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Noncoding SNPs decrease expression of FABP5 during COPD exacerbations

ABSTRACT: Differential susceptibility to recurrent infection and exacerbation in COPD is not well understood. Here we investigated the potential impact of genetic variation in Fatty Acid Binding Protein 5 (FABP5), a metabolic regulator we previously demonstrated to be downregulated in COPD and further downregulated in patients reporting one or more exacerbation. Through negative binomial analysis of the COPDGene SNP dataset, we identified 5 novel linked single nucleotide polymorphisms (SNPs) across the FABP5 locus that were significantly associated with severe exacerbations in a Non-Hispanic White cohort (rs4338057, rs12549270, rs202275, rs202277, and rs202279). We integrated multiple sources of previously published data to prioritize SNPs most likely to exert regulatory function. Ultimately, rs202275 emerged as the lead candidate due to unique alignment with the loading site of a bidirectional RNA Pol II signature of active enhancer utilization in our recently published patient-derived airway epithelial PRO-seq dataset, suggesting a critical regulatory role for the region harboring this variant. Using Micro-C genome-wide chromosome conformation capture, we found that the region harboring rs202275 makes three-dimensional physical contacts with the FABP5 transcription start site (TSS), suggesting the SNP region could regulate FABP5 transcription through a looping mechanism. To examine SNP function, we analyzed previously deposited gene-array data (GEO Accession #GSE42057) from peripheral blood mononuclear cell (PBMC) samples and found that COPD patients carrying the rs202275 risk allele (T) express significantly lower levels of FABP5 compared to non-carrier patients. Seahorse real-time mitochondrial respiration assays in freshly isolated PBMCs further revealed disrupted oxidative phosphorylation in cells from patients carrying the rs202275 risk allele. As macrophage polarization from pro-inflammatory toward pro-resolving phenotype is dependent on oxidative metabolism, the functional impact of the rs202275 risk allele and associated reduction in FABP5 transcription may contribute to increased or prolonged systemic inflammation, thereby increasing susceptibility to exacerbation in COPD.

ORGANISM(S): Homo sapiens

PROVIDER: GSE241294 | GEO | 2024/07/07

REPOSITORIES: GEO

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Project description:Lung adenocarcinoma (LUAD) is the predominant lung cancer subtype. To date, 15 single nucleotide polymorphisms (SNPs) have been reproducibly associated with LUAD susceptibility. However, as most SNPs identified in genome-wide association studies (GWAS) are not located in the coding regions of genes and are co-inherited with hundreds of SNPs in linkage disequilibrium (LD), mechanistic links to disease outcomes remain largely unexplored. We hypothesized that some SNPs increase LUAD risk by affecting enhancers of gene transcription in alveolar epithelial cells (AECs), the purported cells of origin for LUAD. Forty-six LUAD risk-associated SNPs mapped to putative AEC enhancers, and 11 of these were located in FAIRE peaks. Of those, seven were predicted to form transcription factor binding motifs. For four of these, ChIPseq data confirmed the binding of the predicted transcription factors. We chose rs452384, rs6942067 and rs11364096 for functional validation. The reference (risk) allele for rs452384 forms an NKX2-1 binding site that is disrupted by the alternate allele, elicited a 42% increase in activity in H1648 LUAD cells relative to the alternative allele (P = 6.7 x 10-3), and was associated with elevated TERT levels in esophageal tissue (P = 6 x 10-8). The reference (risk) allele for rs6942067 forms an EP300 binding site disrupted by the alternate allele, elicits a 94% increase in enhancer activity relative to the alternative allele in H1648 LUAD cells (P = 2.7 x 10-2), and was associated with higher expression of potential oncogene DCBLD1 in blood (P = 5.2 x 10-16). Lastly, the alternate (risk) allele for rs11364096 disrupts binding sites for FOXA1, HDAC2 and SP1, elicits a 32% decrease in enhancer activity in A549 LUAD cells relative to the reference allele (P = 5.7 x 10-3), and LUAD data from The Cancer Genome Atlas indicates that this SNP is associated with altered expression in LUAD of four genes on other chromosomes. Our analyses provide possible mechanisms for the genetic susceptibility to LUAD, with the identification of three strong functional SNP candidates that appear to affect AEC enhancers. Further investigation of these enhancers and their target genes may ultimately yield more effective and personalized strategies for LUAD risk assessment, prevention and treatment.

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Noncoding SNPs decrease expression of FABP5 during COPD exacerbations

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