- Md Delowar Kobir Jibon
- Professor Joardar DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Asadul Islam
- Professor Joardar DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Eram Hosen
- Biomedical Science and Molecular Biology, College of Medicine and Dentistry, James Cook University, Townsville, Australia
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Rashed Zaman
- Professor Joardar DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Uzzal Kumar Acharjee
- Professor Joardar DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Biswanath Sikdar
- Professor Joardar DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Yewulsew Kebede Tiruneh
- Department of Biology, Biomedical Sciences Stream, Bahir Dar University, P.O.Box=79, Bahir Dar, Ethiopia.
| | - Md Khalekuzzaman
- Professor Joardar DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh.
| | - Motasim Jawi
- Department of Basic Medical Sciences, College of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU) , Riyadh, Saudi Arabia.
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Charles R, Sakurai T, Takahashi N, Elder GA, Gama Sosa MA, Young LJ, Buxbaum JD. Introduction of the human AVPR1A gene substantially alters brain receptor expression patterns and enhances aspects of social behavior in transgenic mice. Dis Model Mech 2014; 7:1013-22. [PMID: 24924430 PMCID: PMC4107330 DOI: 10.1242/dmm.017053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Central arginine vasopressin receptor 1A (AVPR1A) modulates a wide range of behaviors, including stress management and territorial aggression, as well as social bonding and recognition. Inter- and intra-species variations in the expression pattern of AVPR1A in the brain and downstream differential behavioral phenotypes have been attributed to differences in the non-coding regions of the AVPR1A gene, including polymorphic elements within upstream regulatory areas. Gene association studies have suggested a link between AVPR1A polymorphisms and autism, and AVPR1A has emerged as a potential pharmacological target for treatment of social cognitive impairments and mood and anxiety disorders. To further investigate the genetic mechanism giving rise to species differences in AVPR1A expression patterns and associated social behaviors, and to create a preclinical mouse model useful for screening drugs targeting AVPR1A, we engineered and extensively characterized bacterial artificial chromosome (BAC) transgenic mice harboring the entire human AVPR1A locus with the surrounding regulatory elements. Compared with wild-type animals, the humanized mice displayed a more widely distributed ligand-AVPR1A binding pattern, which overlapped with that of primates. Furthermore, humanized AVPR1A mice displayed increased reciprocal social interactions compared with wild-type animals, but no differences in social approach and preference for social novelty were observed. Aspects of learning and memory, specifically novel object recognition and spatial relocation recognition, were unaffected. The biological alterations in humanized AVPR1A mice resulted in the rescue of the prepulse inhibition impairments that were observed in knockout mice, indicating conserved functionality. Although further behavioral paradigms and additional cohorts need to be examined in humanized AVPR1A mice, the results demonstrate that species-specific variations in the genomic content of regulatory regions surrounding the AVPR1A locus are responsible for differential receptor protein expression patterns across species and that they are likely to contribute to species-specific behavioral variation. The humanized AVPR1A mouse is a potential preclinical model for further understanding the regulation of receptor gene expression and the impact of variation in receptor expression on behaviors, and should be useful for screening drugs targeting human AVPR1A, taking advantage of the expression of human AVPR1A in human-relevant brain regions.
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Affiliation(s)
- Rhonda Charles
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takeshi Sakurai
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nagahide Takahashi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gregory A Elder
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Neurology Service, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Miguel A Gama Sosa
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Research and Development Service, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Larry J Young
- Center for Translational Social Neuroscience, Department of Psychiatry and Behavioral Sciences, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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