Abstract

Background: Genetic factors associated with DILI susceptibility have been observed to be largely drug specific. The aim of this study was to identify novel risk factors for Cholestatic-Mixed Drug Induced Liver Injury (CM-DILI).

Methods: Genome-Wide Association (GWAS) and Transcriptome-Wide Association (TWAS) analyses were performed on 927 CM-DILI cases (R value < 5.0) and 10,397 population-based controls of European descent. Associations were confirmed in a validation cohort of 274 CM-DILI cases and 17,836 population-based controls. TWAS analysis was conducted by Fusion using summary statistics from the discovery European GWAS and multi tissues references designed by Context algorithm. CM-DILI cases were also compared to hepatocellular DILI cases. RNA knockdown and analysis of subsequent expression of candidate target genes were performed in three human liver cell lines (HepG2, Huh7, and PH5CH8).

Results: A single nucleotide variant, rs11624069 (C) on chromosome 14, demonstrated a genome-wide significant association with CM-DILI risk in the discovery cohort (OR [95%CI] = 1.33 [1.20-1.46] P=9.3x10^-9). The association was confirmed in the validation cohort (OR [95%CI] = 1.25 [1.06-1.48] P = 0.009). In contrast, hepatocellular DILI cases showed similar allele frequency as population controls. rs11624069 (C) was also overrepresented in Hispanic and African American CM-DILI cases compared to ethnically matched controls. Interestingly, rs11624069 has been associated with risk of Primary Biliary Cholangitis and elevation in serum cholestatic biomarkers in healthy populations. TWAS identified that rs11624069 (C) was colocalized with a cis eQTL signal conserved across tissues, increasing the expression of RP11-736N17.8, a long noncoding RNA (P = 2.3x10^-6). In the liver, rs11624069 (C) was associated with increased expression of RP11-736N17.8 (P= 7.0x10^-10) and also, less strongly, of EXOC3L4 (P = 0.002), a nearby gene selectively expressed in hepatocytes. Knockdown of RP11-736N17.8 expression in the three liver cell lines was found to markedly reduce expression of EXOC3L4.

Conclusion: GWAS identified a regulatory variant for RP11-736N17.8, a long non-coding RNA, which modulates expression of EXOC3L4, as a novel risk factor for CM-DILI due to multiple drugs. Since EXOC3L4 is a component of the exocyst complex, which is involved in tracking of proteins to apical versus basolateral membranes, the association of rs11624069 (C) with CM-DILI may relate to altered membrane trafficking of transporters for bile constituents.