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Noncoding SNPs decrease expression of FABP5 during COPD exacerbations
Manale El Kharbili, Sarah K. Sasse, Lynn Sanford, Sean Jacobson, Katja Aviszus, Arnav Gupta, Claire Guo, Susan M. Majka, Robin D. Dowell, Anthony N. Gerber, Russell P. Bowler, Fabienne Gally
Manale El Kharbili, Sarah K. Sasse, Lynn Sanford, Sean Jacobson, Katja Aviszus, Arnav Gupta, Claire Guo, Susan M. Majka, Robin D. Dowell, Anthony N. Gerber, Russell P. Bowler, Fabienne Gally
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Research Letter Genetics Metabolism

Noncoding SNPs decrease expression of FABP5 during COPD exacerbations

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Abstract

Authors

Manale El Kharbili, Sarah K. Sasse, Lynn Sanford, Sean Jacobson, Katja Aviszus, Arnav Gupta, Claire Guo, Susan M. Majka, Robin D. Dowell, Anthony N. Gerber, Russell P. Bowler, Fabienne Gally

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Figure 1

The rs202275 SNP binds regulatory regions of open chromatin and interacts with the FABP5 transcription start site, decreasing FABP5 expression and reducing oxidative metabolism in mononuclear cells from COPD patients.

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The rs202275 SNP binds regulatory regions of open chromatin and interact...
(A) FABP5 SNPs associated with prospective severe exacerbations in the COPDGene non-Hispanic White cohort. Data were generated using R (https://www.r-project.org/). n = 6,649. (B) SNP locations within the FABP5 locus (black lines) on chromosome 8 (chr8). (C) ATAC-seq profiles (reads per million mapped) at the FABP5 locus showing accessible chromatin at the rs202275 SNP. (D) PRO-seq data at the FABP5 locus showing bidirectionality of the RNA polymerase II loading at rs202275. (E) Micro-C interactions at the FABP5 locus, with arcs (top) and boxes connecting 1-kb interacting regions across genomic space (bottom). TSS, transcription start site. Data in B–E (bottom) were visualized in the UCSC Genome Browser (https://genome.ucsc.edu/) using airway epithelial cells. (F) Normalized gene array expression levels of FABP5 (GEO GSE42057) in 116 noncarrier and 20 SNP carrier PBMCs. (G) Mitochondrial respiration measured by oxygen consumption rate (OCR) in PBMCs by genotype and associated mitochondrial parameters. Data represent 10 COPD noncarrier and 9 COPD SNP carrier donor samples. Data in F and G represent mean ± SEM. *P < 0.05, groups compared via 2-tailed Student’s t test. Experimental details can be found in the Supplemental Methods. All raw data can be found in the supplemental Supporting Data Values file.

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