Combination of single cell sequencing data and GWAS summary statistics reveals genetically-influenced liver cell types for primary biliary cholangitis
Authors: Xiang Bingyu , Deng Chunyu , Li Jingjing , Li Shanshan , Zhang Huifang , Lin Xiuli , Lu Mingqin , Ma Yunlong 
Published: August 2021

Importance

Primary biliary cholangitis (PBC) is a classical autoimmune disease, which is highly influenced by genetic determinants. Many genome-wide association studies (GWAS) have reported that numerous genetic loci were significantly associated with PBC susceptibility. However, the effects of genetic determinants on liver cells and its immune microenvironment for PBC remain unclear.

Objective

To identify genetics-modulated functional liver cell subsets involved in the pathogenesis of PBC.

Design, Setting, and Participants

In this present study, 13,239 European participants were collected from IEU open GWAS project on PBC. There were 1,124,241 qualified SNPs used for GWAS analysis. Expression quantitative trait loci (eQTL) data across 49 tissues were downloaded from the GTEx database. Two single cell RNA sequencing (scRNA-seq) profiles and two bulk-based RNA transcriptomes were downloaded from the GEO database. Data collection and analyses were performed from August 2020 to June 2021.

Main outcomes and measures

We constructed a powerful computational framework to integrate GWAS summary statistics with scRNA-seq data to uncover genetics-modulated liver cell subpopulations.

Results

Based on our multi-omics integrative analysis, we found that 29 risk genes includingORMDL3, GSNK2B, andDDAH2were significantly associated with PBC susceptibility. Gene-property analysis revealed that four immune cell types, including Cst3+dendritic cell, Chil3+macrophage, Trbc2+T cell, and Gzma+T cell, were significantly enriched by PBC-risk genes. By combining GWAS summary statistics with scRNA-seq data, we found that cholangiocytes exhibited a notable enrichment by PBC-related genetic association signals (Permuted P < 0.05). The risk gene ofORMDL3showed the highest expression proportion in cholangiocytes than other liver cells (22.38%). Compared withORMDL3+cholangiocytes, there were 71 significantly highly-expressed genes amongORMDL3-cholangiocytes (FDR < 0.05), such as inflammatory cytokine genesCXCL8, CCL3, IFI16, andIRF1. These highly-expressed genes were significantly enriched in numerous biological pathways and functional terms associated with autoimmune diseases (FDR < 0.05).

Conclusions and relevance

To the best of our knowledge, this is the first study to integrate genetic information with single cell sequencing data for parsing genetics-influenced liver cells for PBC risk. We identified thatORMDL3-cholangiocytes play important immune-modulatory roles in the etiology of PBC.

Key points

Question

Are genetics factors influenced liver cell subpopulations and its immune microenvironment for PBC?

Findings

In this comprehensive genomics study based on multi-omics data, genetic determinants were significantly enriched in cholangiocytes and immune cells including subsets of macrophage, dendritic cells, and T cells.ORMDL3-cholangiocytes have crucial immune-modulatory roles in developing PBC.

Meaning

Findings suggest that integration of single cell sequencing data with GWAS summary statistics contribute to pinpoint PBC-relevant cell types and risk genes.