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Muro-Perez M, González-Martínez G, Martínez-García P, Legaz I, Zafrilla P, Muro M. Analysis of null deletion polymorphism of glutathione S-transferase theta (GSTT-1), associated with anti-GSTT-1 antibodies development in transplantation. Int J Immunogenet 2023; 50:264-271. [PMID: 37612787 DOI: 10.1111/iji.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
Glutathione S-transferase theta 1 (GSTT1) is an enzyme involved in phase II biotransformation processes and a member of a multigene family of detoxifying and clearing reactive oxygen species. GSTT1 is polymorphic like other biotransforming enzymes, allowing variability in hepatic conjugation processes. Immunological recognition of the GSTT1 alloantigen, as evidenced by donor-specific antibodies formation, has previously been observed in recipients lacking GSTT1 protein (called GSTT1-, GSTT*0, null phenotype or homozygous for the GSTT1 deletion) who receive liver or kidney transplants from GSTT1+ donors and is a risk factor for the development of de novo hepatitis following liver transplants from a GSTT1 expressing donor. Antibodies against GSTT1 are demonstrated in patients who are GSTT1 null and received a transplant from a GSTT1+ donor. Understanding the local population frequency of the GSTT1 deletion is of value in understanding the potential clinical risk of developing post-transplant complications, which can be attributed to the nonexpression of GSTT1. A population of 173 healthy donors of the Murcia Region in Southeast Spain was evaluated for a null allele of GSTT1 (n = 173). DNA was extracted, and GSTT-1 null allele detection was performed by real-time polymerase chain reaction. The frequency of the null GSTT1 genotype (nonexpression or deletion of the homozygous polymorphism of the GSTT1 protein) was 17.9% (n = 31 null allele GSTT1/173 total individuals). Our data suggest that the frequency of null GSTT1 mutations in our population in Southeast Spain is 17.9%, lower than in other Caucasoid populations. This would convert our recipient population into more susceptible to nonlocal potential organ donors and less susceptible to local donors. All recipients bearing this GSTT1 deletion homozygous would be without the protein and triggering an alloantigen in the case of transplantation with a donor without deletion.
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Affiliation(s)
- Manuel Muro-Perez
- Immunology Service, University Clinical Hospital "Virgen de la Arrixaca" - IMIB, Murcia, Spain
| | - Gema González-Martínez
- Immunology Service, University Clinical Hospital "Virgen de la Arrixaca" - IMIB, Murcia, Spain
| | - Pedro Martínez-García
- Immunology Service, University Clinical Hospital "Virgen de la Arrixaca" - IMIB, Murcia, Spain
| | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute of Murcia (IMIB), Regional Campus of International Excellence "Campus Mare Nostrum", Faculty of Medicine, University of Murcia (UMU), Murcia, Spain
| | - Pilar Zafrilla
- Faculty of Pharmacy, San Antonio Catholic University of Murcia (UCAM), Murcia, Spain
| | - Manuel Muro
- Immunology Service, University Clinical Hospital "Virgen de la Arrixaca" - IMIB, Murcia, Spain
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Zhang R, Akhtar N, Wani AK, Raza K, Kaushik V. Discovering Deleterious Single Nucleotide Polymorphisms of Human AKT1 Oncogene: An In Silico Study. Life (Basel) 2023; 13:1532. [PMID: 37511907 PMCID: PMC10381612 DOI: 10.3390/life13071532] [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: 03/12/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND AKT1 is a serine/threonine kinase necessary for the mediation of apoptosis, angiogenesis, metabolism, and cell proliferation in both normal and cancerous cells. The mutations in the AKT1 gene have been associated with different types of cancer. Further, the AKT1 gene mutations are also reported to be associated with other diseases such as Proteus syndrome and Cowden syndromes. Hence, this study aims to identify the deleterious AKT1 missense SNPs and predict their effect on the function and structure of the AKT1 protein using various computational tools. METHODS Extensive in silico approaches were applied to identify deleterious SNPs of the human AKT1 gene and assessment of their impact on the function and structure of the AKT1 protein. The association of these highly deleterious missense SNPs with different forms of cancers was also analyzed. The in silico approach can help in reducing the cost and time required to identify SNPs associated with diseases. RESULTS In this study, 12 highly deleterious SNPs were identified which could affect the structure and function of the AKT1 protein. Out of the 12, four SNPs-namely, G157R, G159V, G336D, and H265Y-were predicted to be located at highly conserved residues. G157R could affect the ligand binding to the AKT1 protein. Another highly deleterious SNP, R273Q, was predicted to be associated with liver cancer. CONCLUSIONS This study can be useful for pharmacogenomics, molecular diagnosis of diseases, and developing inhibitors of the AKT1 oncogene.
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Affiliation(s)
- Ruojun Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Vikas Kaushik
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
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Melloni M, Sergi D, Simioni C, Passaro A, Neri LM. Microalgae as a Nutraceutical Tool to Antagonize the Impairment of Redox Status Induced by SNPs: Implications on Insulin Resistance. BIOLOGY 2023; 12:biology12030449. [PMID: 36979141 PMCID: PMC10044993 DOI: 10.3390/biology12030449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Microalgae represent a growing innovative source of nutraceuticals such as carotenoids and phenolic compound which are naturally present within these single-celled organisms or can be induced in response to specific growth conditions. The presence of the unfavourable allelic variant in genes involved in the control of oxidative stress, due to one or more SNPs in gene encoding protein involved in the regulation of redox balance, can lead to pathological conditions such as insulin resistance, which, in turn, is directly involved in the pathogenesis of type 2 diabetes mellitus. In this review we provide an overview of the main SNPs in antioxidant genes involved in the promotion of insulin resistance with a focus on the potential role of microalgae-derived antioxidant molecules as novel nutritional tools to mitigate oxidative stress and improve insulin sensitivity.
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Affiliation(s)
- Mattia Melloni
- Department of Translational Medicine, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy; (M.M.); (D.S.)
| | - Domenico Sergi
- Department of Translational Medicine, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy; (M.M.); (D.S.)
| | - Carolina Simioni
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy;
- Laboratory for Technologies of Advanced Therapies (LTTA)—Electron Microscopy Center, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Angelina Passaro
- Department of Translational Medicine, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy; (M.M.); (D.S.)
- Medical Department, University Hospital of Ferrara Arcispedale Sant’Anna, Via Aldo Moro 8, 44124 Ferrara, Italy
- Research and Innovation Section, University Hospital of Ferrara Arcispedale Sant’Anna, Via Aldo Moro 8, 44124 Ferrara, Italy
- Correspondence: (A.P.); (L.M.N.); Tel.: +39-0532-236291 (A.P.); +39-0532-455940 (L.M.N.)
| | - Luca Maria Neri
- Department of Translational Medicine, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy; (M.M.); (D.S.)
- Laboratory for Technologies of Advanced Therapies (LTTA)—Electron Microscopy Center, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- Correspondence: (A.P.); (L.M.N.); Tel.: +39-0532-236291 (A.P.); +39-0532-455940 (L.M.N.)
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Dos Santos SP, Morissugui SS, Gimenez Martins APD, Fernandes GMDM, Russo A, Galbiatti-Dias ALS, Castanhole-Nunes MMU, Francisco JLE, Pavarino ÉC, Goloni-Bertollo EM. Evaluation of molecular markers GSTM1 and GSTT1 and clinical factors in breast cancer: case-control study and literature review. Xenobiotica 2021; 51:1326-1334. [PMID: 34096444 DOI: 10.1080/00498254.2021.1938291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The study was conducted to evaluate the frequency of polymorphisms in GSTM1 and GSTT1 genes in patients with breast cancer compared with individuals without history of cancer, and the association of these polymorphisms with clinical/epidemiological parameters.There were evaluated 752 women (219 patients and 533 controls). Molecular analysis was performed by the Polymerase Chain Reaction (PCR). Statistical analysis was used multiple logistic regression and descriptive statistics.Age ≥50 years (OR =3.22, 95% CI =2.30 - 4.51, p <0.001) and alcohol consumption (OR =1.60, 95% CI =1.13 - 2.27, p = 0.008) were associated to the development of breast cancer, while smoking and null genotypes GSTM1 and GSTT1 presented no association. GSTM1 and GSTT1 polymorphisms presented no relationship with the clinical and histopathological parameters or molecular subtypes of breast cancer. Ninety-two percent of tumors were invasive ductal, 66% were grade II, 65% were larger than 2 cm, the stages II (35.3%) and III (31.2%) were the most prevalent, and 47.7% were molecular subtype luminal B.Individuals aged ≥50 years and alcohol consumers have more chance to developing breast cancer. GSTM1 and GSTT1 polymorphisms are not associated to the risk of breast cancer.
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Affiliation(s)
- Stéphanie Piacenti Dos Santos
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil
| | - Sabrina Sayuri Morissugui
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil
| | - Ana Paula D'Alarme Gimenez Martins
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil
| | - Glaucia Maria de Mendonça Fernandes
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil
| | - Anelise Russo
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil
| | - Ana Lívia Silva Galbiatti-Dias
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil
| | | | - José Luis Esteves Francisco
- Gynecology and Obstetrics Department, São José do Rio Preto Medical School Fundation - FAMERP/FUNFARME, São José do Rio Preto/SP, Brazil.,São José do Rio Preto Medical School Fundation - FUNFARME, São José do Rio Preto, SP, Brazil
| | - Érika Cristina Pavarino
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil.,São José do Rio Preto Medical School Fundation - FUNFARME, São José do Rio Preto, SP, Brazil
| | - Eny Maria Goloni-Bertollo
- Molecular Biology: Genetics and Molecular Biology Research Unit, São José do Rio Preto Medical School - FAMERP, São Jose do Rio Preto/SP, Brazil.,São José do Rio Preto Medical School Fundation - FUNFARME, São José do Rio Preto, SP, Brazil
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Gusti AMT, Qusti SY, Bahijri SM, Toraih EA, Bokhari S, Attallah SM, Alzahrani A, Alshehri WMA, Alotaibi H, Fawzy MS. Glutathione S-Transferase ( GSTT1 rs17856199) and Nitric Oxide Synthase ( NOS2 rs2297518) Genotype Combination as Potential Oxidative Stress-Related Molecular Markers for Type 2 Diabetes Mellitus. Diabetes Metab Syndr Obes 2021; 14:1385-1403. [PMID: 33790606 PMCID: PMC8006960 DOI: 10.2147/dmso.s300525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Deregulation of the antioxidant enzymes was implicated in pathogenesis and complications of type 2 diabetes mellitus (T2DM). The data relate the genetic variants of these enzymes to T2DM are inconsistent among various populations. PURPOSE We aimed to explore the association of 13 genetic variants of "superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione-S-transferase (GST) and nitric oxide synthase (NOS)" with T2DM susceptibility and the available clinical laboratory data. SUBJECTS AND METHODS A total of 384 individuals were enrolled in this work. Different genotypes of the genes mentioned above were characterized using TaqMan OpenArray Genotyping assays on a Real-Time polymerase chain reaction system. RESULTS After age- and sex-adjustment, among the studied 13 variants, GSTT1 rs17856199 was associated with T2DM under homozygote (OR=3.42; 95% CI:1.04-11.2, p=0.031), and recessive (OR=3.57; 95% CI: 1.11-11.4, p=0.029) comparison models. The NOS2 rs2297518*A allele was more frequent among the T2DM cohort (58.1% vs 35.4%, p<0.001) and showed a dose-response effect; being heterozygote was associated with higher odds for developing DM (OR=4.06, 95% CI=2.13-7.73, p<0.001), whereas being AA homozygote had double the risk (OR=9.06, 95% CI=3.41-24.1, p<0.001). Combined NOS2 rs2297518*A and either GSTT1 rs17856199*A or *C genotype carriers were more likely to develop T2DM. Different associations with sex, BMI, hyperglycemia, and/or hyperlipidemia were evident. The principal component analysis revealed NOS2 rs2297518*G, old age, dyslipidemia, high systolic blood pressure, and elevated HbA1c were the main classifiers of T2DM patients. CONCLUSION The oxidative stress-related molecular markers, GSTT1 rs17856199 and NOS2 rs2297518 variants were significantly associated with T2DM risk and phenotype in the study population.
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Affiliation(s)
- Amani M T Gusti
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory, Biochemistry, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Safaa Y Qusti
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Suhad M Bahijri
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Saudi Diabetes Research Group, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eman A Toraih
- Department of Surgery, Tulane University, School of Medicine, New Orleans, LA, USA
- Department of Histology and Cell Biology (Genetics Unit), Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Samia Bokhari
- Department of Endocrinology and Diabetes, King Fahd Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Sami M Attallah
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
- Department of Clinical Pathology, King Fahd Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Abdulwahab Alzahrani
- Department of Molecular Biology, King Fahd Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Wafaa M A Alshehri
- Department of Chemistry, Faculty of Science, University of Bisha, Al Namas, Saudi Arabia
| | | | - Manal S Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Kingdom of Saudi Arabia
- Correspondence: Manal S Fawzy Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, 41522, EgyptTel + 20 1008584720Fax + 20 64 3216496 Email
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Kim JH, Ahn JB, Kim DH, Kim S, Ma HW, Che X, Seo DH, Kim TI, Kim WH, Cheon JH, Kim SW. Glutathione S-transferase theta 1 protects against colitis through goblet cell differentiation via interleukin-22. FASEB J 2020; 34:3289-3304. [PMID: 31916636 DOI: 10.1096/fj.201902421r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 01/06/2023]
Abstract
The enzyme glutathione S-transferase theta 1 (GSTT1) is involved in detoxifying chemicals, including reactive oxygen species (ROS). Here, we provide a significant insight into the role of GSTT1 in inflammatory bowel disease (IBD). We identified decreased expression of GSTT1 in inflamed colons from IBD patients compared to controls. We intrarectally or intraperitoneally delivered Gstt1 gene to mice with dextran sodium sulfate (DSS)-induced colitis and noted attenuation of colitis through gene transfer of Gstt1 via an IL-22 dependent pathway. Downregulation of GSTT1 by pathogen-associated molecular patterns (PAMPs) of microbes reduced innate defense responses and goblet cell differentiation. The GSTT1 mutation in intestinal epithelial cells (IECs) and IBD patients decreased its dimerization, which was connected to insufficient phosphorylation of signal transducer and activator of transcription-3 and p38/mitogen-activated protein kinase by their common activator, IL-22. GSTT1 ameliorated colitis and contributed as a modulator of goblet cells through sensing pathogens and host immune responses. Its mutations are linked to chronic intestinal inflammation due to its insufficient dimerization. Our results provide new insights into GSTT1 mutations that are linked to chronic intestinal inflammation due to its insufficient dimerization and their functional consequences in IBDs.
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Affiliation(s)
- Jae Hyeon Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Bum Ahn
- Department of Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Da Hye Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Soochan Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Woo Ma
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Xiumei Che
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Dong Hyuk Seo
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Il Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Won Ho Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Won Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
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GPS: Identification of disease genes by rank aggregation of multi-genomic scoring schemes. Genomics 2019; 111:612-618. [DOI: 10.1016/j.ygeno.2018.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 12/19/2022]
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Falomir-Lockhart AH, Villegas-Castagnaso EE, Giovambattista G, Rogberg-Muñoz A. Computational prediction of nsSNPs effects on protein function and structure, a prioritization approach for further in vitro studies applied to bovine GSTP1. Free Radic Biol Med 2018; 129:486-491. [PMID: 30315934 DOI: 10.1016/j.freeradbiomed.2018.10.403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/20/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022]
Abstract
The development of high-throughput technologies in the last decade produced an exponential increase in the amount of biological data available. The case of redox biology and apoptosis is not an exception, and nowadays there is a need to integrate information from multiple "omics" studies. Therefore, validation of proposed discoveries is essential. However, the study in biological systems of the effect of the massive amounts of sequence variation data generated with next-generation sequencing (NGS) technologies can be a very difficult and expensive process. In this context, the present study aimed to demonstrate the advantages of a computational methodology to systematically analyze the structural and functional effects of protein variants, in order to prioritize further studies. This approach stands out for its easy implementation, low costs and low time consumed. First, the possible impact of mutations on protein structure and function was tested by a combination of tools based on evolutionary and structural information. Next, homology modeling was performed to predict and compare the 3D protein structures of unresolved amino acid sequences obtained from genomic resequencing. This analysis applied to the bovine GSTP1 allowed to determine that some of amino acid substitutions may generate important changes in protein structure and function. Moreover, the haplotype analysis highlighted three structure variants worthwhile studying through in vitro or in vivo experiments.
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Affiliation(s)
- A H Falomir-Lockhart
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - E E Villegas-Castagnaso
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - A Rogberg-Muñoz
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina; Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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Al-Aama JY, Banaganapalli B, Aljeaid D, Bakhur K, Verma PK, Al-Ata J, Elango R, Shaik NA. Targeted Molecular Sequencing Revealed Allelic Heterogeneity of BRAF and PTPN11 Genes among Arab Noonan Syndrome Patients. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Al-Shuhaib MBS, Al-Kafajy FR, Badi MA, AbdulAzeez S, Marimuthu K, Al-Juhaishi HAI, Borgio JF. Highly deleterious variations in COX1, CYTB, SCG5, FK2, PRL and PGF genes are the potential adaptation of the immigrated African ostrich population. Comput Biol Med 2018; 100:17-26. [PMID: 29960146 DOI: 10.1016/j.compbiomed.2018.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 11/19/2022]
Abstract
Because of variable inconvenient living conditions in some places around the world, it is difficult to collect reliable physiological data for ostriches. Therefore, this study aims to provide a comprehensive in silico insight for the nature of polymorphism of important genetic loci that are related to physiological and reproductive traits. Sixty-nine mature ostriches ranging over half of Iraq were screened. Six exonic genetic loci, including cytochrome c oxidase I (COX1), cytochrome b (CYTB), secretogranin V (SCG5), feather keratin 2-like (FK2), prolactin (PRL) and placenta growth factor (PGF) were genotyped by PCR-single stranded conformation polymorphism (SSCP). Thirty-six novel SNPs, including seventeen nonsynonymous (ns) SNPs, were observed. Several computational software programs were utilized to assess the extent of the nsSNPs on their corresponding proteins structure, function and stability. The results showed several deleterious functional and stability changes in almost all the proteins studied. The total severity of each missense mutation was evaluated and compared with other nsSNPs accumulatively. It is evident from the extensive cumulative in silico computation that both p.E34D and p.E60K in PGF have the highest deleterious effect. The cumulative predictions from the present study are an impressive guide for the genotypes of African ostriches, which bypassed the expensive protocols for wet laboratory screening, to identify the effects of variants. To the best of our knowledge, this is the first investigation of its kind on the analyses and prediction outcome of missense mutations in African ostrich populations. The highly deleterious nsSNPs in the placenta growth factor are possible adaptive mutations which might be associated with adaptation in extreme and new environments. The flow and protocol of the computational predictions can be extended for various wild animals to identify the molecular nature of adaptations.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Fadhil R Al-Kafajy
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Milad Ali Badi
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Kasi Marimuthu
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, Kedah Darul Aman, Malaysia.
| | | | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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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.
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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
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12
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Václavíková R, Hughes DJ, Souček P. Microsomal epoxide hydrolase 1 (EPHX1): Gene, structure, function, and role in human disease. Gene 2015. [PMID: 26216302 DOI: 10.1016/j.gene.2015.07.071] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Microsomal epoxide hydrolase (EPHX1) is an evolutionarily highly conserved biotransformation enzyme for converting epoxides to diols. Notably, the enzyme is able to either detoxify or bioactivate a wide range of substrates. Mutations and polymorphic variants in the EPHX1 gene have been associated with susceptibility to several human diseases including cancer. This review summarizes the key knowledge concerning EPHX1 gene and protein structure, expression pattern and regulation, and substrate specificity. The relevance of EPHX1 for human pathology is especially discussed.
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Affiliation(s)
- Radka Václavíková
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - David J Hughes
- Centre for Systems Medicine, Department of Physiology, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Plzen, Charles University in Prague, Plzen, Czech Republic.
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13
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Abstract
The computational approaches in determining disease-associated Non-synonymous single nucleotide polymorphisms (nsSNPs) have evolved very rapidly. Large number of deleterious and disease-associated nsSNP detection tools have been developed in last decade showing high prediction reliability. Despite of all these highly efficient tools, we still lack the accuracy level in determining the genotype-phenotype association of predicted nsSNPs. Furthermore, there are enormous questions that are yet to be computationally compiled before we might talk about the prediction accuracy. Earlier we have incorporated molecular dynamics simulation approaches to foster the accuracy level of computational nsSNP analysis roadmap, which further helped us to determine the changes in the protein phenotype associated with the computationally predicted disease-associated mutation. Here we have discussed on the present scenario of computational nsSNP characterization technique and some of the questions that are crucial for the proper understanding of pathogenicity level for any disease associated mutations.
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Matam K, Shaik NA, Aggarwal S, Diwale S, Banaganapalli B, Al-Aama JY, Elango R, Rao P, Hasan Q. Evidence for the presence of somatic mitochondrial DNA mutations in right atrial appendage tissues of coronary artery disease patients. Mol Genet Genomics 2014; 289:533-40. [DOI: 10.1007/s00438-014-0828-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 02/11/2014] [Indexed: 12/31/2022]
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