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Hara A, Lu E, Johnstone L, Wei M, Sun S, Hallmark B, Watkins JC, Zhang HH, Yao G, Chilton FH. Identification of an Allele-Specific Transcription Factor Binding Interaction that May Regulate PLA2G2A Gene Expression. Bioinform Biol Insights 2024; 18:11779322241261427. [PMID: 39081667 PMCID: PMC11287738 DOI: 10.1177/11779322241261427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/24/2024] [Indexed: 08/02/2024] Open
Abstract
The secreted phospholipase A2 (sPLA2) isoform, sPLA2-IIA, has been implicated in a variety of diseases and conditions, including bacteremia, cardiovascular disease, COVID-19, sepsis, adult respiratory distress syndrome, and certain cancers. Given its significant role in these conditions, understanding the regulatory mechanisms impacting its levels is crucial. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs), including rs11573156, that are associated with circulating levels of sPLA2-IIA. The work in the manuscript leveraged 4 publicly available datasets to investigate the mechanism by which rs11573156 influences sPLA2-IIA levels via bioinformatics and modeling analysis. Through genotype-tissue expression (GTEx), 234 expression quantitative trait loci (eQTLs) were identified for the gene that encodes for sPLA2-IIA, PLA2G2A. SNP2TFBS was used to ascertain the binding affinities between transcription factors (TFs) to both the reference and alternative alleles of identified eQTL SNPs. Subsequently, candidate TF-SNP interactions were cross-referenced with the ChIP-seq results in matched tissues from ENCODE. SP1-rs11573156 emerged as the significant TF-SNP pair in the liver. Further analysis revealed that the upregulation of PLA2G2A transcript levels through the rs11573156 variant was likely affected by tissue SP1 protein levels. Using an ordinary differential equation based on Michaelis-Menten kinetic assumptions, we modeled the dependence of PLA2G2A transcription on SP1 protein levels, incorporating the SNP influence. Collectively, our analysis strongly suggests that the difference in the binding dynamics of SP1 to different rs11573156 alleles may underlie the allele-specific PLA2G2A expression in different tissues, a mechanistic model that awaits future direct experimental validation. This mechanism likely contributes to the variation in circulating sPLA2-IIA protein levels in the human population, with implications for a wide range of human diseases.
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Affiliation(s)
- Aki Hara
- School of Nutritional Sciences and Wellness, College of Agriculture and Life Sciences, The University of Arizona, Tucson, AZ, USA
| | - Eric Lu
- Department of Molecular and Cellular Biology, The University of Arizona, Tucson, AZ, USA
| | - Laurel Johnstone
- School of Nutritional Sciences and Wellness, College of Agriculture and Life Sciences, The University of Arizona, Tucson, AZ, USA
| | - Michelle Wei
- Department of Molecular and Cellular Biology, The University of Arizona, Tucson, AZ, USA
| | - Shudong Sun
- Department of Mathematics, The University of Arizona, Tucson, AZ, USA
- Statistics Interdisciplinary Program, The University of Arizona, Tucson, AZ, USA
| | - Brian Hallmark
- BIO5 Institute, The University of Arizona, Tucson, AZ, USA
| | - Joseph C Watkins
- Department of Mathematics, The University of Arizona, Tucson, AZ, USA
- Statistics Interdisciplinary Program, The University of Arizona, Tucson, AZ, USA
| | - Hao Helen Zhang
- Department of Mathematics, The University of Arizona, Tucson, AZ, USA
- Statistics Interdisciplinary Program, The University of Arizona, Tucson, AZ, USA
| | - Guang Yao
- Department of Molecular and Cellular Biology, The University of Arizona, Tucson, AZ, USA
| | - Floyd H Chilton
- School of Nutritional Sciences and Wellness, College of Agriculture and Life Sciences, The University of Arizona, Tucson, AZ, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ, USA
- Center for Precision Nutrition and Wellness, The University of Arizona, Tucson, AZ, USA
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Hara A, Lu E, Johnstone L, Wei M, Sun S, Hallmark B, Watkins JC, Zhang HH, Yao G, Chilton FH. Identification of an allele-specific transcription factor binding interaction that regulates PLA2G2A gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571290. [PMID: 38168258 PMCID: PMC10760018 DOI: 10.1101/2023.12.12.571290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The secreted phospholipase A 2 (sPLA 2 ) isoform, sPLA 2 -IIA, has been implicated in a variety of diseases and conditions, including bacteremia, cardiovascular disease, COVID-19, sepsis, adult respiratory distress syndrome, and certain cancers. Given its significant role in these conditions, understanding the regulatory mechanisms impacting its levels is crucial. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs), including rs11573156, that are associated with circulating levels of sPLA 2 -IIA. Through Genotype-Tissue Expression (GTEx), 234 expression quantitative trait loci (eQTLs) were identified for the gene that encodes for sPLA 2 -IIA, PLA2G2A . SNP2TFBS ( https://ccg.epfl.ch/snp2tfbs/ ) was utilized to ascertain the binding affinities between transcription factors (TFs) to both the reference and alternative alleles of identified SNPs. Subsequently, ChIP-seq peaks highlighted the TF combinations that specifically bind to the SNP, rs11573156. SP1 emerged as a significant TF/SNP pair in liver cells, with rs11573156/SP1 interaction being most prominent in liver, prostate, ovary, and adipose tissues. Further analysis revealed that the upregulation of PLA2G2A transcript levels through the rs11573156 variant was affected by tissue SP1 protein levels. By leveraging an ordinary differential equation, structured upon Michaelis-Menten enzyme kinetics assumptions, we modeled the PLA2G2A transcription's dependence on SP1 protein levels, incorporating the SNP's influence. Collectively, these data strongly suggest that the binding affinity differences of SP1 for the different rs11573156 alleles can influence PLA2G2A expression. This, in turn, can modulate sPLA2-IIA levels, impacting a wide range of human diseases.
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Fonseca AC. The dawn of precision medicine in stroke. Eur J Neurol 2021; 28:3548-3549. [PMID: 34342102 DOI: 10.1111/ene.15047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Catarina Fonseca
- Department of Neurology, Santa Maria Hospital, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
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