A genome-wide association study identifies six novel risk loci for primary biliary cholangitis

Abstract

Primary biliary cholangitis (PBC) is an autoimmune liver disease with a strong hereditary component. Here, we report a genome-wide association study that included 1,122 PBC cases and 4,036 controls of Han Chinese descent, with subsequent replication in a separate cohort of 907 PBC cases and 2,127 controls. Our results show genome-wide association of 14 PBC risk loci including previously identified 6p21 (HLA-DRA and DPB1), 17q12 (ORMDL3), 3q13.33 (CD80), 2q32.3 (STAT1/STAT4), 3q25.33 (IL12A), 4q24 (NF-κB) and 22q13.1 (RPL3/SYNGR1). We also identified variants in IL21, IL21R, CD28/CTLA4/ICOS, CD58, ARID3A and IL16 as novel PBC risk loci. These new findings and histochemical studies showing enhanced expression of IL21 and IL21R in PBC livers (particularly in the hepatic portal tracks) support a disease mechanism in which the deregulation of the IL21 signalling pathway, in addition to CD4 T-cell activation and T-cell co-stimulation are critical components in the development of PBC.

Figure 1. Manhattan plot of PBC GWAS data.

Genome-wide association results from the initial GWA analysis. The genome-wide P-values of the Cochran–Armitage trend test from 796,160 polymorphic SNPs in 1,122 PBC cases and 4,036 controls of Han Chinese ancestry are presented. The chromosomal distribution of all the P-values (−log10 P-values) is shown.

Figure 2. Regional association plots of the six novel loci associated with PBC.

The SNP chromosomal location on genome build hg19 is indicated on the x axis and the −log10 of P-value for each SNP is plotted on the left-hand y axis. Genes and ESTs within the region are shown in the lower panels. The Locus Zoom plots of GWAS P-value and LD (r²) of SNPs with the most significant SNP are shown by the colour codes, depending on their expected degree of correlation (r²) with the top SNP (as estimated internally by LocusZoom on the basis of 1000 Genomes Asian haplotypes from March 2012). The square dots with line to the most significant SNP indicate the combined P-value with the discovery and replication panels. Shown below each Locus Zoom plot is the r²-based LD map that is based on the genotype data of 208 Han Chinese (CHB+CHS) 1000-genome-project samples, using Haploview 4.1 program. (a–f) Chromosome loci 16p12.1 (IL21R), 2q33.2 (CD28-CTLA4), 4q27 (IL21), 1p13.1 (CD58), 19p13.3 (ARID3A) and 15q25.1 (IL16).

Figure 3. Liver immunohistochemical staining of IL21.

(a–d) Representative staining images from patients with PBC, AIH, CHB and HC are shown (× 400). (e) Quantification of hepatic IL21 in PBC (n=30), AIH (n=30), CHB (n=25) and HC (n=6), mean±s.e.m. The frequency of hepatic IL21⁺ cells is positively correlated with hepatic inflammation degrees (f) and fibrosis stages (g) in PBC (*P<0.05, **P<0.01). Scale bars, 20 μm.

Figure 4. Liver immune-histochemical staining of IL21R.

(a–d) Representative staining images from patients with PBC, AIH, CHB and HC are shown (× 400). (e) Quantification of hepatic IL21R⁺ cells in PBC (n=30), AIH (n=30), CHB (n=25) and HC (n=6), mean±s.e.m. The frequency of hepatic IL21R⁺ cells is positively correlated with hepatic inflammation degrees (f) and fibrosis stages (g) in PBC (**P<0.01, ***P<0.001). Scale bars, 20 μm.