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Ryan E, Nishimura S, Lopez G, Tayebi N, Sidransky E. Phenotypic consequences of GBA1 pathological variant R463C (p.R502C). Am J Med Genet A 2024:e63630. [PMID: 38647370 DOI: 10.1002/ajmg.a.63630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/22/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024]
Abstract
Gaucher disease (GD) is an autosomal recessively inherited lysosomal storage disorder caused by biallelic pathological variants in the GBA1 gene. Patients present along a broad clinical spectrum, and phenotypes are often difficult to predict based on genotype alone. The variant R463C (p.Arg502Cys) exemplifies this challenge. To better characterize its different clinical presentations, we examined the records of 25 current and historical patients evaluated at the National Institutes of Health. Nine patients were classified as GD1, 14 were classified as GD3, and two had an ambiguous diagnosis between GD1 and GD3. In addition, we reviewed the published literature in PubMed and Web of Science through December 2023, identifying 62 cases with an R463C variant from 18 countries. Within the NIH cohort, the most common second variants were N370S (p.N409S) and L444P (p.L483P). R463C/L444P was encountered in patients with GD1 and GD3 in both the NIH cohort and worldwide. In the literature, R463C/R463C was also reported in both GD1 and GD3, although sparse phenotypic information was shared. Often the phenotype reflected what might be predicted for the second mutant allele. This diversity of phenotypes emphasizes the need for longitudinal follow-up to assess symptom development and neurological involvement.
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Affiliation(s)
- Emory Ryan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Samantha Nishimura
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Grisel Lopez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Nahid Tayebi
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Ellen Sidransky
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
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2
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Singh S, Gupta A, Singh N, Sengupta PS, Panda SK, Sharma S. Genotyping, in silico screening and molecular dynamics simulation of SNPs of MGMT and ERCC1 gene in lung cancer patients treated with platinum-based doublet chemotherapy. J Biomol Struct Dyn 2023:1-20. [PMID: 37771161 DOI: 10.1080/07391102.2023.2261052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/02/2023] [Indexed: 09/30/2023]
Abstract
Lung cancer, the leading cause of death worldwide, arises from an intricate combination of genetic and environmental factors. Genetic variations can influence the chemotherapeutic response of lung cancer patients in DNA repair genes. This study examines the response to platinum-based drugs among lung cancer patients of North Indian descent who possess genetic variations in the MGMT and ERCC1 genes. P CR-RFLP method was used for genotypic analysis. MedCalc statistical software was used to calculate odds ratios and Median Survival Time (MST). GROMACS software was used to perform Molecular dynamic simulation. ADCC Patients revealed a significant association with MGMT in the heterozygous genotype (HR= 1.56, p=0.02) and also with ERCC1 in both mutant and combined variants (HR= 1.25, p=0.01; HR=0.78, p=0.03). SQCC subjects harbouring ERCC1 polymorphism also reported a 2-fold increase in hazard ratio and a corresponding decrease in survival time for heterozygous and combined variants (HR= 2.55, p=0.02; HR 2.33, p=0.01, respectively). MD simulation results demonstrate a lower RMSD, stable radius of gyration, and lower RMSF, indicating the mutated MGMT protein is more stable than the wild. Further, the docking score for DNA-Wild and DNA-L84F mutants are -201.6 and -131.8, respectively. MD Simulation of the complexes further validated the results. Our study concludes that MGMT and ERCC1 polymorphisms are associated with decreased overall survival. Further, computational analysis of MGMT (rs12917) polymorphism revealed that mutated MGMT cannot bind properly to the DNA and hence cannot properly repair DNA, resulting in lower overall survival.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sidhartha Singh
- Department of Biosciences and Bioengineering, DY Patil International University, Akurdi, Maharashtra, India
| | - Anu Gupta
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Parth Sarthi Sengupta
- Department of Biosciences and Bioengineering, DY Patil International University, Akurdi, Maharashtra, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Sasikumar AP, Ramaswamy S, Sudhir S. A scientific pharmacognosy on Gaucher's disease: an in silico analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:25308-25317. [PMID: 34839442 DOI: 10.1007/s11356-021-17534-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
From ancient times, studies on herbal medicine and pharmacognosy have increased gradually worldwide, due to the increased side effects, adverse drug reactions, and charge lines of modern medicines. Plants are well known for their medicinal effects and nutritional values. They contain bioactive compounds which display a wide spectrum of therapeutic effects. Gaucher's disease (GD) is a rare autosomal recessively inherited metabolic disorder caused due to the defect in Glucosylceramidase beta gene coding for the enzyme acid-β-glucosidase in humans. We revealed the profound binding efficiency of five selected bioactive compounds from different plants against the main enzyme acid-β-glucosidase responsible for GD through molecular docking. An in silico approach along with the ADMET profiles of phytocompounds was done using the Schrodinger software. The preventive measure of GD leads to side effects, inaccessible and unaffordable which put forth the emergence of phytocompounds which have fewer toxic effects, and one such compound is β-D-Glucopyranose with the best docking score (-10.28 kcal/mol) and an excellent binding affinity than other ligands, which could be further analyzed for stability using molecular dynamics study and in vitro. Being a dietary supplement, these compounds could be prepared in any form of formulation as a drug.
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Affiliation(s)
| | | | - Sreeram Sudhir
- PSG College of Arts and Science, Coimbatore, Tamil Nadu, India
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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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Mansouri‐Movahed F, Akhoundi F, Nikpour P, Garshasbi M, Emadi‐Baygi M. Identification of a novel HEXB Mutation in an Iranian Family with suspected patient to GM2-gangliosidoses. Clin Case Rep 2020; 8:2583-2591. [PMID: 33363784 PMCID: PMC7752470 DOI: 10.1002/ccr3.3103] [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: 03/17/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Sandhoff disease is one of the GM2-gangliosidoses which is caused by a mutation in the HEXB preventing the breakdown of GM2-ganglioside. We report a novel HEXB variant in a family with a history of a dead girl with Sandhoff disease which was not found in controls.
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Affiliation(s)
| | - Fatemeh Akhoundi
- Department of GeneticsFaculty of Basic SciencesShahrekord UniversityShahrekordIran
| | - Parvaneh Nikpour
- Department of Genetics and Molecular BiologyFaculty of MedicineIsfahan University of Medical SciencesIsfahanIran
- Child Growth and Development Research CenterResearch Institute for Primordial Prevention of Non‐Communicable DiseaseIsfahan University of Medical SciencesIsfahanIran
| | - Masoud Garshasbi
- Department of Medical GeneticsFaculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | - Modjtaba Emadi‐Baygi
- Department of GeneticsFaculty of Basic SciencesShahrekord UniversityShahrekordIran
- Research Institute of BiotechnologyShahrekord UniversityShahrekordIran
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Michels M, Matte U, Fraga LR, Mancuso ACB, Ligabue-Braun R, Berneira EFR, Siebert M, Sanseverino MTV. Determining the pathogenicity of CFTR missense variants: Multiple comparisons of in silico predictors and variant annotation databases. Genet Mol Biol 2019; 42:560-570. [PMID: 31808782 PMCID: PMC6905453 DOI: 10.1590/1678-4685-gmb-2018-0148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/12/2018] [Indexed: 01/07/2023] Open
Abstract
Pathogenic variants in the Cystic Fibrosis Transmembrane Conductance Regulator
gene (CFTR) are responsible for cystic fibrosis (CF), the
commonest monogenic autosomal recessive disease, and
CFTR-related disorders in infants and youth. Diagnosis of such
diseases relies on clinical, functional, and molecular studies. To date, over
2,000 variants have been described on CFTR (~40% missense).
Since few of them have confirmed pathogenicity, in silico
analysis could help molecular diagnosis and genetic counseling. Here, the
pathogenicity of 779 CFTR missense variants was predicted by
consensus predictor PredictSNP and compared to annotations on CFTR2 and ClinVar.
Sensitivity and specificity analysis was divided into modeling and validation
phases using just variants annotated on CFTR2 and/or ClinVar that were not in
the validation datasets of the analyzed predictors. After validation phase, MAPP
and PhDSNP achieved maximum specificity but low sensitivity. Otherwise, SNAP had
maximum sensitivity but null specificity. PredictSNP, PolyPhen-1, PolyPhen-2,
SIFT, nsSNPAnalyzer had either low sensitivity or specificity, or both. Results
showed that most predictors were not reliable when analyzing
CFTR missense variants, ratifying the importance of
clinical information when asserting the pathogenicity of CFTR
missense variants. Our results should contribute to clarify decision making when
classifying the pathogenicity of CFTR missense variants.
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Affiliation(s)
- Marcus Michels
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Ursula Matte
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Lucas Rosa Fraga
- Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Rodrigo Ligabue-Braun
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Marina Siebert
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação Ciências em Gastroenterologia e Hepatologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Teresa Vieira Sanseverino
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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Thirumal Kumar D, Eldous HG, Mahgoub ZA, George Priya Doss C, Zayed H. Computational modelling approaches as a potential platform to understand the molecular genetics association between Parkinson's and Gaucher diseases. Metab Brain Dis 2018; 33:1835-1847. [PMID: 29978341 DOI: 10.1007/s11011-018-0286-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022]
Abstract
Gaucher's disease (GD) is a genetic disorder in which glucocerebroside accumulates in cells and specific organs. It is broadly classified into type I, type II and type III. Patients with GD are at high risk of Parkinson's disease (PD), and the clinical and pathological presentation of GD patients with PD is almost identical to idiopathic PD. Several experimental models like cell culture, animal models, and transgenic mice models were used to understand the molecular mechanism behind GD and PD association; however, such mechanism remains unclear. In this context, based on literature reports, we identified the most common mutations K198T, E326K, T369M, N370S, V394L, D409H, L444P, and R496H, in the Glucosylceramidase (GBA) protein that are known to cause GD1, and represent a risk of developing PD. However, to date, no computational analyses have designed to elucidate the potential functional role of GD mutations with increased risk of PD. The present computational pipeline allows us to understand the structural and functional significance of these GBA mutations with PD. Based on the published data, the most common and severe mutations were E326K, N370S, and L444P, which further selected for our computational analysis. PredictSNP and iStable servers predicted L444P mutant to be the most deleterious and responsible for the protein destabilization, followed by the N370S mutation. Further, we used the structural analysis and molecular dynamics approach to compare the most frequent deleterious mutations (N370S and L444P) with the mild mutation E326K. The structural analysis demonstrated that the location of E326K and N370S in the alpha helix region of the protein whereas the mutant L444P was in the starting region of the beta sheet, which might explain the predicted pathogenicity level and destabilization effect of the L444P mutant. Finally, Molecular Dynamics (MD) at 50 ns showed the highest deviation and fluctuation pattern in the L444P mutant compared to the two mutants E326K and N370S and the native protein. This was consistent with more loss of intramolecular hydrogen bonds and less compaction of the radius of gyration in the L444P mutant. The proposed study is anticipated to serve as a potential platform to understand the mechanism of the association between GD and PD, and might facilitate the process of drug discovery against both GD and PD.
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Affiliation(s)
- D Thirumal Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Hend Ghasan Eldous
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar
| | - Zainab Alaa Mahgoub
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar
| | - C George Priya Doss
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Hatem Zayed
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar.
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Jin H, Chen J, Li K, Zhang JR, Gu CC, Mao CJ, Yang YP, Wang F, Liu CF. A novel p.L216I mutation in the glucocerebrosidase gene is associated with Parkinson's disease in Han Chinese patients. Neurosci Lett 2018. [PMID: 29530815 DOI: 10.1016/j.neulet.2018.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Pathogenic mutations in the glucocerebrosidase (GBA) gene are associated with Parkinson's disease (PD), of which L444P and N370S are the most frequently observed in patients with PD. The aim of this study was to systematically explore variations in the coding regions of GBA in Han Chinese patients with PD, as well as to expand the GBA mutation spectrum. MATERIAL AND METHODS A total of 213 Han Chinese patients with PD and 348 controls were enrolled in the study. Whole coding regions of GBA were captured and sequenced by target region sequencing. Sanger sequencing was also used to confirm the identified variants. RESULTS We identified a novel variant (c. C646A; p.L216I; NM_001171811.1) of GBA in two unrelated patients, which was not observed in the controls. Both patients had early-onset PD and neither exhibited any motor-related symptoms. However, we did not find an L444P or N370S mutations in our patients. CONCLUSIONS The p.L216I mutation is a novel GBA mutation, which we identified in two Han Chinese patients with PD. The patients exhibited similar characteristics, which differed from those seen in patients with other GBA mutations. Future work is needed to investigate this mutation further, as well as larger cohort studies to explore other GBA mutations associated with PD in the Han Chinese and in other populations.
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Affiliation(s)
- Hong Jin
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Chen
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Kai Li
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jin-Ru Zhang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chen-Chen Gu
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng-Jie Mao
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ya-Ping Yang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China; Institute of Neuroscience, Soochow University, Suzhou 215123, China
| | - Feng Wang
- Institute of Neuroscience, Soochow University, Suzhou 215123, China
| | - Chun-Feng Liu
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China; Institute of Neuroscience, Soochow University, Suzhou 215123, China; Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, China; Parkinson Disease Center of Beijing Institute for Brain Disorders, Beijing, China.
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9
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Genetic analysis of CLDN14 in the Chinese population affected with non-syndromic hearing loss. Int J Pediatr Otorhinolaryngol 2018; 105:6-11. [PMID: 29447821 DOI: 10.1016/j.ijporl.2017.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/15/2017] [Accepted: 11/18/2017] [Indexed: 12/22/2022]
Abstract
OBJECTIVE The CLDN14 gene, encoding the tight junction protein Claudin-14, has been proposed as a candidate causative gene affecting autosomal recessive non-syndromic hearing loss (ARNSHL). Genetic analysis of nonsynonymous single-nucleotide variations (nsSNVs) in CLDN14 has been performed in different populations. The role of CLDN14 nsSNVs in contributing to hearing loss in Chinese populations would be investigated in this study. METHODS Target screening for CLDN14 variations were conducted in 500 unrelated patients diagnosed with non-syndromic hearing loss (NSHL). RESULTS No reported pathogenic CLDN14 nsSNVs in heterozygote or homozygote were detected in this study, however, we identified 4 heterozygous nsSNVs [c.11C > T, p.(Thr4Met); c.16G > A, p.(Val6Met); c.68T > C, p.(Ile23Thr); c.367A > C, p.(Thr123Pro)] in CLDN14. The 4 nsSNVs are located at claudin-14 transmembrane domains, but assessed to be poorly conservative and non-pathogenic via multiple in silico algorithms. The structure-based analysis also suggested that the 4 nsSNVs had less structural and functional impact on claudin-14. CONCLUSION Our findings indicated that CLDN14 might not be a major causative gene for NSHL in Chinese populations, which would contribute to fully understanding the genetic cause of NSHL in the East Asian populations.
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Song J, Yang Y, Mauvais-Jarvis F, Wang YP, Niu T. KCNJ11, ABCC8 and TCF7L2 polymorphisms and the response to sulfonylurea treatment in patients with type 2 diabetes: a bioinformatics assessment. BMC MEDICAL GENETICS 2017; 18:64. [PMID: 28587604 PMCID: PMC5461698 DOI: 10.1186/s12881-017-0422-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 05/11/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Type 2 diabetes (T2D) is a worldwide epidemic with considerable health and economic consequences. Sulfonylureas are widely used drugs for the treatment of patients with T2D. KCNJ11 and ABCC8 encode the Kir6.2 (pore-forming subunit) and SUR1 (regulatory subunit that binds to sulfonylurea) of pancreatic β cell KATP channel respectively with a critical role in insulin secretion and glucose homeostasis. TCF7L2 encodes a transcription factor expressed in pancreatic β cells that regulates insulin production and processing. Because mutations of these genes could affect insulin secretion stimulated by sulfonylureas, the aim of this study is to assess associations between molecular variants of KCNJ11, ABCC8 and TCF7L2 genes and response to sulfonylurea treatment and to predict their potential functional effects. METHODS Based on a comprehensive literature search, we found 13 pharmacogenetic studies showing that single nucleotide polymorphisms (SNPs) located in KCNJ11: rs5219 (E23K), ABCC8: rs757110 (A1369S), rs1799854 (intron 15, exon 16 -3C/T), rs1799859 (R1273R), and TCF7L2: rs7903146 (intron 4) were significantly associated with responses to sulfonylureas. For in silico bioinformatics analysis, SIFT, PolyPhen-2, PANTHER, MutPred, and SNPs3D were applied for functional predictions of 36 coding (KCNJ11: 10, ABCC8: 24, and TCF7L2: 2; all are missense), and HaploReg v4.1, RegulomeDB, and Ensembl's VEP were used to predict functions of 7 non-coding (KCNJ11: 1, ABCC8: 1, and TCF7L2: 5) SNPs, respectively. RESULTS Based on various in silico tools, 8 KCNJ11 missense SNPs, 23 ABCC8 missense SNPs, and 2 TCF7L2 missense SNPs could affect protein functions. Of them, previous studies showed that mutant alleles of 4 KCNJ11 missense SNPs and 5 ABCC8 missense SNPs can be successfully rescued by sulfonylurea treatments. Further, 3 TCF7L2 non-coding SNPs (rs7903146, rs11196205 and rs12255372), can change motif(s) based on HaploReg v4.1 and are predicted as risk factors by Ensembl's VEP. CONCLUSIONS Our study indicates that a personalized medicine approach by tailoring sulfonylurea therapy of T2D patients according to their genotypes of KCNJ11, ABCC8, and TCF7L2 could attain an optimal treatment efficacy.
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Affiliation(s)
- Jingwen Song
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Yunzhong Yang
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Franck Mauvais-Jarvis
- Division of Endocrinology and Metabolism, Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112 USA
| | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA 70118 USA
| | - Tianhua Niu
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
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12
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In silico analysis of deleterious single nucleotide polymorphisms in human BUB1 mitotic checkpoint serine/threonine kinase B gene. Meta Gene 2016; 9:142-50. [PMID: 27331020 PMCID: PMC4913181 DOI: 10.1016/j.mgene.2016.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 11/23/2022] Open
Abstract
One of the major challenges in the analysis of human genetic variation is to distinguish mutations that are functionally neutral from those that contribute to disease. BubR1 is a key protein mediating spindle-checkpoint activation that plays a role in the inhibition of the anaphase-promoting complex/cyclosome (APC/C), delaying the onset of anaphase and ensuring proper chromosome segregation. Owing to the importance of BUB1B gene in mitotic checkpoint a functional analysis using different in silico approaches was undertaken to explore the possible associations between genetic mutations and phenotypic variation. In this work we found that 3 nsSNPs I82N, P334L and R814H have a functional effect on protein function and stability. A literature search revealed that R814H was already implicated in human diseases. Additionally, 2 SNPs in the 5' UTR region was predicted to exhibit a pattern change in the internal ribosome entry site (IRES), and eight MicroRNA binding sites were found to be highly affected due to 3' UTR SNPs. These in silico predictions will provide useful information in selecting the target SNPs that are likely to have functional impact on the BUB1B gene.
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Ghosh A, Kaur N, Kumar A, Goswami C. Why individual thermo sensation and pain perception varies? Clue of disruptive mutations in TRPVs from 2504 human genome data. Channels (Austin) 2016; 10:339-345. [PMID: 26962677 DOI: 10.1080/19336950.2016.1162365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Every individual varies in character and so do their sensory functions and perceptions. The molecular mechanism and the molecular candidates involved in these processes are assumed to be similar if not same. So far several molecular factors have been identified which are fairly conserved across the phylogenetic tree and are involved in these complex sensory functions. Among all, members belonging to Transient Receptor Potential (TRP) channels have been widely characterized for their involvement in thermo-sensation. These include TRPV1 to TRPV4 channels which reveal complex thermo-gating behavior in response to changes in temperature. The molecular evolution of these channels is highly correlative with the thermal response of different species. However, recent 2504 human genome data suggest that these thermo-sensitive TRPV channels are highly variable and carry possible deleterious mutations in human population. These unexpected findings may explain the individual differences in terms of complex sensory functions.
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Affiliation(s)
- Arijit Ghosh
- a School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus , Bhubaneswar , Orissa , India.,b School of Biological Sciences, National Institute of Science Education and Research, Jatni Campus , Bhubaneswar , Orissa , India
| | - Navneet Kaur
- c School of Biotechnology, KIIT University , Bhubaneswar , Orissa , India
| | - Abhishek Kumar
- d Molecular Genetic Epidemiology, Deutsches Krebsforschungszentrum (DKFZ) , Heidelberg , Germany
| | - Chandan Goswami
- a School of Biological Sciences, National Institute of Science Education and Research, Institute of Physics Campus , Bhubaneswar , Orissa , India.,b School of Biological Sciences, National Institute of Science Education and Research, Jatni Campus , Bhubaneswar , Orissa , India
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Timson DJ. Value of predictive bioinformatics in inherited metabolic diseases. World J Med Genet 2015; 5:46-51. [DOI: 10.5496/wjmg.v5.i3.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/28/2015] [Accepted: 05/18/2015] [Indexed: 02/06/2023] Open
Abstract
Typically, inherited metabolic diseases arise from point mutations in genes encoding metabolic enzymes. Although some of these mutations directly affect amino acid residues in the active sites of these enzymes, the majority do not. It is now well accepted that the majority of these disease-associated mutations exert their effects through alteration of protein stability, which causes a reduction in enzymatic activity. This finding suggests a way to predict the severity of newly discovered mutations. In silico prediction of the effects of amino acid sequence alterations on protein stability often correlates with disease severity. However, no stability prediction tool is perfect and, in general, better results are obtained if the predictions from a variety of tools are combined and then interpreted. In addition to predicted alterations to stability, the degree of conservation of a particular residue can also be a factor which needs to be taken into account: alterations to highly conserved residues are more likely to be associated with severe forms of the disease. The approach has been successfully applied in a variety of inherited metabolic diseases, but further improvements are necessary to enable robust translation into clinically useful tools.
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