Single Cell Sequencing Analysis Identifies Genetics-Modulated ORMDL3+ Cholangiocytes Having Higher Metabolic Effects On Primary Biliary Cholangitis

Abstract

Background: 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. Results: We constructed a powerful computational framework to integrate GWAS summary statistics with scRNA-seq data to uncover genetics-modulated liver cell subpopulations for PBC. Based on our multi-omics integrative analysis, 29 risk genes including ORMDL3, GSNK2B, and DDAH2 were significantly associated with PBC susceptibility. 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 of ORMDL3 showed the highest expression proportion in cholangiocytes than other liver cells (22.38%). The ORMDL3+ cholangiocytes have prominently higher metabolism activity score than ORMDL3- cholangiocytes (P = 1.383×10-15). Compared with ORMDL3- cholangiocytes, there were 77 significantly differentially expressed genes among ORMDL3+ cholangiocytes (FDR < 0.05), and these significant genes were associated with autoimmune diseases-related functional terms or pathways. The ORMDL3+ cholangiocytes exhibited relatively high communications with macrophage and monocyte. Compared with ORMDL3- cholangiocytes, the VEGF signaling pathway is specific for ORMDL3+ cholangiocytes to interact with other cell populations. Conclusions: 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 that ORMDL3+ cholangiocytes with higher metabolism activity play important immune-modulatory roles in the etiology of PBC.

Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19

“…Second, the identification of COVID-19-relevant cell types or subpopulations does not imply causality but may reflect indirect discovery of causal phenotype-cell associations, analogous to earlier studies [24,56]. Third, we removed the MHC region from all genomic analyses to reduce the influence of the complex genetic architecture and extensively high levels of LD, parallel to previous studies [8,24]. However, it should be noted that COVID-19-relevent genetic signals in this locus might be ignored.…”

“…First, the power of the cell-type-level integration analysis is limited by the lack of scRNA-seq data and matched genetic information in each sample for discerning COVID-19-relevant cell types. To diminish the impact of this limitation, we adopted a powerful approach by incorporating a large-scale GWAS summary dataset and human organoids scRNA-seq data with a large amount of cells, as reference to previous studies [8,23,24,27,56].…”

“…Although having incredibly powerful capabilities, human organoids are biomimetic and heterogeneous model systems with complicated cell types and states, which is intractable to analyze through the conventional technologies, e.g., immunohistochemistry. Advancing single-cell RNA sequencing (scRNA-seq) technique provides an unprecedented opportunity to dissect the cellular and molecular heterogeneity in primary human organs/tissues [8][9][10]. Compared with transcriptome measurements from bulk samples, single-cell sequencing methods not only generate cell states and transcription regulatory programs in these 3D model systems at single-cell resolution, but also gain insights into the disease-related processes and complex cellular interactions [11][12][13].…”

Unraveling the Complexity of Liver Disease One Cell at a Time

“…Interrogation of PBC susceptibility-associated gene variants in an scRNA-seq dataset revealed the immune-modulatory role of ORMDL3 expression in cholangiocytes. 58 ORMDL3 + cholangiocytes were highly metabolically active and interacted with macrophages and monocytes via the vascular endothelial growth factor (VEGF) pathway. In PSC, scRNA-seq studies identified the expansion of a unique population of naive-like CD4 + T-cells with the potential to develop into Th17 cells.…”

“…For example, genome-wide association studies (GWAS) have clarified the role of the host genetic background in many disease states, like ulcerative colitis, PSC, PBC, and CLD. 58 100 101 102 103 In the future, a unique application of scRNA-seq in combination with such GWAS analyses could delineate the precise cellular source of such disease-associated gene variants. 104 105 While these combined analyses are still being refined, they have previously clarified the cellular origins for genetic alterations of interest in ulcerative colitis 105 and could be applied to autoimmune liver diseases.…”