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Dubey PK, Dubey S, Singh S, Bhat PD, Pogwizd S, Krishnamurthy P. Identification and development of Tetra-ARMS PCR-based screening test for a genetic variant of OLA1 (Tyr254Cys) in the human failing heart. PLoS One 2024; 19:e0293105. [PMID: 38889130 PMCID: PMC11185490 DOI: 10.1371/journal.pone.0293105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/01/2024] [Indexed: 06/20/2024] Open
Abstract
Obg-like ATPase 1 (OLA1) protein has GTP and ATP hydrolyzing activities and is important for cellular growth and survival. The human OLA1 gene maps to chromosome 2 (locus 2q31.1), near Titin (TTN), which is associated with familial dilated cardiomyopathy (DCM). In this study, we found that expression of OLA1 was significantly downregulated in failing human heart tissue (HF) compared to non-failing hearts (NF). Using the Sanger sequencing method, we characterized the human OLA1 gene and screened for mutations in the OLA1 gene in patients with failing and non-failing hearts. Among failing and non-failing heart patients, we found 15 different mutations in the OLA1 gene, including two transversions, one substitution, one deletion, and eleven transitions. All mutations were intronic except for a non-synonymous 5144A>G, resulting in 254Tyr>Cys in exon 8 of the OLA1 gene. Furthermore, haplotype analysis of these mutations revealed that these single nucleotide polymorphisms (SNPs) are linked to each other, resulting in disease-specific haplotypes. Additionally, to screen the 254Tyr>Cys point mutation, we developed a cost-effective, rapid genetic screening PCR test that can differentiate between homozygous (AA and GG) and heterozygous (A/G) genotypes. Our results demonstrate that this PCR test can effectively screen for OLA1 mutation-associated cardiomyopathy in human patients using easily accessible cells or tissues, such as blood cells. These findings have important implications for the diagnosis and treatment of cardiomyopathy.
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Affiliation(s)
- Praveen K. Dubey
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shubham Dubey
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sarojini Singh
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Purnima Devaki Bhat
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Steven Pogwizd
- Comprehensive Cardiovascular Center, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Dubey PK, Dubey S, Singh S, Bhat PD, Pogwizd S, Krishnamurthy P. Identification and development of Tetra-ARMS PCR-based screening test for a genetic variant of OLA1 (Tyr254Cys) in the human failing heart. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.16.23296746. [PMID: 37905026 PMCID: PMC10615000 DOI: 10.1101/2023.10.16.23296746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Obg-like ATPase 1 (OLA1) protein has GTP and ATP hydrolyzing activities and is important for cellular growth and survival. The human OLA1 gene maps on chromosome 2, at the locus 1q31, close to the Titin (TTN) gene, which is associated with familial dilated cardiomyopathy (DCM). In this study, we found that expression of OLA1 was significantly downregulated in human failing heart tissue (HF) as compared to in non-failing heart tissues (NF). Moreover, using the Sanger sequencing method, we characterized the human OLA1 gene and screened genetic mutations in patients with heart-failing and non-failing. Among failing and non-failing heart patients, we found a total of 15 mutations, including two transversions, one substitution, one indel, and eleven transition mutations in the OLA1 gene. All the mutations were intronic except for a non-synonymous mutation, 5144A>G, resulting in 254Tyr>Cys in exon 8 of the OLA1 gene. Furthermore, haplotype analysis of these mutations revealed that these single nucleotide polymorphisms (SNPs) are linked to each other, resulting in disease-specific haplotypes. Additionally, to screen for the 254Tyr>Cys point mutation, we developed a cost-effective, rapid genetic screening PCR test that can differentiate between homozygous (AA and GG) and heterozygous (A/G) genotypes. Our results show that this test can be used as a genetic screening tool for human cardiomyopathy. These findings have important implications for the diagnosis and treatment of cardiomyopathy.
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Affiliation(s)
- Praveen K Dubey
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, AL, USA
| | - Shubham Dubey
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, AL, USA
| | - Sarojini Singh
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, AL, USA
| | - Purnima Devaki Bhat
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, AL, USA
| | - Steven Pogwizd
- Comprehensive Cardiovascular Center, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, AL, USA
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Rout AK, Acharya V, Maharana D, Dehury B, Udgata SR, Jena R, Behera B, Parida PK, Behera BK. Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach. PLoS One 2021; 16:e0245358. [PMID: 33444377 PMCID: PMC7808660 DOI: 10.1371/journal.pone.0245358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
The toll-like receptor 5 (TLR5) is the most conserved important pattern recognition receptors (PRRs) often stimulated by bacterial flagellins and plays a major role in the first-line defense against invading pathogenic bacteria and in immune homeostasis. Experimental crystallographic studies have shown that the extracellular domain (ECD) of TLR5 recognizes flagellin of bacteria and functions as a homodimer in model organism zebrafish. However, no structural information is available on TLR5 functionality in the major carp Cirrhinus mrigala (mrigala) and its interaction with bacterial flagellins. Therefore, the present study was undertaken to unravel the structural basis of TLR5-flagellin recognition in mrigala using structural homodimeric TLR5-flagellin complex of zebrafish as reference. Integrative structural modeling and molecular dynamics simulations were employed to explore the structural and mechanistic details of TLR5 recognition. Results from structural snapshots of MD simulation revealed that TLR5 consistently formed close interactions with the three helices of the D1 domain in flagellin on its lateral side mediated by several conserved amino acids. Results from the intermolecular contact analysis perfectly substantiate with the findings of per residue-free energy decomposition analysis. The differential recognition mediated by flagellin to TLR5 in mrigala involves charged residues at the interface of binding as compared to the zebrafish complex. Overall our results shows TLR5 of mrigala involved in innate immunity specifically recognized a conserved site on flagellin which advocates the scientific community to explore host-specific differences in receptor activation.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Varsha Acharya
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Diptimayee Maharana
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sheela Rani Udgata
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Rajkumar Jena
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, Odisha, India
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, Odisha, India
| | - Pranaya Kumar Parida
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- * E-mail: (BKB); (PKP)
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology & Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- * E-mail: (BKB); (PKP)
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Goyal S, Dubey P, Sahoo B, Mishra S, Niranjan S, Singh S, Mahajan R, Kataria R. Sequence based structural characterization and genetic diversity analysis across coding and promoter regions of goat Toll-like receptor 5 gene. Gene 2014; 540:238-45. [DOI: 10.1016/j.gene.2014.01.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 01/17/2014] [Accepted: 01/31/2014] [Indexed: 11/16/2022]
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Novák K. Functional polymorphisms in Toll-like receptor genes for innate immunity in farm animals. Vet Immunol Immunopathol 2013; 157:1-11. [PMID: 24268689 DOI: 10.1016/j.vetimm.2013.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 10/21/2013] [Accepted: 10/28/2013] [Indexed: 01/05/2023]
Abstract
The exploitation of the genetic factors affecting the health status of farm animals represents an alternative approach to controlling the diseases caused by microbial pathogens. The determination of innate immunity based on the genotype of the germplasm cells is a constraint for specificity but becomes an advantage in breeding schemes. The structural deviations among Toll-like receptors (TLRs), as the most frequently studied innate immunity components, have been documented at all levels, i.e., interspecific, inter- and intravarietal, in the main farm species. The current computational methods facilitate the prediction of the functional consequences of the observed mutations. Subsequently, these predictions can be verified through immunological responsiveness and population-wide association studies. The frequency and haplotype grouping of individual polymorphisms are used to track the origin and selection coefficient as independent indicators of functional changes. The Toll-like receptor variants associated with mastitis and mycobacterial infection have been identified in cattle, consequently, the targeting of these proteins in breeding could contribute to disease control. The range of infections affected by TLR polymorphisms suggests that the improvement of innate resistance is feasible in more species. Thus, the traditional breeds and wild populations should be regarded as the resources of genetic variability accessible for these purposes.
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Affiliation(s)
- Karel Novák
- Department of Molecular Genetics, Institute of Animal Science, Prague-Uhříněves, Czech Republic.
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Goyal S, Dubey PK, Kumari N, Niranjan SK, Kathiravan P, Mishra BP, Mahajan R, Kataria RS. Caprine Toll-like receptor 8 gene sequence characterization reveals close relationships among ruminant species. Int J Immunogenet 2013; 41:81-9. [PMID: 23829591 DOI: 10.1111/iji.12075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 05/28/2013] [Accepted: 06/06/2013] [Indexed: 02/06/2023]
Abstract
TLR8 mediates antiviral immunity by recognizing ssRNA viruses and triggers potent antiviral and antitumor immune responses. In this study, approximately 3.5 Kb nucleotide sequence data of caprine TLR8 gene were generated from one sample each of twelve different Indian goat breeds belonging to different geographical regions. Cloning and characterization of cDNA synthesized from RNA purified from goat spleen revealed TLR8 ORF to be of 3102 nucleotides long coding for 1033 amino acids similar to other ruminant species, that is sheep, buffalo and cattle. The sequence analysis at nucleotide level revealed goat TLR8 to be closer to buffalo sharing 99.6% homology, followed by cattle and sheep. Simple Modular Architecture Research Tool (SMART) used for the structural analysis of goat TLR8 showed the presence of 16 leucine-rich repeats (LRRs) along with single Toll/interleukin-1 receptor (TIR) domain. TIR domain when compared with other livestock species was found to be conserved in ruminant species goat, sheep, cattle and buffalo. The phylogenetic analysis also revealed grouping of all ruminant species together, goat being closer to buffalo followed by cattle and sheep. Total 4 polymorphic sites were observed in TLR8 gene of one specimen goat representing each of 12 different breeds studied, all of which were synonymous and present within the coding region. Of these 4 SNPs, two were in ectodomains, one in TIR domain and one was found to be present in transmembrane domain. PCR-RFLP genotyping of two of the SNPs indicated variations in allele frequencies among different goat breeds. The expression profiling in 13 tissues of goat showed maximum expression of TLR8 gene in kidney followed by spleen, lung and lymph node. Overall, our results indicate conservation of TLR8 gene among the ruminant species and low variation within Indian goat breeds.
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Affiliation(s)
- S Goyal
- National Bureau of Animal Genetic Resources, Karnal, India
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