A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease

Abstract

Background: Elucidation of the genetic factors underlying chronic liver disease may reveal new therapeutic targets.

Methods: We used exome sequence data and electronic health records from 46,544 participants in the DiscovEHR human genetics study to identify genetic variants associated with serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Variants that were replicated in three additional cohorts (12,527 persons) were evaluated for association with clinical diagnoses of chronic liver disease in DiscovEHR study participants and two independent cohorts (total of 37,173 persons) and with histopathological severity of liver disease in 2391 human liver samples.

Results: A splice variant (rs72613567:TA) in HSD17B13, encoding the hepatic lipid droplet protein hydroxysteroid 17-beta dehydrogenase 13, was associated with reduced levels of ALT (P=4.2×10^-12) and AST (P=6.2×10^-10). Among DiscovEHR study participants, this variant was associated with a reduced risk of alcoholic liver disease (by 42% [95% confidence interval {CI}, 20 to 58] among heterozygotes and by 53% [95% CI, 3 to 77] among homozygotes), nonalcoholic liver disease (by 17% [95% CI, 8 to 25] among heterozygotes and by 30% [95% CI, 13 to 43] among homozygotes), alcoholic cirrhosis (by 42% [95% CI, 14 to 61] among heterozygotes and by 73% [95% CI, 15 to 91] among homozygotes), and nonalcoholic cirrhosis (by 26% [95% CI, 7 to 40] among heterozygotes and by 49% [95% CI, 15 to 69] among homozygotes). Associations were confirmed in two independent cohorts. The rs72613567:TA variant was associated with a reduced risk of nonalcoholic steatohepatitis, but not steatosis, in human liver samples. The rs72613567:TA variant mitigated liver injury associated with the risk-increasing PNPLA3 p.I148M allele and resulted in an unstable and truncated protein with reduced enzymatic activity.

Conclusions: A loss-of-function variant in HSD17B13 was associated with a reduced risk of chronic liver disease and of progression from steatosis to steatohepatitis. (Funded by Regeneron Pharmaceuticals and others.).

Figure 1.. Association of Single-Nucleotide Variants with Aminotransferase Levels in the GHS Discovery Cohort.

Each panel includes a Manhattan plot (left) and quantile–quantile plot (right). Variants that are indicated by gene name, including HSD17B13, remained significantly associated with levels of alanine aminotransferase or aspartate aminotransferase in a replication meta-analysis of three separate cohorts of persons of European ancestry (Table S3 in the Supplementary Appendix). GHS denotes Geisinger Health System.

Figure 2.. Associations of HSD17B13 rs72613567:TA with Phenotypes of Alcoholic and Nonalcoholic Liver Disease in the GHS Discovery Cohort and in the Dallas Liver Study.

In the GHS discovery cohort (Panel A), allelic odds ratios were calculated with the use of logistic regression, with adjustment for age, age squared, sex, body-mass index (BMI), and the first four principal components of ancestry. Genotypic odds ratios for reference allele homozygotes (T/T), heterozygotes (T/TA), and alternate allele homozygotes (TA/TA) are also shown. All reported P values correspond to the allelic model. In the Dallas Liver Study (Panel B), allelic odds ratios were calculated with the use of logistic regression, with adjustment for age, age squared, sex, BMI, and patient-reported ethnic group.

Figure 3.. Association of HSD17B13 rs72613567 with Aminotransferase Levels in Persons with Each PNPLA3 p.I148M Genotype.

Effect estimates were calculated with the use of linear regression, with adjustment for age, age squared, sex, BMI, and the first four principal components of ancestry. PNPLA3 rs738409 genotypes on the x axis indicate reference allele homozygotes (C/C), heterozygotes (C/G), and alternate allele homozygotes (G/G). The rs738409:G allele corresponds to the p.I148M amino acid change. The P values for interaction between HSD17B13 rs72613567:TA and PNPLA3 rs738409:G (p.I148M) in association analyses of levels of alanine aminotransferase and aspartate aminotransferase were P=0.002 and P=0.004, respectively. The numbers above the circles indicate the number of persons with each genotype combination. I bars indicate 95% confidence intervals.

Figure 4.. Associations of HSD17B13 rs72613567:TA with Liver Pathology in Patients Undergoing Bariatric Surgery.

Panel A shows the prevalence of histopathologically characterized liver disease according to HSD17B13 rs72613567 genotype in 2391 persons with liver biopsies from the GHS bariatric-surgery cohort. Panel B shows associations of HSD17B13 rs72613567:TA with liver pathology in the GHS bariatric-surgery cohort, according to logistic regression with adjustment for age, age squared, sex, BMI, and the first four principal components of ancestry. NASH denotes nonalcoholic steatohepatitis

Figure 5.. Expression and Subcellular Localization of a Novel HSD17B13 Transcript.

Panel A shows the expression of HSD17B13 ranscripts A and D in rs72613567 reference allele homozygotes (T/T), heterozygotes (T/TA), and alternate allele homozygotes (TA/TA). Coding regions are indicated in red, untranslated regions as thick black lines, and introns as thin black lines. The asterisk in transcript D indicates the A insertion from rs72613567. Box plots show the median and interquartile range (IQR) of fragments per kilobase of transcript per 1 million mapped reads (FPKM). The length of the whiskers is 1.5 times the IQR. Dots represent individual messenger RNA expression levels. Panel B shows the results of Western blot analysis of human liver and HEK293 cell samples. Human liver samples were from T/T, T/TA, and TA/TA carriers of the HSD17B13 rs72613567 splice variant. Cell samples were from HEK293 cells overexpressing nontagged HSD17B13 transcripts A and D. Panel C shows levels of HSD17B13 isoform A (isoA) and isoform D (IsoD) protein in human liver samples. ND denotes not determined. Panel D shows localization of HSD17B13 isoforms A and D. HepG2 cells stably overexpressing HSD17B13 transcripts A or D were labeled with boron-dipyrromethene (BODIPY) to show lipid droplets and anti-Myc to show HSD17B13 localization. All figures are magnified to the same extent. Insets represent 4× amplification of the original images.