DataSheet_1_Integration of Candida albicans-induced single-cell gene expression data and secretory protein concentrations reveal genetic regulators of inflammation.docx

Both gene expression and protein concentrations are regulated by genetic variants. Exploring the regulation of both eQTLs and pQTLs simultaneously in a context- and cell-type dependent manner may help to unravel mechanistic basis for genetic regulation of pQTLs. Here, we performed meta-analysis of Candida albicans-induced pQTLs from two population-based cohorts and intersected the results with Candida-induced cell-type specific expression association data (eQTL). This revealed systematic differences between the pQTLs and eQTL, where only 35% of the pQTLs significantly correlated with mRNA expressions at single cell level, indicating the limitation of eQTLs use as a proxy for pQTLs. By taking advantage of the tightly co-regulated pattern of the proteins, we also identified SNPs affecting protein network upon Candida stimulations. Colocalization of pQTLs and eQTLs signals implicated several genomic loci including MMP-1 and AMZ1. Analysis of Candida-induced single cell gene expression data implicated specific cell types that exhibit significant expression QTLs upon stimulation. By highlighting the role of trans-regulatory networks in determining the abundance of secretory proteins, our study serve as a framework to gain insights into the mechanisms of genetic regulation of protein levels in a context-dependent manner.