Genome-wide association and replication studies of anti-tubercular and anti-retroviral drugs-induced liver injury in Ethiopian TB/HIV patients
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Date
2019-10
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Addis Abeba University
Abstract
Background: Drug-induced liver injury (DILI) is a well-recognized adverse effect of anti-
tubercular drugs (ATD) and antiretroviral therapy (ART) possibly associated with genetic
variations. Liver injury induced by these drugs carries numerous risks that include morbidity and
mortality due to liver failure, disease progression resulting from discontinuation of drug therapy,
and drug resistance related to treatment interruption. Genome-wide association study (GWAS) is
a genetic study used to identify single nucleotide polymorphisms (SNPs) that contribute to
disease risk. Genetic risk variants identified by pharmacogenomic GWAS, and confirmed
through replication studies can serve as biomarkers to predict treatment response, and advance
clinical care through personalized medicine. The objective of this study was to identify and
validate SNPs associated with ATD and ART-induced liver injury through GWAS and
subsequent replication studies, and also to investigate the association of human leukocyte antigen
(HLA)-B alleles with ATD and ART co-treatment induced liver injury in Ethiopian TB/HIV co-
infected patients.
Methods: The present study had a case-control design using cases and controls obtained from a
prospective cohort study conducted to determine the incidence and predictors for ATD and ART-
induced liver injury in Ethiopia. Cases were those study participants who developed DILI due to
ATD and/or ART in the follow up period. DNA samples from a total of 1,055 patients were
used. The three treatment groups for the current study were TB patients treated with first-line
ATD (75 cases, 571 controls), HIV patients without TB co-infection treated with Efavirenz-
based ART (21 cases, 368 controls), and TB/HIV co-infected patients treated with both ATD and
efavirenz-based ART concurrently (46 cases, 292 controls). Whole genome genotyping was done
using Illumina Omni Express Exome BeadChip genotyping array on a total 89 cases and 488 controls. Replication study was carried out for the top SNPs with the lowest P-values in the
GWAS using an independent cohort consisting of 45 cases and 425 controls. For the HLA study,
genomic DNA from 46 cases, and sex and age matched controls from ATD and ART co-
treatment group were typed for HLA-B alleles using low resolution Olerup SSP
typing kit. High resolution sub-typing was performed for HLA-B alleles that showed significant
association with DILI. The association analysis for the GWAS and replication studies were done
using Plink v 1.07, and we used SPSS v 22 for the HLA-B typing analysis.
Results: In the combined analysis of the GWAS and the replication study, the top SNP identified
in the ATD treatment group was rs10946737 (P = 4.4×10
-6
®
HLA-B DNA
, odds ratio (OR) = 3.4, 95% CI = 2.2-
5.3) located in the intron region of family with sequence similarity-65 member-B (FAM65B). In
addition, we identified cluster of SNPs with suggestive genome-wide significance in the intron of
ATP/GTP binding protein like-4 (AGBL4). We identified a missense SNP rs199650082 (R919Q,
P = 1.4×10
-6
, OR = 18.2, 95% CI = 7.1-46.9) in an endoplasmic reticulum to nucleus signaling-1
(ERN1) gene in the ART group. In the ATD and ART co-treatment group, we identified
rs4842407 (P = 5.3×10
-7
, OR = 5.4, 95% CI = 2.8-10.3) a long intergenic non-coding RNA
(lincRNA) transcript variant. In our HLA typing study, proportion of HLA-B
the cases was significantly higher compared with the controls (P = 0.002). From HLA-B
alleles detected, HLA-B
*
57:02 and HLA-B
*
*
57 allele carriers in
57:03 accounted for 41.7 and 58.3%, respectively.
Conclusion: We identified genetic variants that may be associated with ATD and ART-induced
liver injuries. Further studies with larger sample sizes are essential to confirm the findings.
Description
Keywords
AGBL4, Anti-tubercular drugs, Anti-retroviral therapy, DILI, ERN1, Ethiopians, FAM65B, GWAS, Hepatotoxicity, HLA-B * 57, LincRNA