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C.W. Thorball et al.
blood or peripheral blood mononuclear cells (PBMC) from multiple publicly available datasets, including GTEx,37 GEUVADIS38 and the Milieu Intérieur Consortium39 (Online Supplementary Figure S3). Of note, CXCL12 expression levels were very low in all datasets (Online Supplementary Figure S4A).
Using allele-specific expression analysis in the GTEx dataset, we observed a significant effect in individuals heterozygous of rs7919208, with increased allelic imbal- ance of CXCL12 in fibroblasts (false discovery rate adjusted P=0.0006, one-sided rank sum test), which was not observed in other tissues (Online Supplementary Figure 4B).
HIV infection causes many profound transcriptomic changes.40 Thus, in order to examine the effect of rs7919208 on CXCL12 in the context of HIV infection, we
extracted RNA from PBMC of 452 individuals in the SHCS with available genotyping data and sequenced them using the Bulk RNA Barcoding and sequencing (BRB-seq) approach.41 However, the expression levels of CXCL12 were below the limit of detection for most indi- viduals, preventing an expression quantitative trait loci (eQTL) analysis.
Multiple isoforms of CXCL12 exist, with variable degrees of expression and potency described in the con- text of HIV infection.42 We observed a single significant correlation between rs7919208 and CXCL12 transcript usage, which was restricted to visceral adipose tissue. The presence of the rs7919208 minor allele was associat- ed with higher relative expression of the longer and rarer transcript isoform ENST00000374429.6 (Online Supplementary Figure S5).
AB
C
Figure 1. Genome-wide association analysis. (A) Schematic of analysis pipeline. (B) Quantile-quantile plot of the observed -log (P-value) (black dots, y-axis) vs. expect-
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(P-values) under the null hypothesis (red line) to check for any genomic inflation of the observed P-values. No genomic inflation is observed, with the genomic inflation factor λ=0.99. (C) Manhattan plot of all obtained P-values for each variant included in the meta-analysis. The genome-wide threshold (P=5e-8) for signifi-
ed -log
cance is marked by a dotted line. Only variants at the CXCL12 locus were found to be significant.
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haematologica | 2021; 106(8)