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Sharma K, Hema K, Bhatraju NK, Kukreti R, Das RS, Gupta MD, Syed MA, Pasha MAQ. The deleterious impact of a non-synonymous SNP on protein structure and function is apparent in hypertension. J Mol Model 2021; 28:14. [PMID: 34961886 DOI: 10.1007/s00894-021-04997-6] [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: 01/20/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022]
Abstract
Essential hypertension (EH) is a significant health issue around the globe. The indifferent therapy regimen suggests varied physiological functions due to the lifestyle and genetic presentations of an individual. The endothelial nitric oxide synthase (NOS3) gene is a crucial vascular system marker in EH that contributes significantly to the phenotype. Hence, the present study aimed to employ the candidate gene approach and investigate the association between NOS3 single nucleotide polymorphism (SNP) E298D (G894T/rs1799983) by applying several in silico tools and validation through human samples screening. We corroborated computational findings through a case-control study comprising 294 controls and 299 patients; the 894T allele emerged significantly as the risk allele (odds ratio=2.07; P=6.38E-05). The in silico analyses highlighted the significance of E298D on the native structure and function of NOS3. The dynamics simulation study revealed that the variant type 298D caused structural destabilization of the protein to alter its function. Plasma nitrite levels were reduced in patients (P=0.0002), and the same correlated with the 894T allele. Furthermore, correlations were apparent between clinical, genotype, and routine biochemical parameters. To conclude, the study demonstrated a perceptible association between the SNP E298D and NOS3 protein structure stability that appears to have a bearing on the enzyme's function with a deleterious role in EH.
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Affiliation(s)
- Kavita Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India.,Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India
| | - Kanipakam Hema
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
| | - Naveen Kumar Bhatraju
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
| | - Rajat Subhra Das
- All India Institute of Medical Sciences, Raebareli, Uttar Pradesh, 229405, India.,Agartala Government Medical College, Kunjaban, Agartala, Tripura, India
| | - Mohit Dayal Gupta
- GB Pant Institute of Post Graduate Medical Education and Research, New Delhi, India
| | - Mansoor Ali Syed
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India.
| | - M A Qadar Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India.
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Kumar R, Lee MH, Mickael C, Kassa B, Pasha Q, Tuder R, Graham B. Pathophysiology and potential future therapeutic targets using preclinical models of COVID-19. ERJ Open Res 2020; 6:00405-2020. [PMID: 33313306 PMCID: PMC7720688 DOI: 10.1183/23120541.00405-2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/27/2020] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) gains entry into the lung epithelial cells by binding to the surface protein angiotensin-converting enzyme 2. Severe SARS-CoV-2 infection, also known as coronavirus disease 2019 (COVID-19), can lead to death due to acute respiratory distress syndrome mediated by inflammatory immune cells and cytokines. In this review, we discuss the molecular and biochemical bases of the interaction between SARS-CoV-2 and human cells, and in doing so we highlight knowledge gaps currently precluding development of new effective therapies. In particular, discovery of novel treatment targets in COVID-19 will start from understanding pathologic changes based on a large number of autopsy lung tissue samples. Pathogenetic roles of potential molecular targets identified in human lung tissues must be validated in established animal models. Overall, this stepwise approach will enable appropriate selection of candidate therapeutic modalities targeting SARS-CoV2 and the host inflammatory response.
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Affiliation(s)
- Rahul Kumar
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael H. Lee
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Claudia Mickael
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Biruk Kassa
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Qadar Pasha
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rubin Tuder
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brian Graham
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
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Impact on Longevity of Genetic Cardiovascular Risk and Lifestyle including Red Meat Consumption. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:1305413. [PMID: 32714484 PMCID: PMC7354649 DOI: 10.1155/2020/1305413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/02/2020] [Indexed: 12/25/2022]
Abstract
Background Cardiovascular risk (CVR) underlies aging process and longevity. Previous work points to genetic and environmental factors associated with this risk. Objectives The aim of this research is to look for any CVR gene-gene and gene-multifactorial/lifestyle interactions that may impact health and disease and underlie exceptional longevity. Methods A case-control study involving 521 both gender individuals, 253 centenarians (100.26 ± 1.98 years), and 268 controls (67.51 ± 3.25 years), low (LCR, n = 107) and high (HCR, n = 161) CVR. Hypertension, diabetes, obesity (BMI, kg·m−2), and impaired kidney function were defined according to standard criteria. CVR was calculated using Q risk®. DNA was genotyping (ACE-rs4646994, AGT-rs4762, AGR1-rs5182, GRK4-rs2960306, GRK4-rs1024323, NOS3-rs1799983, and SLC12A3-rs13306673) through iPlex-MassARRAY®, read by MALDI-TOF mass spectrometry, and analyzed by EARTDECODE®. Results Antilongevity factors consisted (OR 95% CI, p < 0.05) BMI 1.558 (1.445-1.680), hypertension 2.358 (1.565-3.553), smoking habits 4.528 (2.579-7.949), diabetes 5.553 (2.889-10.675), hypercholesterolemia 1.016 (1.010-1.022), and regular consumption of red meat 22.363 (13.987-35.755). Genetic aspects particularly for HCR individuals ACE II (OR: 3.96 (1.83-8.56), p < 0.0001) and NOS3 TT (OR: 3.11 (1.70-5.70), p < 0.0001) genotypes were also risk associate. Obesity, smoking, hypercholesterolemia, and frequent consumption of red meat have an additive action to hypertension in the longevity process. There was a synergistic interaction between the endothelial NOS3 genotypes and the severity of arterial hypertension. An epistatic interaction between functional genetic variants of GRK4 and angiotensinogen was also observed. Conclusions Cardiovascular risk-related genetic and multifactorial or predominantly lifestyle aspects and its interactions might influence the aging process and contribute to exceptional longevity in Portuguese centenarians. Besides lifestyle, the activity of nitrite oxide synthase may be one of the main physiologic regulators of cardiovascular protection in the path of longevity.
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Evidence for gene-gene epistatic interactions between susceptibility genes for Mycobacterium avium subsp. paratuberculosis infection in cattle. Livest Sci 2017. [DOI: 10.1016/j.livsci.2016.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Kohli S, Kumar R, Gupta M, Tyagi S, Pasha MAQ. Impact of interactions between risk alleles on clinical endpoints in hypertension. HEART ASIA 2016; 8:83-9. [PMID: 27326240 DOI: 10.1136/heartasia-2016-010723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/28/2016] [Accepted: 04/08/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Impairment of the renin-angiotensinogen-aldosterone system (RAAS), one of the characteristics of essential hypertension (EH), imbalances vascular homeostasis. Despite inconsistent reports on individual single nucleotide polymorphisms (SNPs) as a major predictor of EH, interactions among RAAS genetic variants are rarely investigated. METHODS Using SNP markers, we studied potential interactions between angiotensin 1 converting enzyme (ACE), angiotensinogen (AGT), angiotensin II-type 1 receptor (AGTR1), and α adducin (ADD1) variants and their correlation with clinical endpoints in 545 individuals with hypertension and 400 age- and ethnicity-matched unrelated controls. Generalised multifactor dimensionality reduction (GMDR) analysis identified the models for genotype interaction. RESULTS Although the results on single genes were significant, gene-gene interactions were more reliable and promising as markers in predisposing hypertension. The best models to represent association of multi-locus interactions with augmented hypertension susceptibility were: (a) within gene 4-locus model comprised of AGT SNPs -217G/A, -20A/C, -6G/A and 235M/T (p=0.022, OR 6.1); and (b) between genes 5-locus model comprised of AGT -217G/A, -20A/C, -6G/A, 235M/T and ACE I/D (p=0.05, OR 4.6). Stratification of 4- and 5-locus GMDR models on the basis of risk alleles from ≤1 to ≥7 increased the ORs from 2.8 to 36.1 and from 0.9 to 16.1, respectively. Moreover, compared to ≤1 risk alleles the ≥7 interacting risk alleles in both 4- and 5-locus models showed an increment of 14.2% and 11.1% in systolic blood pressure, 7.7% and 1.1% in diastolic blood pressure, and 10.5% and 5.1% in mean arterial pressure, respectively, in patients. CONCLUSIONS Interactions among the genetic loci of RAAS components may be used as a predictor for susceptibility to hypertension.
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Affiliation(s)
- Samantha Kohli
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India; Academy of Scientific and Innovative Research, New Delhi, Delhi, India
| | - Rahul Kumar
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India; Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Denver, USA
| | - Mohit Gupta
- Department of Cardiology , G.B. Pant Hospital , New Delhi, Delhi , India
| | - Sanjay Tyagi
- Department of Cardiology , G.B. Pant Hospital , New Delhi, Delhi , India
| | - M A Qadar Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India; Academy of Scientific and Innovative Research, New Delhi, Delhi, India
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Kumar R, Kohli S, Ali Z, Duhan K, Ram R, Gupta M, Tyagi S, Mohammad G, Pasha MQ. CYBA (p22phox) variants associate with blood pressure and oxidative stress markers in hypertension: a replication study in populations of diverse altitudes. Hypertens Res 2015; 38:498-506. [PMID: 25787042 DOI: 10.1038/hr.2015.31] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/27/2014] [Accepted: 12/11/2014] [Indexed: 02/07/2023]
Abstract
CYBA (p22(phox)) is an integral constituent of the NADPH oxidases and is consequently a main component of oxidative stress, which is strongly associated with hypertension. This study investigates the contribution of CYBA polymorphisms toward the complex etiology of hypertension in two ethnically different populations, one located at a high altitude and the other at a low altitude. The significance of CYBA single nucleotide polymorphisms and their correlation with clinical and biochemical phenotypes were investigated in age- and ethnicity-matched unrelated permanent high-altitude residents (>3500 m) comprising 245 controls and 241 patients. The results were replicated in a second population comprising 935 controls and 545 patients who lived at a low altitude (<200 m). The analysis of covariance revealed that CYBA risk alleles and their haplotypes, rs8854A/rs9932581G/rs4873C and rs8854G/rs9932581G/rs4873C, were positively correlated with clinical parameters, for example, systolic blood pressure (SBP), diastolic blood pressure (DBP) and mean arterial pressure (MAP), and biochemical parameters, for example, 8-isoPGF2α level, and inversely correlated with catalase activity in patients compared with controls (P⩽0.01, each). Conversely, the protective alleles and their haplotype, rs8854G/rs9932581A/rs4873T, were inversely correlated with SBP, DBP, MAP and 8-isoPGF2α level, and positively correlated with catalase activity (P⩽0.001, each). Furthermore, correlation analysis between the clinical and biochemical parameters revealed a positive correlation of SBP, DBP and MAP with 8-isoPGF2α levels and a negative correlation with catalase activity in both populations (P<0.0001, each). CYBA (p22(phox)) variants influence the markers of oxidative stress and are associated with hypertension.
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Affiliation(s)
- Rahul Kumar
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Samantha Kohli
- 1] Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India [2] Academy of Scientific and Innovative Research, New Delhi, India
| | - Zahara Ali
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Kanika Duhan
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rekhbala Ram
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mohit Gupta
- Department of Cardiology, G.B. Pant hospital, New Delhi, India
| | - Sanjay Tyagi
- Department of Cardiology, G.B. Pant hospital, New Delhi, India
| | | | - Ma Qadar Pasha
- 1] Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India [2] Academy of Scientific and Innovative Research, New Delhi, India
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Kumar R, Kohli S, Mishra A, Garg R, Alam P, Stobdan T, Nejatizadeh A, Gupta M, Tyagi S, Pasha MAQ. Interactions between the genes of vasodilatation pathways influence blood pressure and nitric oxide level in hypertension. Am J Hypertens 2015; 28:239-47. [PMID: 25159081 DOI: 10.1093/ajh/hpu130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND This study investigates the contribution of genetic interactions between the β-2 adrenergic receptor (ADRB2) and nitric oxide synthase (NOS3) genes to the complex etiology of hypertension. METHODS Using single nucleotide polymorphism (SNP) markers, we studied potential interactions between ADRB2 and NOS3 variants and their correlation with clinical, biochemical, and expression levels in 546 individuals with hypertension and 884 age-, sex-, and ethnicity-matched unrelated control subjects. Generalized multifactor dimensionality reduction (GMDR) analysis identified the models for genotype interaction. RESULTS The best models to represent association of genotypes with augmented hypertension susceptibility were the 4- and 5-locus interacting GMDR models of ADRB2 and NOS3 compared with within-gene 6-locus ADRB2 and 2-locus NOS3 (odds ratio (OR) = 4.8, P = 0.04; OR = 5.6, P = 0.02, respectively). Stratification of 4- and 5-locus GMDR models on the basis of risk alleles (in increasing order) increased the ORs from 1.26 to 14.17 and from 0.81 to 14.18, respectively, and correlated linearly with increased systolic blood pressure, diastolic blood pressure, and mean arterial pressure and decreased nitric oxide level (P ≤ 0.0004). We performed various analyses, such as single-locus, genetic interactions, sliding-window, and comparative analysis. Each analysis consistently revealed the 46A allele of ADRB2 46G/A SNP and 4a allele of NOS3 4b/4a SNP to be associated with risk of hypertension. These risk-conferring markers were associated with decreased ADRB2 and NOS3 expression and decreased nitric oxide level in the patients (P ≤ 0.04). CONCLUSIONS Evidence of interaction between the genetic loci of ADRB2 and NOS3 points to varied clinical, biochemical, and expression levels and a role in hypertension susceptibility.
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Affiliation(s)
- Rahul Kumar
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Present address: Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Denver, Colorado (R.K.); Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, California (T.S.); Research Center for Molecular Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran (A.N.)
| | - Samantha Kohli
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research, New Delhi, India
| | - Aastha Mishra
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Ritu Garg
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Perwez Alam
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Tsering Stobdan
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Present address: Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Denver, Colorado (R.K.); Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, California (T.S.); Research Center for Molecular Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran (A.N.)
| | - Azim Nejatizadeh
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Present address: Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Denver, Colorado (R.K.); Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, California (T.S.); Research Center for Molecular Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran (A.N.)
| | - Mohit Gupta
- Department of Cardiology, Govind Ballabh Pant Hospital, New Delhi, India
| | - Sanjay Tyagi
- Department of Cardiology, Govind Ballabh Pant Hospital, New Delhi, India
| | - M A Qadar Pasha
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research, New Delhi, India;
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