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Akhtar F, Ruiz JH, Liu YG, Resendez RG, Feliers D, Morales LD, Diaz-Badillo A, Lehman DM, Arya R, Lopez-Alvarenga JC, Blangero J, Duggirala R, Mummidi S. Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564937. [PMID: 37961304 PMCID: PMC10635030 DOI: 10.1101/2023.10.31.564937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles:A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles:_C>T) in the CCL2 3' untranslated region (3' UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated a role for HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. The presence of the rs1024611G-rs13900T conferred a distinct transcriptomic signature related to inflammation and immunity. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and explain the interindividual differences in CCL2-mediated disease susceptibility.
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Affiliation(s)
- Feroz Akhtar
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Joselin Hernandez Ruiz
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Ya-Guang Liu
- Department of Pathology, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Roy G. Resendez
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Denis Feliers
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Liza D. Morales
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Alvaro Diaz-Badillo
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Donna M. Lehman
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Rector Arya
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Juan Carlos Lopez-Alvarenga
- Department of Population Health and Biostatistics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Ravindranath Duggirala
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Srinivas Mummidi
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
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Alizada A, Khyzha N, Wang L, Antounians L, Chen X, Khor M, Liang M, Rathnakumar K, Weirauch MT, Medina-Rivera A, Fish JE, Wilson MD. Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals. Nat Commun 2021; 12:567. [PMID: 33495464 PMCID: PMC7835376 DOI: 10.1038/s41467-020-20765-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
The regulatory elements controlling gene expression during acute inflammation are not fully elucidated. Here we report the identification of a set of NF-κB-bound elements and common chromatin landscapes underlying the acute inflammatory response across cell-types and mammalian species. Using primary vascular endothelial cells (human/mouse/bovine) treated with the pro-inflammatory cytokine, Tumor Necrosis Factor-α, we identify extensive (~30%) conserved orthologous binding of NF-κB to accessible, as well as nucleosome-occluded chromatin. Regions with the highest NF-κB occupancy pre-stimulation show dramatic increases in NF-κB binding and chromatin accessibility post-stimulation. These 'pre-bound' regions are typically conserved (~56%), contain multiple NF-κB motifs, are utilized by diverse cell types, and overlap rare non-coding mutations and common genetic variation associated with both inflammatory and cardiovascular phenotypes. Genetic ablation of conserved, 'pre-bound' NF-κB regions within the super-enhancer associated with the chemokine-encoding CCL2 gene and elsewhere supports the functional relevance of these elements.
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Affiliation(s)
- Azad Alizada
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nadiya Khyzha
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- University Health Network, Toronto General Hospital Research Institute, Toronto, Canada
| | - Liangxi Wang
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Lina Antounians
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Melvin Khor
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- University Health Network, Toronto General Hospital Research Institute, Toronto, Canada
| | - Minggao Liang
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kumaragurubaran Rathnakumar
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada
- University Health Network, Toronto General Hospital Research Institute, Toronto, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Alejandra Medina-Rivera
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Jason E Fish
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- University Health Network, Toronto General Hospital Research Institute, Toronto, Canada.
- University Health Network, Peter Munk Cardiac Centre, Toronto, Canada.
| | - Michael D Wilson
- Hospital for Sick Children, Genetics and Genome Biology, Toronto, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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Bai XY, Li S, Wang M, Qu X, Hu G, Xu Z, Chen M, He GW, Wu H. Association of monocyte chemoattractant protein-1 (MCP-1)-2518A>G polymorphism with susceptibility to coronary artery disease: a meta-analysis. Ann Hum Genet 2015; 79:173-87. [PMID: 25875728 DOI: 10.1111/ahg.12105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/03/2015] [Indexed: 12/29/2022]
Abstract
We attempted to systematically elucidate the association between monocyte chemoattractant protein-1 (MCP-1) -2518A>G polymorphism and risk of coronary artery disease (CAD). Eligible studies were identified through PubMed, EBSCO, and Web of Science Databases. The magnitude of MCP-1 polymorphism effect and its possible mode of action on CAD were estimated. The odds ratio (OR) with 95% confidence intervals (CI) were pooled in a specific genetic model to assess the association. A total of 21 studies were involved. There was significant gene effect on CAD risk in the overall population (likelihood ratio test: p < 0.0001). Patients with GG and AG genotypes had 1.435 (95% CI: 1.183-1.740) and 1.087 (95% CI: 1.008-1.172) times higher risk of CAD than those with AA genotype. These gene effects suggested a recessive model to be appropriate. The pooled OR was 1.362 (95% CI: 1.137-1.631; puncorrected = 0.001, pFDR = 0.005) in the recessive model. In the ethnicity-stratified analysis, significant association was observed in the Caucasian population (OR = 1.492; 95% CI: 1.106-2.014; puncorrected = 0.009, pFDR = 0.015), whereas no statistical significant association was detected in the Asian population (adjusted p = 0.124). The results suggested that MCP-1 -2518A>G polymorphism may be associated with susceptibility to CAD, especially in Caucasians.
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Affiliation(s)
- Xiao-Yan Bai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
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Ballana E, Esté JA. Insights from host genomics into HIV infection and disease: Identification of host targets for drug development. Antiviral Res 2013; 100:473-86. [PMID: 24084487 DOI: 10.1016/j.antiviral.2013.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023]
Abstract
HIV susceptibility and disease progression show a substantial degree of individual heterogeneity, ranging from fast progressors to long-term non progressors or elite controllers, that is, subjects that control infection in the absence of therapy. Recent years have seen a significant increase in understanding of the host genetic determinants of susceptibility to HIV infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale functional screens. These studies have identified common variants in host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogue of genes and pathways involved in viral replication. This review highlights the potential of host genomic influences in antiviral therapy by pointing to promising novel drug targets but also providing the basis of the identification and validation of host mechanisms that might be susceptible targets for novel antiviral therapies.
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Affiliation(s)
- Ester Ballana
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
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The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. PLoS One 2012; 7:e49498. [PMID: 23166687 PMCID: PMC3500309 DOI: 10.1371/journal.pone.0049498] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/09/2012] [Indexed: 01/16/2023] Open
Abstract
CC chemokine ligand 2 (CCL2) is the most potent monocyte chemoattractant and inter-individual differences in its expression level have been associated with genetic variants mapping to the cis-regulatory regions of the gene. An A to G polymorphism in the CCL2 enhancer region at position -2578 (rs1024611; A>G), was found in most studies to be associated with higher serum CCL2 levels and increased susceptibility to a variety of diseases such as HIV-1 associated neurological disorders, tuberculosis, and atherosclerosis. However, the precise mechanism by which rs1024611influences CCL2 expression is not known. To address this knowledge gap, we tested the hypothesis that rs1024611G polymorphism is associated with allelic expression imbalance (AEI) of CCL2. We used haplotype analysis and identified a transcribed SNP in the 3'UTR (rs13900; C>T) can serve as a proxy for the rs1024611 and demonstrated that the rs1024611G allele displayed a perfect linkage disequilibrium with rs13900T allele. Allele-specific transcript quantification in lipopolysaccharide treated PBMCs obtained from heterozygous donors showed that rs13900T allele were expressed at higher levels when compared to rs13900C allele in all the donors examined suggesting that CCL2 is subjected to AEI and that that the allele containing rs1024611G is preferentially transcribed. We also found that AEI of CCL2 is a stable trait and could be detected in newly synthesized RNA. In contrast to these in vivo findings, in vitro assays with haplotype-specific reporter constructs indicated that the haplotype bearing rs1024611G had a lower or similar transcriptional activity when compared to the haplotype containing rs1024611A. This discordance between the in vivo and in vitro expression studies suggests that the CCL2 regulatory region polymorphisms may be functioning in a complex and context-dependent manner. In summary, our studies provide strong functional evidence and a rational explanation for the phenotypic effects of the CCL2 rs1024611G allele.
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Abstract
HIV host genetic studies seek to describe as comprehensively as possible the effect of human genetic variation on the individual response to HIV type-1 (HIV-1) infection. Many associations between specific gene variants and HIV-1 disease outcomes have been reported over the past 15 years. Although most of them have yet to be confirmed or have been proven false-positives, the identification of several definitive genotype-phenotype associations has shed new light on HIV-1 pathogenesis. This review discusses these results in the context of the new genome-wide approaches that now make it possible to globally assess the influence of the host genome on HIV-1-related outcomes.
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Affiliation(s)
- Jacques Fellay
- Center for Human Genome Variation, Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA.
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