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. 2018 Aug 13;14(8):e1007532.
doi: 10.1371/journal.pgen.1007532. eCollection 2018 Aug.

A Genome-Wide Association Study Identifies a Susceptibility Locus for Biliary Atresia on 2p16.1 Within the Gene EFEMP1

Free PMC article

A Genome-Wide Association Study Identifies a Susceptibility Locus for Biliary Atresia on 2p16.1 Within the Gene EFEMP1

Ying Chen et al. PLoS Genet. .
Free PMC article


Biliary atresia (BA) is a rare pediatric cholangiopathy characterized by fibrosclerosing obliteration of the extrahepatic bile ducts, leading to cholestasis, fibrosis, cirrhosis, and eventual liver failure. The etiology of BA remains unknown, although environmental, inflammatory, infectious, and genetic risk factors have been proposed. We performed a genome-wide association study (GWAS) in a European-American cohort of 343 isolated BA patients and 1716 controls to identify genetic loci associated with BA. A second GWAS was performed in an independent European-American cohort of 156 patients with BA and other extrahepatic anomalies and 212 controls to confirm the identified candidate BA-associated SNPs. Meta-analysis revealed three genome-wide significant BA-associated SNPs on 2p16.1 (rs10865291, rs6761893, and rs727878; P < 5 ×10-8), located within the fifth intron of the EFEMP1 gene, which encodes a secreted extracellular protein implicated in extracellular matrix remodeling, cell proliferation, and organogenesis. RNA expression analysis showed an increase in EFEMP1 transcripts from human liver specimens isolated from patients with either BA or other cholestatic diseases when compared to normal control liver samples. Immunohistochemistry demonstrated that EFEMP1 is expressed in cholangiocytes and vascular smooth muscle cells in liver specimens from patients with BA and other cholestatic diseases, but it is absent from cholangiocytes in normal control liver samples. Efemp1 transcripts had higher expression in cholangiocytes and portal fibroblasts as compared with other cell types in normal rat liver. The identification of a novel BA-associated locus, and implication of EFEMP1 as a new BA candidate susceptibility gene, could provide new insights to understanding the mechanisms underlying this severe pediatric disorder.

Conflict of interest statement

The authors have declared that no competing interests exist.


Fig 1
Fig 1. SNPs associated with susceptibility to BA.
(A) Manhattan plot of GWAS results in the isolated BA cohort. X-axis: genomic coordinates of tested SNPs. Y-axis: significance level on a -log10 scale. The genome-level significance threshold is indicated by the red horizontal line (P = 5 × 10−8) and the suggestive significance threshold is indicated by the blue horizontal line (P = 1 × 10−5). (B) Regional association plot of 2p16.1 after meta-analysis. P-values (left Y-axis) obtained from additive frequentist association test on genotyped and imputed SNPs. The recombination rate (right Y-axis) is calculated from the 1000 Genomes Phase 3 European ancestry dataset. The top BA-associated SNP is imputed SNP rs6761893 (purple circle), located in the fifth intron of the gene EFEMP1. The colors refer to r-square correlation of each SNP to rs6761893 based on the 1000 Genomes Phase 3 European ancestry dataset. The circles represent the genotyped markers and squares represent imputed markers.
Fig 2
Fig 2. EFEMP1 gene expression in human and rat liver.
(A) ddPCR showing relative expression of EFEMP1 transcripts in human liver specimens. Fold change of EFEMP1 was determined by normalizing to the reference gene, TBP. Error bars indicate standard deviation. (B) Relative expression of Efemp1 transcripts in six cell populations from normal rat livers. Rat gene Rsp12 was used as reference gene. Error bars indicate standard deviation of technical triplicates (cholangiocytes, portal fibroblasts, hepatocytes, Kupffer cells, and sinusoidal endothelial cells) or technical duplicates (hepatic stellate cells).
Fig 3
Fig 3. Localization of EFEMP1 in control and cholestatic disease human liver samples.
(A) EFEMP1 is expressed in SMA positive smooth muscle cells, but not (B) CK19 positive intrahepatic cholangiocytes in control liver. EFEMP1 is expressed in both smooth muscle cells and intrahepatic cholangiocytes in (C, D) BA, (E, F) TPN, and (G, H) ARPKD liver. Scale bar = 25 μm. (A-F) were taken at a lower magnification and correspond to the scale bar in (F). (G, H) were taken at a higher magnification and correspond to the scale bar in (H). Arrowheads indicate vascular smooth muscle cells and arrows indicate cholangiocytes.
Fig 4
Fig 4. EFEMP1 expression in BA extrahepatic bile ducts.
EFEMP1 is expressed in both (A) SMA positive smooth muscle cells and (B) CK19 positive extrahepatic cholangiocytes in BA liver. Scale bar = 25 μm.

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