Single-cell and spatial transcriptomics reveal the fibrosis-related immune landscape of biliary atresia.

ABSTRACT:

Background

Biliary atresia (BA) is a devastating inflammatory and fibrosing cholangiopathy of neonates with unknown aetiology. We aim to investigate the relationship between these two main characteristics.

Methods

Single-cell RNA sequencing and spatial transcriptomics were performed on liver samples from a cohort of 14 objects (BA: n = 6; control: n = 8). We conducted data integration and cell-type annotation based on gene expression profiling. Furthermore, we identified fibrosis-related immune cells according to their spatial locations, GO and KEGG analysis. Finally, SPOTlight and CIBERSORTx were used to deconvolute ST data and microarray data of the GSE46960 cohorts, respectively.

Results

Immune subpopulations inhabiting the 'fibrotic niche' (areas of scarring), com

SUBMITTER: Ye C 

PROVIDER: S-EPMC9636046 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature