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Batool L, Hariharan K, Xu Y, Kaßmann M, Tsvetkov D, Gohlke BO, Kaden S, Gossen M, Nürnberg B, Kurtz A, Gollasch M. An inactivating human TRPC6 channel mutation without focal segmental glomerulosclerosis. Cell Mol Life Sci 2023; 80:265. [PMID: 37615749 PMCID: PMC10449997 DOI: 10.1007/s00018-023-04901-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023]
Abstract
Transient receptor potential cation channel-6 (TRPC6) gene mutations cause familial focal segmental glomerulosclerosis (FSGS), which is inherited as an autosomal dominant disease. In patients with TRPC6-related FSGS, all mutations map to the N- or C-terminal TRPC6 protein domains. Thus far, the majority of TRPC6 mutations are missense resulting in increased or decreased calcium influx; however, the fundamental molecular mechanisms causing cell injury and kidney pathology are unclear. We report a novel heterozygous TRPC6 mutation (V691Kfs*) in a large kindred with no signs of FSGS despite a largely truncated TRPC6 protein. We studied the molecular effects of V691Kfs* TRPC6 mutant using the tridimensional cryo-EM structure of the tetrameric TRPC6 protein. The results indicated that V691 is localized at the pore-forming transmembrane region affecting the ion conduction pathway, and predicted that V691Kfs* causes closure of the ion-conducting pathway leading to channel inactivation. We assessed the impact of V691Kfs* and two previously reported TRPC6 disease mutants (P112Q and G757D) on calcium influx in cells. Our data show that the V691Kfs* fully inactivated the TRCP6 channel-specific calcium influx consistent with a complete loss-of-function phenotype. Furthermore, the V691Kfs* truncation exerted a dominant negative effect on the full-length TRPC6 proteins. In conclusion, the V691Kfs* non-functional truncated TRPC6 is not sufficient to cause FSGS. Our data corroborate recently characterized TRPC6 loss-of-function and gain-of-function mutants suggesting that one defective TRPC6 gene copy is not sufficient to cause FSGS. We underscore the importance of increased rather than reduced calcium influx through TRPC6 for podocyte cell death.
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Affiliation(s)
- Lilas Batool
- BIH Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Krithika Hariharan
- BIH Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Fraunhofer-Institute for Biomedical Engineering (IBMT), Fraunhofer Project Center for Stem Cell Process Engineering, Würzburg, Germany
| | - Yao Xu
- Klinik und Poliklinik für Innere Medizin D-Geriatrie, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Greifswald, Germany
| | - Mario Kaßmann
- Klinik und Poliklinik für Innere Medizin D-Geriatrie, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Greifswald, Germany
| | - Dmitry Tsvetkov
- Klinik und Poliklinik für Innere Medizin D-Geriatrie, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Greifswald, Germany
| | - Björn-Oliver Gohlke
- Department of Information Technology, Science-IT, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Kaden
- Electron Microscopy Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Manfred Gossen
- BIH Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Institut für Aktive Polymere, Hereon TeltowAbteilung Stammzellmodifikation und Biomaterialien, Teltow, Germany
| | - Bernd Nürnberg
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomics, University of Tübingen, Tübingen, Germany
| | - Andreas Kurtz
- BIH Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- Biomedical Data and Bioethics, Fraunhofer-Institute for Biomedical Engineering (IBMT), Berlin, Germany.
| | - Maik Gollasch
- Klinik und Poliklinik für Innere Medizin D-Geriatrie, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Greifswald, Germany.
- Klinik für Nephrologie und Internistische Intensivmedizin, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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2
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Irfan M, Iqbal T, Hashmi S, Ghani U, Bhatti A. Insilico prediction and functional analysis of nonsynonymous SNPs in human CTLA4 gene. Sci Rep 2022; 12:20441. [PMID: 36443461 PMCID: PMC9705290 DOI: 10.1038/s41598-022-24699-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
The CTLA4 receptor is an immune checkpoint involved in the downregulation of T cells. Polymorphisms in this gene have been found to be associated with different diseases like rheumatoid arthritis, autosomal dominant immune dysregulation syndrome, juvenile idiopathic arthritis and autoimmune Addison's disease. Therefore, the identification of polymorphisms that have an effect on the structure and function of CTLA4 gene is important. Here we identified the most damaging missense or non-synonymous SNPs (nsSNPs) that might be crucial for the structure and function of CTLA4 using different bioinformatics tools. These in silico tools included SIFT, PROVEAN, PhD-SNP, PolyPhen-2 followed by MutPred2, I-Mutant 2.0 and ConSurf. The protein structures were predicted using Phyre2 and I-TASSER, while the gene-gene interactions were predicted by GeneMANIA and STRING. Our study identified three damaging missense SNPs rs1553657429, rs1559591863 and rs778534474 in coding region of CTLA4 gene. Among these SNPs the rs1553657429 showed a loss of potential phosphorylation site and was found to be highly conserved. The prediction of gene-gene interaction showed the interaction of CTlA4 with other genes and its importance in different pathways. This investigation of damaging nsSNPs can be considered in future while studying CTLA4 related diseases and can be of great importance in precision medicine.
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Affiliation(s)
- Muhammad Irfan
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Talha Iqbal
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Sakina Hashmi
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Uzma Ghani
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Attya Bhatti
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
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3
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Rafaee A, Kashani-Amin E, Meybodi AM, Ebrahim-Habibi A, Sabbaghian M. Structural modeling of human AKAP3 protein and in silico analysis of single nucleotide polymorphisms associated with sperm motility. Sci Rep 2022; 12:3656. [PMID: 35256641 PMCID: PMC8901789 DOI: 10.1038/s41598-022-07513-9] [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: 09/27/2020] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
AKAP3 is a member of the A-kinase anchoring proteins and it is a constituent of the sperm fibrous sheath. AKAP3 is needed for the formation of sperm flagellum structure, sperm motility, and male fertility. This study aims to model the AKAP3 tertiary structure and identify the probable impact of four mutations characterized in infertile men on the AKAP3 structure. The T464S, I500T, E525K, and I661T substitutions were analyzed using in silico methods. The secondary structure and three-dimensional model of AKAP3 were determined using PSI-BLAST based secondary structure prediction and Robetta servers. The TM-score was used to quantitatively measure the structural similarities between native and mutated models. All of the desired substitutions were classified as benign. I-Mutant results showed all of the substitutions decreased AKAP3 stability; however, the I500T and I661T were more effective. Superposition and secondary structure comparisons between native and mutants showed no dramatic deviations. Our study provided an appropriate model for AKAP3. Destabilization of AKAP3 caused by these substitutions did not appear to induce structural disturbances. As AKAP3 is involved in male infertility, providing more structural insights and the impact of mutations that cause protein functional diversity could elucidate the etiology of male fertility problems at molecular level.
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Affiliation(s)
- Alemeh Rafaee
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Anahita Mohseni Meybodi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Sabbaghian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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Thakor JM, Parmar G, Mistry KN, Gang S, Rank DN, Joshi CG. Mutational landscape of TRPC6, WT1, LMX1B, APOL1, PTPRO, PMM2, LAMB2 and WT1 genes associated with Steroid resistant nephrotic syndrome. Mol Biol Rep 2021; 48:7193-7201. [PMID: 34546508 DOI: 10.1007/s11033-021-06711-4] [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: 07/24/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Nephrotic syndrome appears as a group of symptoms like proteinuria, edema and hyperlipidemia. Identification of monogenic forms revealed the physiology and pathogenesis of the SRNS. METHODS AND RESULTS We performed Illumina panel sequencing of seven genes in 90 Indian patients to determine the role of these genetic mutations in nephrotic syndrome prognosis. Samtool was used for variants calling, and SnpEff and Snpsift did variants annotation. Clinical significance and variant classification were performed by the ClinVar database. In SSNS and SRNS patients, we found 0.78% pathogenic and 3.41% likely pathogenic mutations. Pathogenic mutations were found in LAMB2, LMX1B and WT1 genes, while likely pathogenic mutations were found in (6/13) LAMB2, (2/13) LMX1B, (2/13) TRPC6, (2/13) PTPRO and (1/13) PMM2 genes. Approximately 46% likely pathogenic mutations were contributed to the LAMB2 gene in SSNS and SRNS patients. We also detect 30 VUS (variants of uncertain significance), which were found (17/30) pathogenic and (13/30) likely pathogenic by different prediction tools. CONCLUSIONS Multigene panels were used for genetic screening of heterogeneous disorders like nephrotic syndrome in the Indian population. We found pathogenic, likely pathogenic and certain VUS, which were responsible for the pathogenesis of the disease. Therefore, mutational analysis of SSNS and SRNS is necessary to avoid adverse effects of corticosteroids, modify the intensity of immunosuppressing agents, and prevent the disease's progression.
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Affiliation(s)
- Jinal M Thakor
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India
| | - Glory Parmar
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India
| | - Kinnari N Mistry
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India.
| | - Sishir Gang
- Muljibhai Patel Urological Hospital, Dr. V.V. Desai Road, Nadiad, 387001, Gujarat, India
| | - Dharamshibhai N Rank
- Department of Animal Breeding and Genetics, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, 388110, Gujarat, India
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Singh SK, Reddy MS. Computational prediction of the effects of non-synonymous single nucleotide polymorphisms on the GPI-anchor transamidase subunit GPI8p of Plasmodium falciparum. Comput Biol Chem 2021; 92:107461. [PMID: 33667975 DOI: 10.1016/j.compbiolchem.2021.107461] [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] [Received: 09/18/2019] [Revised: 11/03/2020] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
Drug resistance is increasingly evolving in malaria parasites; hence, it is important to discover and establish alternative drug targets. In this context, GPI-anchor transamidase (GPI-T) is a potential drug target primarily of its crucial role in the development and survival of the parasite in the GPI anchor biosynthesis pathway. The present investigation was undertaken to explore the plausible effects of nsSNP on the structure and functions of GPI-T subunit GPI8p of Plasmodium falciparum. The GPI8p (PF3D7_1128700) was analyzed using various sequence-based and structure-based computational tools such as SIFT, PROVEAN, PredictSNP, SNAP2, I-Mutant, MuPro, ConSurf, NetSurfP, MUSTER, COACH server and STRING server. Of the 34 nsSNPs submitted for functional analysis, 18 nsSNPs (R124 L, N143 K, Y145 F, V157I, T195S, K379E, I392 K, I437 T, Y438H, N439D, Y441H, N442D, N448D, N451D, D457A, D457Y, I458 L and N460 K) were predicted to have deleterious effects on the protein GPI8p. Additionally, I-Mutant 2.0 and MuPro both showed a decrease in stability after mutation as a result of these nsSNPs, suggesting the destabilization of protein. ConSurf findings suggest that most of the regions were highly conserved. In addition, COACH server was used to predict the ligand binding sites. It was found that no mutation was present at the predicted ligand binding site. The results of the STRING database showed that the protein GPI8p interacts with those proteins which either involve the biosynthetic process of attaching GPI anchor to protein or GPI anchor. The present study suggested that the GPI8p could be a novel target for anti-malarial drugs, which provides significant details for further experimentation.
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Affiliation(s)
- Sanjay Kumar Singh
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India.
| | - M Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India.
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6
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Sunkar S, Aravind M, Reddy SSC, Neeharika D. Genetic variations and their impact on protein function: Study on deleterious nsSNPs in Cancer related genes of Wnt pathway. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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7
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Zamani M, Eslami M, Nezafat N, Hosseini SV, Ghasemi Y. Evaluating the effect of BDNF Val66Met polymorphism on complex formation with HAP1 and Sortilin1 via structural modeling. Comput Biol Chem 2019; 78:282-289. [PMID: 30602138 DOI: 10.1016/j.compbiolchem.2018.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
Brain derived neurotrophic factor (BDNF) has a critical role in the neurogenesis, differentiation, survival of the neurons, regulation of the appetite, and energy homeostasis. Two key proteins, Huntingtin associated protein-1 (HAP1) and sortilin1, regulate the intracellular trafficking and stabilization of the precursor proBDNF through interaction with its prodomain region and mark it for secretion. Evidence suggests that the most frequent single nucleotide polymorphism (SNP) of BDNF gene (rs6265) has been associated with different psychiatric, neurodegenerative and eating disorders. In this study, structural bioinformatics and molecular dynamics (MD) simulations were applied, in order to get precise insights into the impact of Val66Met polymorphism on the proBDNF structure and its interaction with HAP1 and Sortilin1. Homology modeling, structure validation, refinement and also protein-protein docking were performed using appropriate servers. The stability, the fluctuations and the compactness of protein complexes were measured by MD simulation parameters including root mean square deviation (RMSD), root mean square fluctuation (RMSF) and Radius of gyration (Rg), respectively. The mutant proBDNF complexes with HAP1 and Sortilin1 revealed higher RMSD and RMSF values and also variable Rg over time compared with wild-type proBDNF. These computational results indicated that, wild-type proBDNF possessed more stable structure in binding with HAP1 and Sortilin1 compared with its mutant form. Therefore, Val66Met SNP could be deleterious due to making structural changes. It may cause a decrease in proBDNF secretion, which could possibly lead to different psychiatric, neurodegenerative and eating disorders. Further experimental lab studies are required for a more accurate conclusion.
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Affiliation(s)
- Mozhdeh Zamani
- Colorectal Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahboobeh Eslami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | | | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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8
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Mutation screening of the BRCA1 gene in sporadic breast cancer in the Central of Iran. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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9
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Al-Shuhaib MBS, Al-Kafajy FR, Badi MA, AbdulAzeez S, Marimuthu K, Al-Juhaishi HAI, Borgio JF. Highly deleterious variations in COX1, CYTB, SCG5, FK2, PRL and PGF genes are the potential adaptation of the immigrated African ostrich population. Comput Biol Med 2018; 100:17-26. [PMID: 29960146 DOI: 10.1016/j.compbiomed.2018.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 11/19/2022]
Abstract
Because of variable inconvenient living conditions in some places around the world, it is difficult to collect reliable physiological data for ostriches. Therefore, this study aims to provide a comprehensive in silico insight for the nature of polymorphism of important genetic loci that are related to physiological and reproductive traits. Sixty-nine mature ostriches ranging over half of Iraq were screened. Six exonic genetic loci, including cytochrome c oxidase I (COX1), cytochrome b (CYTB), secretogranin V (SCG5), feather keratin 2-like (FK2), prolactin (PRL) and placenta growth factor (PGF) were genotyped by PCR-single stranded conformation polymorphism (SSCP). Thirty-six novel SNPs, including seventeen nonsynonymous (ns) SNPs, were observed. Several computational software programs were utilized to assess the extent of the nsSNPs on their corresponding proteins structure, function and stability. The results showed several deleterious functional and stability changes in almost all the proteins studied. The total severity of each missense mutation was evaluated and compared with other nsSNPs accumulatively. It is evident from the extensive cumulative in silico computation that both p.E34D and p.E60K in PGF have the highest deleterious effect. The cumulative predictions from the present study are an impressive guide for the genotypes of African ostriches, which bypassed the expensive protocols for wet laboratory screening, to identify the effects of variants. To the best of our knowledge, this is the first investigation of its kind on the analyses and prediction outcome of missense mutations in African ostrich populations. The highly deleterious nsSNPs in the placenta growth factor are possible adaptive mutations which might be associated with adaptation in extreme and new environments. The flow and protocol of the computational predictions can be extended for various wild animals to identify the molecular nature of adaptations.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Fadhil R Al-Kafajy
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Milad Ali Badi
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Kasi Marimuthu
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, Kedah Darul Aman, Malaysia.
| | | | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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Kaur T, Thakur K, Singh J, Kamboj SS, Kaur M. Identification of functional SNPs in human LGALS3 gene by in silico analyses. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2017. [DOI: 10.1016/j.ejmhg.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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11
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Joshi BB, Mistry KN, Gang S, Koringa PG, Joshi CG. Characterization of NPHS2 gene polymorphisms associated to steroid resistance nephrotic syndrome in Indian children. Gene 2017; 628:134-140. [PMID: 28712774 DOI: 10.1016/j.gene.2017.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/02/2017] [Accepted: 07/10/2017] [Indexed: 11/18/2022]
Abstract
Nephrotic syndrome (NS) is the common glomerular disease in children. These children are treated with steroids, depending upon their behavior. They are either steroid sensitive (SSNS) or steroid resistant (SRNS). NPHS2 gene mutants are linked to the risk of autosomal recessive SRNS and in some cases to SSNS. The present study has been performed to screen single nucleotide polymorphisms (SNPs) of the NPHS2 gene in a group of 90 Indian children suffering with NS (30 SSNS, 30 SRNS and 30 Controls) by PCR method followed by direct exon sequencing. Effect of SNPs on fold expression changes at transcript level of podocin was checked using quantitative real time PCR (qRT-PCR). SNPs identified through sequencing helps to carry out in-silico analysis. Overall 17 SNPs were identified in NPHS2 gene where 6 were found novel. Three missense SNPs p.R299Q, p.P20L and p.G35D were also identified in this population where SNP, p.G35D was found novel. In addition to sequencing analysis, results of in silico analysis shows that a mutant with these three missense SNPs has least ligand binding efficiency compared to native model. Moreover the significant observation of this study included two intronic SNPs c.451+23C>T and c.451+58A>T present in SRNS group of patients. These SNPs has shown high level of clinical significance within genomic and allelic frequency along with haplotypes and linkage disequilibrium count. The qRT-PCR analysis shows, down expression of podocin protein at transcript level in SRNS patients compared to SSNS patients. All these results support the fact that SNPs present in this population could affect the protein structural stability. Thus it is concluded that the polymorphisms predicted in this study might be disease causing in the NPHS2 gene and may have influence on the therapeutic response of NS patients.
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Affiliation(s)
- Bhoomi B Joshi
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), Sardar Patel University, Vallabh Vidyanagar, Gujarat 388120, India
| | - Kinnari N Mistry
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), Sardar Patel University, Vallabh Vidyanagar, Gujarat 388120, India.
| | - Sishir Gang
- Muljibhai Patel Urological Hospital, Dr. V.V. Desai Road, Nadiad 387 001, Gujarat, India
| | - Prakash G Koringa
- College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, India
| | - Chaitanya G Joshi
- College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, India
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12
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Desai M, Chauhan JB. Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene. Comput Biol Chem 2017; 70:7-14. [PMID: 28734179 DOI: 10.1016/j.compbiolchem.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/20/2017] [Accepted: 07/09/2017] [Indexed: 11/24/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand.
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Affiliation(s)
- Mansi Desai
- Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Science (ARIBAS), Affiliated to Sardar Patel University, New Vallabh Vidyanagar 388121, Gujarat, India.
| | - J B Chauhan
- Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Science (ARIBAS), Affiliated to Sardar Patel University, New Vallabh Vidyanagar 388121, Gujarat, India.
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13
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Chakrapani V, Rasal KD, Kumar S, Mohapatra SD, Sundaray JK, Jayasankar P, Barman HK. In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C. Interdiscip Sci 2017; 10:641-652. [PMID: 28660537 DOI: 10.1007/s12539-017-0247-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 11/29/2022]
Abstract
Immune response mediated by toll-like receptor 22 (TLR22), only found in teleost/amphibians, is triggered by double-stranded RNA binding to its LRR (leucine-rich repeats) ecto-domain. Accumulated evidences suggested that missense mutations in TLR genes affect its function. However, information on mutation linked pathogen recognition for TLR22 was lacking. The present study was commenced for predicting the effect of non-synonymous single-nucleotide polymorphisms (nsSNPs) on the pathogen recognizable LRR domain of TLR22 of farmed carp, Labeo rohita. The sequence-based algorithms (SIFT, PROVEAN and I-Mutant2.0) indicated that three SNPs (out of 27) such as p.L159F (rs76759876) and p.L529P (rs749355507) of LRR, and p.I836M (rs750758397) of intracellular motifs could potentially disrupt protein function. The 3D structure was generated using MODELLER 9.13 and further validated by SAVEs server. The simulated molecular docking of native TLR22 and mutants with poly I:C ligand indicated that mutations positioned at p.L159F and p.L529P of the LRR region affects the binding affinity significantly. This is the first kind of study of predicting nsSNPs of teleost TLR22 with disturbed ligand binding affinity with its extra-cellular LRR domain and thereby likely hindrance in subsequent signal transduction. This study serves as a guide for in vivo evaluation of impact of mutation on immune response mediated by teleost TLR22 gene.
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Affiliation(s)
- Vemulawada Chakrapani
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Sunil Kumar
- ICAR, National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, 275103, India
| | - Shibani D Mohapatra
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Jitendra K Sundaray
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Hirak K Barman
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India.
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Ozmen O, Kul S, Risvanli A, Ozalp G, Sabuncu A, Kul O. Somatic SNPs of the BRCA2 gene at the fragments encoding RAD51 binding sites of canine mammary tumors. Vet Comp Oncol 2017; 15:1479-1486. [PMID: 28133886 DOI: 10.1111/vco.12293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/29/2022]
Abstract
Mammary tumors are the most common tumor type both in women and in female dogs. In women, heritable breast cancers have been linked mutations in the breast cancer susceptibility gene BRCA2 and it contains eight BRC repeats in exon 11 that bind to RAD51. In this study, we investigated the sequence variations of BRC1-BRC8 and C-terminus of canine BRCA2 gene. From a total of 64 canine patients with mammary tumors, 31 mammary tumors with benign and malign carcinomas and the 3 normal mammary glands were used for the study. In this study, 19 SNPs of exon 11 of BRCA2 in canine mammary tumors were detected for the first time. The c.2383A>C (T1425P) SNP was found to be the most probable disease-associated nsSNP. Our findings suggest that T1425P variation in BRC3 to be the most probable disease-associated nsSNP and may affect RAD51 binding strength.
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Affiliation(s)
- O Ozmen
- Ankara University, Faculty of Veterinary Medicine, Department of Genetics, Ankara, Turkey
| | - S Kul
- Firat University, Faculty of Veterinary Medicine, Department of Animal Breeding, Elazig, Turkey
| | - A Risvanli
- Firat University, Faculty of Veterinary Medicine, Department of Obstetrics and Gynecology, Elazig, Turkey
| | - G Ozalp
- Uludag University, Faculty of Veterinary Medicine, Department of Obstetrics and Gynecology, Bursa, Turkey
| | - A Sabuncu
- Istanbul University, Faculty of Veterinary Medicine, Department of Obstetrics and Gynecology, Istanbul, Turkey
| | - O Kul
- Kirikkale University, Faculty of Veterinary Medicine, Department of Pathology, Kirikkale, Turkey
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