1
|
Vetriselvan Y, Manoharan A, Murugan M, Jayakumar S, Govindasamy C, Ravikumar S. In Silico Characterization of Pathogenic Homeodomain Missense Mutations in the PITX2 Gene. Biochem Genet 2024:10.1007/s10528-024-10836-z. [PMID: 38802693 DOI: 10.1007/s10528-024-10836-z] [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: 02/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Paired homologous domain transcription factor 2 (PITX2) is critically involved in ocular and cardiac development. Mutations in PITX2 are consistently reported in association with Axenfeld-Rieger syndrome, an autosomal dominant genetic disorder and atrial fibrillation, a common cardiac arrhythmia. In this study, we have mined missense mutations in PITX2 gene from NCBI-dbSNP and Ensembl databases, evaluated the pathogenicity of the missense variants in the homeodomain and C-terminal region using five in silico prediction tools SIFT, PolyPhen2, GERP, Mutation Assessor and CADD. Fifteen homeodomain mutations G42V, G42R, R45W, S49Y, R53W, E53D, E55V, R62H, P65S, R69H, G75R, R84G, R86K, R87W, R91P were found to be highly pathogenic by both SIFT, PolyPhen2 were further functionally characterized using I-Mutant 2.0, Consurf, MutPred and Project Hope. The findings of the study can be used for prioritizing mutations in the context of genetic studies.
Collapse
Affiliation(s)
- Yogesh Vetriselvan
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Aarthi Manoharan
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Manoranjani Murugan
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Swetha Jayakumar
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, 11433, Riyadh, Saudi Arabia
| | - Sambandam Ravikumar
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India.
| |
Collapse
|
2
|
Hossain MU, Ahammad I, Moniruzzaman M, Akter Lubna M, Bhattacharjee A, Mahmud Chowdhury Z, Ahmed I, Hosen MB, Biswas S, Chandra Das K, Keya CA, Salimullah M. Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database. Cancer Rep (Hoboken) 2023; 6:e1906. [PMID: 37867380 PMCID: PMC10728505 DOI: 10.1002/cnr2.1906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/29/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. AIM The aim of this study is to examine the nsSNP in GC-associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC-associated genes and their impacts. METHODS AND RESULTS A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named "GasCanBase" was developed to make data available to researchers. CONCLUSION The findings of this study and the "GasCanBase" database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/.
Collapse
Affiliation(s)
| | - Ishtiaque Ahammad
- Bioinformatics DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Md. Moniruzzaman
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | | | | | | | - Istiak Ahmed
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md. Billal Hosen
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Shourov Biswas
- Department of Clinical OncologyBangabandhu Sheikh Mujib Medical UniversityDhakaBangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and MicrobiologyNorth South UniversityDhakaBangladesh
| | - Md. Salimullah
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| |
Collapse
|
3
|
Surati U, Mohan M, Jayakumar S, Verma A, Niranjan SK. Genome-wide in silico analysis leads to identification of deleterious L290V mutation in RBBP5 gene in Bos indicus. Anim Biotechnol 2023; 34:4851-4859. [PMID: 37051916 DOI: 10.1080/10495398.2023.2199502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Genome-wide deleterious mutations were identified in zebu cattle (Bos indicus) using in silico approach. The ddRAD sequence data of Sahiwal cattle were annotated and aligned with the cattle reference genome (ARS-UCD1.2). A total of 279,383 SNPs were identified at Read Depth10, which were further filtered to 692 missense SNPs. These SNPs were further analyzed, for functional consequences, by using Variant Effect Predictor, PolyPhen, PROVEAN, and PANTHER tools. A total of 18 SNPs, were finally identified as deleterious, and among these, 12 SNPs were mapped on nine different genes. ERRAT, ProSA-web, Project HOPE, TM-Align, and YASSARA tools, further confirmed the protein malfunctioning of one missense (L290V) mutation of Retinoblastoma binding protein-5 (RBBP5) gene, transcribing a cell cycle regulatory protein and associated with Retinoblastoma in human. This derived bioinformatics pipeline may be useful for preliminarily identifying the deleterious DNA mutations in livestock, specifically in absence of any genetic disease records.
Collapse
Affiliation(s)
- Utsav Surati
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | - M Mohan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | - S Jayakumar
- ICAR-Directorate of Poultry Research, Hyderabad, India
| | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
| | | |
Collapse
|
4
|
Structural Consequences of IRS-2 nsSNPs and Implication for Insulin Receptor Substrate-2 Protein Stability. Biochem Genet 2023; 61:69-86. [PMID: 35727487 DOI: 10.1007/s10528-022-10247-y] [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: 11/29/2021] [Accepted: 06/07/2022] [Indexed: 01/24/2023]
Abstract
Single-Nucleotide Polymorphisms (SNPs) are common genetic variations implicated in human diseases. The non-synonymous SNPs (nsSNPs) affect the proteins' structures and their molecular interactions with other interacting proteins during the accomplishment of biochemical processes. This ultimately causes proteins functional perturbation and disease phenotypes. The Insulin receptor substrate-2 (IRS-2) protein promotes glucose absorption and participates in the biological regulation of glucose metabolism and energy production. Several IRS-2 SNPs are reported in association with type 2 diabetes and obesity in human populations. However, there are no comprehensive reports about the protein structural consequences of these nsSNPs. Keeping in view the pathophysiological consequences of the IRS-2 nsSNPs, we designed the current study to understand their possible structural impact on coding protein. The prioritized list of the deleterious IRS-2 nsSNPs was acquired from multiple bioinformatics resources, including VEP (SIFT, PolyPhen, and Condel), PROVEAN, SNPs&GO, PMut, and SNAP2. The protein structure stability assessment of these nsSNPs was performed by MuPro and I-Mutant-3.0 servers via structural modeling approaches. The atomic-level structural and molecular dynamics (MD) impact of these nsSNPs were examined using GROMACS 2019.2 software package. The analyses initially predicted 8 high-risk nsSNPs located in the highly conserved regions of IRS-2. The MD simulation analysis eventually prioritized the N232Y, R218C, and R104H nsSNPs that predicted to significantly compromise the structure stability and may affect the biological function of IRS-2. These nsSNPs are predicted as high-risk candidates for diabetes and obesity. The validation of protein structural impact of these shortlisted nsSNPs may provide biochemical insight into the IRS-2-mediated type-2 diabetes.
Collapse
|
5
|
Shinwari K, Rehman HM, Xiao N, Guojun L, Khan MA, Bolkov MA, Tuzankina IA, Chereshnev VA. Novel high-risk missense mutations identification in FAT4 gene causing Hennekam syndrome and Van Maldergem syndrome 2 through molecular dynamics simulation. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
|
6
|
Mahmood MS, Afzal M, Batool H, Saif A, Aqdas T, Ashraf NM, Saleem M. Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach. Bioinform Biol Insights 2022; 16:11779322221115547. [PMID: 35966807 PMCID: PMC9373111 DOI: 10.1177/11779322221115547] [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: 03/14/2022] [Accepted: 06/11/2022] [Indexed: 11/15/2022] Open
Abstract
LHPP gene encodes a phospholysine phosphohistidine inorganic pyrophosphate phosphatase, which functions as a tumor-suppressor protein. The tumor suppression by this protein has been confirmed in various cancers, including hepatocellular carcinoma (HCC). LHPP downregulation promotes cell growth and proliferation by modulating the PI3K/AKT signaling pathway. This study identifies potentially deleterious missense single nucleotide variants (SNVs) associated with the LHPP gene using multiple computational tools based on different algorithms. A total of 4 destabilizing mutants are identified as L22P, I212T, G227R, and G236R, from the conserved region of the phosphatase. The 3-dimensional (3D) modeling and structural comparison of variants with the native protein reveals significant structural and conformational variations after mutations, suggesting disruption in the function of phospholysine phosphohistidine inorganic pyrophosphate phosphatase. The identified mutations might, therefore, participate in the cause of HCC.
Collapse
Affiliation(s)
- Malik Siddique Mahmood
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan.,Department of Biochemistry, NUR International University, Lahore, Pakistan
| | - Maryam Afzal
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Hina Batool
- Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Amara Saif
- Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Tahreem Aqdas
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry & Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
7
|
Mia MA, Uddin MN, Akter Y, Jesmin, Wal Marzan L. Exploring the Structural and Functional Effects of Nonsynonymous SNPs in the Human Serotonin Transporter Gene Through In Silico Approaches. Bioinform Biol Insights 2022; 16:11779322221104308. [PMID: 35706533 PMCID: PMC9189512 DOI: 10.1177/11779322221104308] [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: 01/24/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
The sodium-dependent serotonin transporter SLC6A4 (solute carrier family 6 member 4) gene encodes an intrinsic membrane protein that transmits the serotonin neurotransmitter from synaptic clefts into presynaptic neurons. The product of the SLC6A4 gene is related to the regulation of mood and social behavior, sleep, appetite, memory, digestion, and sexual desire. This protein is a target for antidepressant and psychostimulant drugs, thus prolonged neurotransmitter signaling remains blocked. In this study, the functional consequences of nsSNPs in the human SLC6A4 gene were explored through computational tools: PhD-SNP, SIFT, Align GVGD, PROVEAN, PMut, nsSNP Analyzer, SNPs&GO, SNAP2, PolyPhen2, and PANTHER to identify the most deleterious and damaging nsSNPs. Then the mutant protein stabilities were assessed using I-Mutant, MUpro, and MutPred2; amino acid conservation using ConSurf, and posttranslational modification analysis using MusiteDEEP and PROSPER. Furthermore, the 3-dimensional (3D) model of the mutated proteins was predicted and validated using SPARKS-X, Verify3D, and PROCHECK. The protein–ligand binding sites were analyzed using the COACH meta-server. Results from this study predicted that T192M, G342E, R607C, W282S, R104C, P131L, P156L, and N351S were the most structurally and functionally significant nsSNPs in the human SLC6A4 gene. Arg607 and Pro156 were the predicted sites for posttranslational modifications, and Thr192 and Try282 were the ligand-binding sites in the human SLC6A4 gene. The analyzed data also suggested that R104C, P131L, P156L, T192M, G342E, and W282S mutants might affect the binding of sodium ions with this protein. Taken together, this study provided important information on structurally and functionally important nsSNPs of the human SLC6A4 gene for further experimental validation. In the future, these damaging nsSNPs of the SLC6A4 gene have the potential to be evaluated as prognostic biomarkers for SLC6A4-related disorder diagnosis and research.
Collapse
Affiliation(s)
- Md Arzo Mia
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Md Nasir Uddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Yasmin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Jesmin
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Lolo Wal Marzan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| |
Collapse
|
8
|
Alymatiri CM, Gkegka GT, Gavriatopoulou M, Terpos E, Dimopoulos MA, Sergentanis TN, Psaltopoulou T. Association Of -308G/A, -238G/A TNF-α Polymorphisms with Multiple Myeloma Risk and Survival: A Systematic Review and Meta-Analysis. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2022; 22:e96-e115. [PMID: 34642126 DOI: 10.1016/j.clml.2021.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/26/2021] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Tumor necrosis factor alpha (TNF-α) is a cytokine with a key role in proinflammation and multiple diseases, including cancer. The gene encoding TNF-α is located within a highly polymorphic region on chromosome 6p21.3; two polymorphisms -308G/A (rs1800629) and -238G/A (rs361525) have been associated with occurrence of human diseases. There is a debate in recent meta-analyses that reached discrepant conclusions regarding the potential role of TNF-α polymorphisms in multiple myeloma (MM) risk. The aim of this systematic review and meta-analysis is to investigate the association between the aforementioned two polymorphisms with the risk and survival of MM. MATERIALS AND METHODS Eligible articles were identified through an extensive search in PubMed database (end of search: June 18, 2020). The pooled effect estimates were calculated following the random-effects models by Der Simonian and Laird. Separate analyses were conducted by ethnicity. Between-study heterogeneity was quantified, and the deviation of genotype frequencies in controls from the Hardy-Weinberg equilibrium was evaluated. RESULTS Eighteen studies (2934 cases, 4291 controls) have been included in the quantitative synthesis examining risk and 5 studies for survival (557 cases). No association was found between -308G/A and -238G/A TNF-α polymorphisms and MM susceptibility in all genetic models for both Caucasian and East Asian populations. There was no association between -308G/A and -238G/A TNF-α polymorphisms and survival (overall or progression-free) of MM. CONCLUSION This systematic review and meta-analysis did not reveal a significant effect of -308G/A and -238G/A TNF-α polymorphisms upon risk or survival of MM.
Collapse
Affiliation(s)
- Christina M Alymatiri
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgia T Gkegka
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gavriatopoulou
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros N Sergentanis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodora Psaltopoulou
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
9
|
Nkansah EO, Ahenkorah J, Adutwum-Ofosu K, Adjei RL, Adu-Aryee NA, Tagoe EA, Koney NKK, Aryee NA, Hottor BA, Blay RM, Clegg-Lamptey JN, Arko-Boham B. BRCA1 gene polymorphism and finger dermatoglyphic patterns in Ghanaian breast cancer patients: a quantitative cross-sectional approach. Pan Afr Med J 2022; 43:209. [PMID: 36942145 PMCID: PMC10024563 DOI: 10.11604/pamj.2022.43.209.33136] [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: 01/06/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022] Open
Abstract
Introduction breast cancer development is linked to mutant single nucleotide polymorphism of breast cancer type 1 (BRCA1) gene usually harboured within exon 11. It has also been linked to finger dermatoglyphics where certain patterns have been associated with breast cancer. This study suggests a possible relationship between finger dermatoglyphic patterns and single nucleotide polymorphism of BRCA1 gene. Methods in a quantitative cross-sectional approach, finger dermatoglyphic patterns were obtained using the ink method from 70 female breast cancer patients and 70 age-matched apparently healthy females. Approximately 5 ml of venous blood was obtained from each participant from which DNA was extracted from the white blood cells collected after centrifugation. DNA was amplified and sequenced and the data aligned with the wildtype template of BRCA1 gene. Fingerprint patterns were analyzed with Chi-square. Mean frequency of fingerprint patterns was analyzed with independent student's t-test. Differences in data set with p<0.05 were statistically significant. Results luminal B was the predominant breast cancer molecular subtype among the patients. The predominant fingerprint pattern among breast cancer participants was the loop. Six or more loops had higher frequency among breast cancer females. The predominant BRCA1 gene variant locations were c.34311, c.34320, and c.34321 with c.34311A>C being the predominant variant. Higher percentage frequency of six or more loops in relation to c.34311A>C was observed in apparently healthy females compared to breast cancer females. Conclusion the study reports for the very first time in Ghana, BRCA1 gene variants and finger dermatoglyphics among breast cancer patients. Although the results are preliminary and inconclusive it creates an avenue for extended studies.
Collapse
Affiliation(s)
- Emmanuel Osei Nkansah
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - John Ahenkorah
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Kevin Adutwum-Ofosu
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Raymond Lovelace Adjei
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Accra, Ghana
| | - Nii Armah Adu-Aryee
- Department of Surgery, University of Ghana Medical School, University of Ghana, Accra, Ghana
- Department of Surgery, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Emmanuel Ayitey Tagoe
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Nii Koney-Kwaku Koney
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Nii Ayite Aryee
- Department of Medical Biochemistry, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Bismark Afedo Hottor
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Richard Michael Blay
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Joe-Nat Clegg-Lamptey
- Department of Surgery, University of Ghana Medical School, University of Ghana, Accra, Ghana
- Department of Surgery, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Benjamin Arko-Boham
- Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana
- Corresponding author: Benjamin Arko-Boham, Department of Anatomy, University of Ghana Medical School, University of Ghana, Accra, Ghana.
| |
Collapse
|
10
|
In silico screening and exploration into phenotypic alterations of deleterious oncogenic single nucleotide polymorphisms in HSPB1 gene. Genomics 2021; 113:2812-2825. [PMID: 34129932 DOI: 10.1016/j.ygeno.2021.06.017] [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: 12/09/2019] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 11/20/2022]
Abstract
A small heat shock protein, HSP27, encoded by HSPB1 gene strongly favors survival, proliferation and metastasis of cancer cells and its expression is dependent on post-translational modifications like phosphorylation. This study performed an extensive in silico screening of 20 deleterious non-synonymous SNPs in the coding region of HSPB1 gene, among which four were identified to be cancer associated. The SNP variant I181S introduced a new phosphorylation site in position 181, which might elevate the protein's activation potential. Emergence of other post-translational modifications was also observed in SNP variants: L144P and E130K.Significant conformational changes were observed in I181S, L144P and E130K SNP variants with respect to wild-type HSP27. These SNPs appear in one among 105 individuals, making them more susceptible towards cancer. This study would therefore, instigate development of novel biomarkers for cancer risk detection and would provide a detailed understanding towards varied cancer susceptibility of human population.
Collapse
|
11
|
Buainain RP, Boschiero MN, Camporeze B, de Aguiar PHP, Marson FAL, Ortega MM. Single-Nucleotide Variants in microRNAs Sequences or in their Target Genes Might Influence the Risk of Epilepsy: A Review. Cell Mol Neurobiol 2021; 42:1645-1658. [PMID: 33666796 DOI: 10.1007/s10571-021-01058-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
Single-nucleotide variant (SNV) is a single base mutation at a specific location in the genome and may play an import role in epilepsy pathophysiology. The aim of this study was to review case-control studies that have investigated the relationship between SNVs within microRNAs (miRs) sequences or in their target genes and epilepsy susceptibility from January 1, 2010 to October 31, 2020. Nine case-control studies were included in the present review. The mainly observed SNVs associated with drug-resistant epilepsy (DRE) risk were SNVs n.60G > C (rs2910164) and n.-411A > G (rs57095329), both located at miR-146a mature sequence and promoter region, respectively. In addition, the CC haplotype (rs987195-rs969885) and the AA genotype at rs4817027 in the MIR155HG/miR-155 tagSNV were also genetic susceptibility markers for early-onset epilepsy. MiR-146a has been observed as upregulated in human astrocytes in epileptogenesis and it regulates inflammatory process through NF-κB signaling by targeting tumor necrosis factor-associated factor 6 (TRAF6) gene. The SNVs rs2910164 and rs57095329 may modify the expression level of mature miR-146a and the risk for epilepsy and SNVs located at rs987195-rs969885 haplotype and at rs4817027 in the MIR155HG/miR-155 tagSNV could interfere in the miR-155 expression modulating inflammatory pathway genes involved in the development of early-onset epilepsy. In addition, SNVs rs662702, rs3208684, and rs35163679 at 3'untranslated region impairs the ability of miR-328, let-7b, and miR-200c binding affinity with paired box protein PAX-6 (PAX6), BCL2 like 1 (BCL2L1), and DNA methyltransferase 3 alpha (DNMT3A) target genes. The SNV rs57095329 might be correlated with DRE when a larger number of patients are evaluated. Thus, we concluded that the main drawback of most of studies is the small number of individuals enrolled, which lacks sample power.
Collapse
Affiliation(s)
- Renata Parissi Buainain
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University (USF), Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, USF, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil
| | - Matheus Negri Boschiero
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University (USF), Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, USF, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil
| | - Bruno Camporeze
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University (USF), Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, USF, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil
| | - Paulo Henrique Pires de Aguiar
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University (USF), Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, USF, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.,Departament of Neurosurgery, Hospital Santa Paula, São Paulo, São Paulo, Brazil
| | - Fernando Augusto Lima Marson
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University (USF), Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, USF, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil
| | - Manoela Marques Ortega
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University (USF), Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil. .,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, USF, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.
| |
Collapse
|
12
|
In silico analysis of Single Nucleotide Polymorphisms in human GCH1 gene. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
13
|
Computational discovery and assessment of non-synonymous single nucleotide polymorphisms from target gene pool associated with Parkinson's disease. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
14
|
Venkata Subbiah H, Ramesh Babu P, Subbiah U. In silico analysis of non-synonymous single nucleotide polymorphisms of human DEFB1 gene. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00110-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Abstract
Background
Single nucleotide polymorphisms (SNPs) play a significant role in differences in individual’s susceptibility to diseases, and it is imperative to differentiate potentially harmful SNPs from neutral ones. Defensins are small cationic antimicrobial peptides that serve as antimicrobial and immunomodulatory molecules, and SNPs in β-defensin 1 (DEFB1 gene) have been associated with several diseases. In this study, we have determined deleterious SNPs of the DEFB1 gene that can affect the susceptibility to diseases by using different computational methods. Non-synonymous SNPs (nsSNPs) of the DEFB1 gene that have the ability to affect protein structure and functions were determined by several in silico tools—SIFT, PolyPhen v2, PROVEAN, SNAP, PhD-SNP, and SNPs&GO. Then, nsSNPs identified to be potentially deleterious were further analyzed by I-Mutant and ConSurf. Post-translational modifications mediated by nsSNPs were predicted by ModPred, and gene-gene interaction was studied by GeneMANIA. Finally, nsSNPs were submitted to Project HOPE analysis.
Results
Ten nsSNPs of the DEFB1 gene were found to be potentially deleterious: rs1800968, rs55874920, rs56270143, rs140503947, rs145468425, rs146603349, rs199581284, rs201260899, rs371897938, rs376876621. I-Mutant server showed that nsSNPs rs140503947 and rs146603349 decreased stability of the protein, and ConSurf analysis revealed that SNPs were located in conserved regions. The physiochemical properties of the polymorphic amino acid residues and their effect on structure were determined by Project HOPE.
Conclusion
This study has determined high-risk deleterious nsSNPs of β-defensin 1 and could increase the knowledge of nsSNPs towards the impact of mutations on structure and functions mediated by β-defensin 1 protein.
Collapse
|
15
|
Stalin A, Lin D, Josephine Princy J, Feng Y, Xiang H, Ignacimuthu S, Chen Y. Computational analysis of single nucleotide polymorphisms (SNPs) in PPAR gamma associated with obesity, diabetes and cancer. J Biomol Struct Dyn 2020; 40:1843-1857. [DOI: 10.1080/07391102.2020.1835724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Antony Stalin
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Ding Lin
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | | | - Yue Feng
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Haiping Xiang
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | | | - Yuan Chen
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| |
Collapse
|
16
|
Wang Y, Zhang H, Chen Q, Jiao F, Shi C, Pei M, Lv J, Zhang H, Wang L, Gong Z. TNF-α/HMGB1 inflammation signalling pathway regulates pyroptosis during liver failure and acute kidney injury. Cell Prolif 2020; 53:e12829. [PMID: 32419317 PMCID: PMC7309595 DOI: 10.1111/cpr.12829] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Acute kidney injury (AKI) is a common complication of acute liver failure (ALF). Pyroptosis is a necrosis type related to inflammation. This study aimed to investigate the role of TNF-α/HMGB1 pathway in pyroptosis during ALF and AKI. METHODS An ALF and AKI mouse model was generated using LPS/D-Gal, and a TNF-α inhibitor, CC-5013, was used to treat the mice. THP-1 cells were induced to differentiate into M1 macrophages, then challenged with either CC-5013 or an HMGB1 inhibitor, glycyrrhizin. pLVX-mCMVZsGreen-PGK-Puros plasmids containing TNF-α wild-type (WT), mutation A94T of TNF-α and mutation P84L of TNF-α were transfected into M1 macrophages. RESULTS Treatment with CC-5013 decreased the activation of TNF-α/HMGB1 pathway and pyroptosis in the treated mice and cells compared with the control mice and cells. CC-5013 also ameliorated liver and kidney pathological changes and improved liver and renal functions in treated mice, and the number of M1 macrophages in the liver and kidney tissues also decreased. The activation of TNF-α/HMGB1 pathway and pyroptosis increased in the M1 macrophage group compared with the normal group. Similarly, the activation of TNF-α/HMGB1 pathway and pyroptosis in the LPS + WT group also increased. By contrast, the activation of the TNF-α/HMGB1 pathway and pyroptosis decreased in the LPS + A94T and LPS + P84L groups. Moreover, glycyrrhizin inhibited pyroptosis. CONCLUSION The TNF-α/HMGB1 inflammation signalling pathway plays an important role in pyroptosis during ALF and AKI.
Collapse
Affiliation(s)
- Yao Wang
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Haiyue Zhang
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Qian Chen
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Fangzhou Jiao
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Chunxia Shi
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Maohua Pei
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Jian Lv
- Department of PharmacyRenmin Hospital of Wuhan UniversityWuhanChina
| | - Hong Zhang
- Department of PharmacyRenmin Hospital of Wuhan UniversityWuhanChina
| | - Luwen Wang
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| | - Zuojiong Gong
- Department of Infectious DiseasesRenmin Hospital of Wuhan UniversityWuhanChina
| |
Collapse
|
17
|
CYP2R1 and CYP27A1 genes: An in silico approach to identify the deleterious mutations, impact on structure and their differential expression in disease conditions. Genomics 2020; 112:3677-3686. [PMID: 32344004 DOI: 10.1016/j.ygeno.2020.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/22/2019] [Accepted: 04/23/2020] [Indexed: 01/27/2023]
Abstract
Mutations in CYP2R1 and CYP27A1 involved in the conversion of Cholecalciferol into Calcidiol were associated with the impaired 25-hydroxylase activity therefore affecting the Vitamin D metabolism. Hence, this study attempted to understand the influence of genetic variations at the sequence and structural level via computational approach. The non-synonymous mutations retrieved from dbSNP database were assessed for their pathogenicity, stability as well as conservancy using various computational tools. The above analysis predicted 11/260 and 35/489 non-synonymous mutations to be deleterious in CYP2R1 and CYP27A1 genes respectively. Native and mutant forms of the corresponding proteins were modeled. Further, interacting native and mutant proteins with cholecalciferol showed difference in hydrogen bonds, hydrophobic bonds and their binding affinities suggesting the possible influence of these mutations in their function. Also, expression of these genes in various disease conditions was investigated using GEO datasets which predicted that there is a differential expression in cancer and arthritis.
Collapse
|
18
|
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
|
19
|
Pandey S, Dhusia K, Katara P, Singh S, Gautam B. An in silico analysis of deleterious single nucleotide polymorphisms and molecular dynamics simulation of disease linked mutations in genes responsible for neurodegenerative disorder. J Biomol Struct Dyn 2019; 38:4259-4272. [DOI: 10.1080/07391102.2019.1682047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sapna Pandey
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
| | - Kalyani Dhusia
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
- Department of Biomedical Engineering, Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Pramod Katara
- Centre of Bioinformatics, University of Allahabad, Allahabad, India
| | - Satendra Singh
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
| | - Budhayash Gautam
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
| |
Collapse
|
20
|
Alidoost S, Habibi M, Noormohammadi Z, Hosseini J, Azargashb E, Pouresmaeili F. Association between tumor necrosis factor-alpha gene rs1800629 (-308G/A) and rs361525 (-238G > A) polymorphisms and prostate cancer risk in an Iranian cohort. Hum Antibodies 2019; 28:65-74. [PMID: 31594215 DOI: 10.3233/hab-190397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Prostate cancer (PCa) as the first men's common cancer in the world and the third cancer in Iranian men is a heterogeneous disorder which sometimes several biopsies are needed for its diagnosis. OBJECTIVES The aim of current study is finding new biomarkers in order to diagnose of PCa at the earliest possible stage. Hence, the relationship between rs1800629 and rs361525 polymorphisms of TNF-α gene with PCa was investigated. MATERIALS AND METHODS Blood DNA samples were collected from 100 patients with PCa, 110 with BPH, and 110 controls. Collected samples were examined using PCR-RFLP and Tetra-ARMS-PCR techniques to detect the desired polymorphisms. RESULTS The frequency of rs1800629 genotypes in smokers was significantly different from non-smokers with PCa (p= 0.001). Logistic regression analysis results showed that GA heterozygotes in comparison to GG homozygotes had higher risk of developing Benign Prostatic Hyperplasia (BPH) or prostate cancer. However, no significant correlation was considered between the risk of PCa and the TNF-α gene polymorphisms (rs1800629 and rs361525). CONCLUSIONS Although, the achieved results of this investigation demonstrated that the two examined genetic variants do not seem to be suitable markers for early diagnosis of prostate cancer in this pilot study; however increased risk for the disease is shown in GA heterozygotes and smokers which is indicative of some epigenetic factors influence on prostate cancer etiology.
Collapse
Affiliation(s)
- Saeideh Alidoost
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohsen Habibi
- Central Laboratory, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Jalil Hosseini
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Eznollah Azargashb
- Department of Social Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
21
|
In silico analysis of non-synonymous single nucleotide polymorphism in a human KLK-2 gene associated with prostate cancer. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
22
|
In silico Identification of potential Drug Target and Analysis of Effective Single Nucleotide Polymorphisms for autism spectrum Disorder. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
23
|
Agnihotry S, Dhusia K, Srivastav AK, Upadhyay J, Verma V, Shukla PK, Ramteke PW, Gautam B. Biochemical regulation and structural analysis of copper‐transporting ATPase in a human hepatoma cell line for Wilson disease. J Cell Biochem 2019; 120:18826-18844. [DOI: 10.1002/jcb.29199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shikha Agnihotry
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio‐Engineering, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Kalyani Dhusia
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio‐Engineering, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Ajeet K. Srivastav
- Photobiology Laboratory, System Toxicology and Health Risk Assessment GroupCSIR‐Indian Institute of Toxicology Research (CSIR‐IITR) Lucknow Uttar Pradesh India
| | - Jaya Upadhyay
- Department of GastroenterologySanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow Uttar Pradesh India
| | - Vinod Verma
- Department of Hematology, Stem Cell Research CentreSanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow Uttar Pradesh India
| | - Pradeep K. Shukla
- Department of Biological Sciences, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Pramod W. Ramteke
- Department of Biological Sciences, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Budhayash Gautam
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio‐Engineering, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| |
Collapse
|
24
|
J CP, D TK, P S, R S, W CEJ, C GPD, Zayed H. An integrative bioinformatics pipeline to demonstrate the alteration of the interaction between the ALDH2*2 allele with NAD + and Disulfiram. J Cell Biochem 2019; 120:17030-17041. [PMID: 31104322 DOI: 10.1002/jcb.28964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/07/2019] [Accepted: 03/15/2019] [Indexed: 11/07/2022]
Abstract
Alcohol use disorder (AUD) is a multifactorial psychiatric behavior disorder. Disulfiram is the first approved drug by the Food and Drug Administration for alcohol-dependent patients, which targets the ALDH2 enzyme. Several genes are known to be involved in alcohol metabolism; mutations in any of these genes are known to be associated with AUD. The E504K mutation in the ALDH2 of the precursor protein or the E487K of the mature protein (E504K/E487K; ALDH2*2 allele) is carried by approximately 8% of the world population. In this study, we aimed to test the known inactive allele ALDH2*2, to validate the use of our extensive computational pipeline (in silico tools, molecular modeling, and molecular docking) for testing the interaction between the ALDH2*2 allele, NAD+, and Disulfiram. In silico predictions showed that the E504K variant of ALDH2 to be pathogenic and destabilizing with the maximum number of prediction in silico tools. Consequently, we studied the effect of this mutation mainly on the interaction between NAD+ -E504K and Disulfiram-E504K complexes using molecular docking technique, and molecular dynamics (MD) analysis. From the molecular docking analysis with NAD+ , we observed that the interaction affinity of the NAD+ decreases with the impact of E504K variant. On the other hand, the drug Disulfiram showed similar interaction in both the native and mutant ALDH2 proteins. Further, the comprehensive MD analysis predicted that the E504K destabilizes the protein and influences the NAD+ and Disulfiram interactions. Our findings reveal that the interaction of NAD+ to the protein is disturbed by the E504K/E487K variant whereas the drug Disulfiram has a similar effect as both native ALDH2 and ALDH2 bearing E504K/E487K variant. This study provides a platform to understand the effect of E504K/E487K on the molecular interaction with NAD+ and Disulfiram.
Collapse
Affiliation(s)
- Christy Priyadharshini J
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Thirumal Kumar D
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Sneha P
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Siva R
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Charles Emmanuel Jebaraj W
- Department of Biotechnology, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai-600116, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, P. O. Box:2713, Qatar
| |
Collapse
|
25
|
Lv J, Zhang H, Wang L, Gao J, Fan Y. Effects of A94T and P84L Polymorphisms Within theTNF-αGene on Proliferation and Activation of Hepatic Stellate Cells. DNA Cell Biol 2019; 38:162-169. [PMID: 30526018 DOI: 10.1089/dna.2018.4452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jian Lv
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Hong Zhang
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Li Wang
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Jiefang Gao
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Yueying Fan
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| |
Collapse
|
26
|
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
|
27
|
Polymorphisms of TNF- α -308 G/A and IL-8 -251 T/A Genes Associated with Urothelial Carcinoma: A Case-Control Study. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3148137. [PMID: 29951534 PMCID: PMC5987345 DOI: 10.1155/2018/3148137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/01/2018] [Accepted: 04/10/2018] [Indexed: 01/19/2023]
Abstract
Cigarette smoking and exposure to environmental tobacco smoke are well-known risk factors for urothelial carcinoma (UC). We conducted a hospital-based case-control study involving 287 UC cases and 574 cancer-free controls to investigate the joint effects of cigarette smoking and polymorphisms of inflammatory genes on UC risk. Tumor necrosis factor alpha (TNF-α) -308 G/A and interleukin-8 (IL-8) -251 T/A polymorphisms were determined using a polymerase chain reaction-restriction fragment length polymorphism method. People who had ever smoked and those who were exposed to environmental tobacco smoke had significantly increased UC odds ratios (ORs) of 1.65 and 1.68, respectively. Participants who had smoked more than 18 pack-years had a significantly increased UC OR of 2.64. People who had ever smoked and who carried the A/A genotype of the TNF-α -308 G/A polymorphism had a significantly higher UC OR (10.25) compared to people who had never smoked and who carried the G/G or G/A genotype. In addition, people who had ever smoked and who carried the IL-8 -251 T/T genotype had a significantly increased UC OR (3.08) compared to people who had never smoked and who carried the T/A or A/A genotype. In a combined analysis of three major risk factors (cumulative cigarette smoking, the TNF-α -308 A/A genotype, and the IL-8 -251 T/T genotype), subjects with any one, any two, and all three risk factors experienced significantly increased UC ORs of 1.55, 2.89, and 3.77, respectively, compared to individuals with none of the risk factors. Conclusions. Our results indicate that the combined effects of cumulative cigarette exposure and the TNF-α -308 A/A genotype and/or the IL-8 -251 T/T genotype on UC OR showed a significant dose-response relationship.
Collapse
|
28
|
Wankhede DP, Aravind J, Mishra SP. Identification of Genic SNPs from ESTs and Effect of Non-synonymous SNP on Proteins in Pigeonpea. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s40011-018-0973-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
29
|
Single nucleotide polymorphisms of microRNA in cardiovascular diseases. Clin Chim Acta 2018; 478:101-110. [DOI: 10.1016/j.cca.2017.12.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 12/15/2022]
|
30
|
Sang P, Hu W, Ye YJ, Li LH, Zhang C, Xie YH, Meng ZH. In silico screening, molecular docking, and molecular dynamics studies of SNP-derived human P5CR mutants. J Biomol Struct Dyn 2017; 35:2441-2453. [PMID: 27677826 DOI: 10.1080/07391102.2016.1222967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/07/2016] [Indexed: 01/13/2023]
Abstract
Pyrroline-5-carboxylate reductase (P5CR) encoded by PYCR1 gene is a housekeeping enzyme that catalyzes the reduction of P5C to proline using NAD(P)H as the cofactor. In this study, we used in silico approaches to examine the role of nonsynonymous single-nucleotide polymorphisms in the PYCR1 gene and their putative functions in the pathogenesis of Cutis Laxa. Among the 348 identified SNPs, 15 were predicted to be potentially damaging by both SIFT and PolyPhen tools; of them two SNP-derived mutations, R119G and G206W, have been previously reported to correlate with Cutis Laxa. These two mutations were therefore selected to be mapped to the wild-type (WT) P5CR structure for further structural and functional analyses. The results of comparative computational analyses using I-Mutant and Autodock reveal reductions in both stability and cofactor binding affinity of these two mutants. Comparative molecular dynamics (MD) simulations were performed to evaluate the changes in dynamic properties of P5CR upon mutations. The results reveal that the two mutations enhance the rigidity of P5CR structure, especially that of cofactor binding site, which could result in decreased kinetics of cofactor entrance and egress. Comparison between the structural properties of the WT and mutants during MD simulations shows that the enhanced rigidity of mutants results most likely from the increased number of inter-atomic interactions and the decreased number of dynamic hydrogen bonds. Our study provides novel insight into the deleterious effects of the R119G and G206W mutations on P5CR, and sheds light on the mechanisms by which these mutations mediate Cutis Laxa.
Collapse
Affiliation(s)
- Peng Sang
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Wei Hu
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Yu-Jia Ye
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Lin-Hua Li
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Chao Zhang
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Yue-Hui Xie
- b Department of Computer Science, The Faculty of Basic Medicine , Kunming Medical University , Kunming , P.R China
| | - Zhao-Hui Meng
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Solayman M, Saleh MA, Paul S, Khalil MI, Gan SH. In silico analysis of nonsynonymous single nucleotide polymorphisms of the human adiponectin receptor 2 (ADIPOR2) gene. Comput Biol Chem 2017; 68:175-185. [PMID: 28359874 DOI: 10.1016/j.compbiolchem.2017.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 11/17/2022]
Abstract
Polymorphisms of the ADIPOR2 gene are frequently linked to a higher risk of developing diseases including obesity, type 2 diabetes and cardiovascular diseases. Though mutations of the ADIPOR2 gene are detrimental, there is a lack of comprehensive in silico analyses of the functional and structural impacts at the protein level. Considering the involvement of ADIPOR2 in glucose uptake and fatty acid oxidation, an in silico functional analysis was conducted to explore the possible association between genetic mutations and phenotypic variations. A genomic analysis of 82 nonsynonymous SNPs in ADIPOR2 was initiated using SIFT followed by the SNAP2, nsSNPAnalyzer, PolyPhen-2, SNPs&GO, FATHMM and PROVEAN servers. A total of 10 mutations (R126W, L160Q, L195P, F201S, L235R, L235P, L256R, Y328H, E334K and Q349H) were predicted to have deleterious effects on the ADIPOR2 protein and were therefore selected for further analysis. Theoretical models of the variants were generated by comparative modeling via MODELLER 9.16. A protein structural analysis of these amino acid variants was performed using SNPeffect, I-Mutant, ConSurf, Swiss-PDB Viewer and NetSurfP to explore their solvent accessibility, molecular dynamics and energy minimization calculations. In addition, FTSite was used to predict the ligand binding sites, while NetGlycate, NetPhos2.0, UbPerd and SUMOplot were used to predict post-translational modification sites. All of the variants showed increased free energy, though F201S exhibited the highest energy increase. The root mean square deviation values of the modeled mutants strongly indicated likely pathogenicity. Remarkably, three binding sites were detected on ADIPOR2, and two mutations at positions 328 and 201 were found in the first and second binding pockets, respectively. Interestingly, no mutations were found at the post-translational modification sites. These genetic variants can provide a better understanding of the wide range of disease susceptibility associated with ADIPOR2 and aid the development of new molecular diagnostic markers for these diseases. The findings may also facilitate the development of novel therapeutic elements for associated diseases.
Collapse
Affiliation(s)
- Md Solayman
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh.
| | - Md Abu Saleh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh.
| | - Sudip Paul
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.
| | - Md Ibrahim Khalil
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| | - Siew Hua Gan
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| |
Collapse
|
33
|
Li S, Zhao L, Wan XH. A Missense Variant rs4645843 in TNF-α Gene Is a Risk Factor of Polycystic Ovary Syndrome in the Uygur Population. TOHOKU J EXP MED 2017; 243:95-100. [DOI: 10.1620/tjem.243.95] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Shan Li
- Department of Obstetrics, First Affiliated Hospital of Xinjiang Medical University
| | - Lei Zhao
- Department of Gynecology, First Affiliated Hospital of Xinjiang Medical University
| | - Xiao-Hui Wan
- Department of Reproductive Medicine, First Affiliated Hospital of Xinjiang Medical University
| |
Collapse
|
34
|
Basharat Z, Messaoudi A, Ruba S, Yasmin A. NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach. Gene 2016; 591:14-20. [DOI: 10.1016/j.gene.2016.06.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/12/2016] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
|
35
|
Thakur R, Shankar J. In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens. Front Microbiol 2016; 7:192. [PMID: 26941719 PMCID: PMC4763014 DOI: 10.3389/fmicb.2016.00192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/04/2016] [Indexed: 01/13/2023] Open
Abstract
Pentraxin-3 (PTX-3) protein is an evolutionary conserved protein that acts as a soluble pattern-recognition receptor for pathogens and plays important role in innate immune response. It recognizes various pathogens by interacting with extracellular moieties such as glactomannan of conidia (Aspergillus fumigatus), lipopolysaccharide of Pseudomonas aeruginosa, Streptococcus pneumonia and Salmonella typhimurium. Thus, PTX-3 protein helps to clear these pathogens by activating downstream innate immune process. In this study, computational methods were used to analyze various non-synonymous single nucleotide polymorphisms (nsSNPs) in PTX-3 gene. Three different databases were used to retrieve SNP data sets followed by seven different in silico algorithms to screen nsSNPs in PTX-3 gene. Sequence homology based approach was used to identify nsSNPs. Conservation profile of PTX-3 protein amino acid residues were predicted by ConSurf web server. In total, 10 high-risk nsSNPs were identified in pentraxin-domain of PTX-3 gene. Out of these 10 high-risk nsSNPs, 4 were present in the conserved structural and functional residues of the pentraxin-domain, hence, selected for structural analyses. The results showed alteration in the putative structure of pentraxin-domain. Prediction of protein–protein interactions analysis showed association of PTX-3 protein with C1q component of complement pathway. Different functional and structural residues along with various putative phosphorylation sites and evolutionary relationship were also predicted for PTX-3 protein. This is the first extensive computational analyses of pentraxin protein family with nsSNPs and will serve as a valuable resource for future population based studies.
Collapse
Affiliation(s)
- Raman Thakur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology Solan, India
| | - Jata Shankar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology Solan, India
| |
Collapse
|
36
|
Cheng Y, Huang C, Tsai HJ. Relationship of bovine TNF-α gene polymorphisms with the risk of bovine tuberculosis in Holstein cattle. J Vet Med Sci 2016; 78:727-32. [PMID: 26876219 PMCID: PMC4905823 DOI: 10.1292/jvms.15-0506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Many studies suggest significant genetic variation in the resistance of cattle and humans
to infection with Mycobacterium bovis (M. bovis), the
causative agent of zoonotic tuberculosis. TNF-α promotes inflammation and induces
apoptosis in response to mycobacterial infection. The aim of the present study was to
investigate the influence of single nucleotide polymorphisms of the TNF-α
gene on bovine tuberculosis (bTB) susceptibility. We genotyped the TNF-α
gene in 74 bTB-infected Holstein cows and 90 healthy control animals. The influence in the
exon 3 region of TNF-α polymorphisms on bTB susceptibility was
subsequently investigated by association analysis. Our finding demonstrated that the
g.27534932A>C polymorphism of the TNF-α is associated with bTB in
Holstein cattle. The susceptibility of cattle with the g.27534932A>C genotype compared
with the CC genotype was 4.11-fold (95% CI, 1.27–13.36; P=0.02) higher.
The g.27534932A>C polymorphism located in exon 3 of the TNF-α gene,
and the functional consequence was missense. The deduced amino acid sequence for the
protein product revealed an arginine to serine conversion at position 159, which may
affect initiation of protein synthesis and disrupt normal TNF-α function
that protects animals against mycobacterial infection. A significant association was
observed with the A allele as a risk factor for bTB susceptibility (OR, 3.84; 95% CI,
1.21–12.17; P=0.02). In conclusion, this is the first report showing that
the g.27534932A>C polymorphism may contribute to TNF-α-mediated bTB
susceptibility.
Collapse
Affiliation(s)
- Yafen Cheng
- School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | | | | |
Collapse
|
37
|
Joshi BB, Koringa PG, Mistry KN, Patel AK, Gang S, Joshi CG. In silico analysis of functional nsSNPs in human TRPC6 gene associated with steroid resistant nephrotic syndrome. Gene 2015; 572:8-16. [DOI: 10.1016/j.gene.2015.06.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/15/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
|
38
|
Wang S, Zhang X, Chen F, Cui D. A Single-Nucleotide Polymorphism of TaGS5 Gene Revealed its Association with Kernel Weight in Chinese Bread Wheat. FRONTIERS IN PLANT SCIENCE 2015; 6:1166. [PMID: 26779195 PMCID: PMC4688388 DOI: 10.3389/fpls.2015.01166] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/07/2015] [Indexed: 05/21/2023]
Abstract
TaGS5 genes were cloned from bread wheat and were physically mapped on 3AS and 3DS. Sequencing results revealed that a SNP was found in the sixth exon of TaGS5-A1 gene. The SNP resulted in amino acid change from alanine to serine at the 303 bp position of TaGS5-A1. These two alleles were designated as TaGS5-A1a (alanine at the 303 bp position) and TaGS5-A1b genes (serine at the 303-bp position). Analysis of association of TaGS5-A1 alleles with agronomic traits indicated that cultivars with TaGS5-A1b possessed wider kernel width and higher thousand-kernel weight, as well as significantly lower plant height, spike length, and internode length below spike than those of cultivars with TaGS5-A1a over 3 years. These trait differences between TaGS5-A1a and TaGS5-A1b genotypes were larger in landraces than in modern cultivars. This finding suggested that TaGS5 gene played an important role in modulating yield-related traits in the landraces, which possibly resulted from numerous superior genes gathering in modern cultivars after strong artificial selection. The preferred TaGS5-A1b haplotype underwent very strong positive selection in Chinese modern wheat breeding, but not in Chinese landraces. Expression analysis of the TaGS5-A1 gene indicated that TaGS5-A1b allele possessed significantly higher expression level than TaGS5-A1b allele in differently developmental seeds. This study could provide relatively superior genotype in view of agronomic traits in wheat breeding programs. Likewise, this study could offer important information for the dissection of molecular and genetic basis of yield-related traits.
Collapse
|