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), comprising ‘intermediate’ CD14
++
CD16
+
monocytes, scar‐associated macrophages, natural killer T cells, transitional B cells and FCN3
+
neutrophils were identified. GO and KEGG analyses showed that pathways including ‘positive regulation of smooth muscle cell/fibroblast proliferation’ and ‘positive regulation of/response to VEGFR/VEGF/EGFR/FGF’ were enriched in these cell types. Interactions analysis showed that communication among ‘FGF_FGFR’, ‘RPS19‐C5AR1’, ‘CD74_COPA/MIF/APP’ and ‘TNFRSF1A/B_GRN’ was extensive. Finally, the results of deconvolution for ST data and microarray data validated that the proportions of certain identified fibrosis‐related cell types we identified were increased in BA.
Discussion
Fibrosis is an important feature of BA, in which the immune system plays an important role. Our work reveals the subpopulations of immune cells enriched in the fibrotic niche of BA liver, as well as key related pathways and molecules; some are highlighted for the first time in liver fibrosis. These newly identified interactions might partly explain why the rate of liver fibrosis occurs much faster in BA than in other liver diseases.
Conclusion
Our study revealed the molecular, cellular and spatial immune microenvironment of the fibrotic niche of BA.
Background
Hirschsprung's disease (HSCR) is a relatively common congenital disability. Accumulating extracellular matrix (ECM) prompts intestinal fibrosis remodelling in the aganglionic segments of HSCR. The contributions of various cellular subsets in the fibrogenesis of HSCR segments are poorly understood.
Methods
Single‐cell transcriptomics from 8 aganglionic segments and 5 normal segments of 7 HSCR subjects and 26 healthy segments of seven healthy donors were analysed. Fibrotic phenotype and alterations were explored using differential expression analysis and single‐cell trajectory analysis. Fibrosis‐related transcription factors were inferred through single‐cell regulatory network inference. Bulk transcriptomic data, proteomic data, immunohistochemistry (IHC) and real‐time polymerase chain reaction were used to validate the alterations in the HSCR intestine.
Results
Various collagen, fibronectin and laminin protein‐coding genes expression were up‐regulated in the stromal and glial cells of the HSCR intestine. The number of fibroblasts and myofibroblasts in the aganglionic segments increased, and more myofibroblasts were activated at an earlier stage in HSCR segments, which infers that there is an intestinal fibrosis phenotype in HSCR segments. The fibrotic regulators
POSTN
,
ANXA1
and
HSP70
were highly expressed in the ECM‐related cellular subsets in the transitional segments and aganglionic segments. The transcription factor regulatory network revealed that fibrosis‐related and megacolon‐related
NR2F1
in the fibroblasts and glial subsets was up‐regulated in the aganglionic segment.
Conclusions
This work identifies intestinal fibrosis and related regulators in aganglionic segments of HSCR; hence, anti‐fibrotic therapy may be considered to prevent HSCR‐associated enterocolitis (HAEC), relieve intestinal stricture and improve cell therapy.
Whether N6-methyladenosine (m6A) is involved in biliary atresia (BA) remains undefined. Herein, we comprehensively evaluated the m6A profile in BA. When compared with normal controls, BA had an elevated m6A level with upregulated m6A writers. The m6A level was correlated with liver function, stage of fibrosis and jaundice clearance in BA. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) demonstrated an altered m6A topology in BA. MeRIP-seq and RNA sequencing filtered out 130 m6A-modified genes, which were enriched in fibrogenetic pathways. MeRIP-qPCR in vivo and interventions of LX-2 and primary HSCs in vitro validated the regulatory role of m6A on COL1A1 and THY1. THY1+ myofibroblasts expanded in portal area of BA, and highly expressed profibrogenic genes (COL1A1, MMP2, PDGFRA, and DCN). THY1 was correlated with liver fibrosis and jaundice clearance in BA. Bulk array (GSE46960, GSE15235), single-cell RNA sequencing (GSE136103), primary HSC interventions, and co-immunoprecipitation revealed that THY1 was correlated with extracellular matrix organization, promoted HSC activation, showed higher interactions with integrins on myeloid cells in cholestatic fibrosis, and was correlated with native liver survival in BA. Our study highlights the significance of m6A in BA-induced liver fibrogenesis by regulating THY1, shedding new light on the novel therapies to alleviate liver fibrosis by targeting m6A/THY1 axis in BA.
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