Comprehensive characterization of inflammatory cells reveals novel molecular typing of biliary atresia

Abstract Objectives: Biliary Atresia (BA) is a severe cholangiopathy that affects the liver's bile ducts in pediatric patients. Ongoing research has identified a range of factors that may be contributing to the development of BA, with inflammation and fibrosis being among the most widely studied. However, it is essential to acknowledge that not all patients present with these etiological mechanisms. The significance of inflammation-associated cells as a contributing factor in BA is increasingly being recognized. Our approach to re-classifying BA involves integrating gene microarray data and scRNA-seq data, enabling us to provide customized clinical treatment and facilitating mechanistic studies. Methods: The BA microarray dataset GSE15235, containing gene expression data from BA and normal liver, was downloaded from the Gene Expression Omnibus (GEO) database. To validate our findings, we used an additional dataset (GSE46960) as a replication cohort. By analysis of the immune microenvironment, eight types of inflammation-associated immune cells were used for typing research. The combination of enrichment analysis and clinical data revealed the characteristics of each subtype. An effective method for identifying BA typing through machine learning algorithms. The immune landscape of biliary atresia T and NK cells was further analyzed by combining scRNA-seq datasets. Results: Two novel subtypes of inflammation were identified, the highly immune-activated C1 subtype and the lowly immune-activated C2 subtype. The C1 subtype exhibits an enhanced inflammatory response accompanied by a high infiltration of neutrophils and macrophages M1. On the other hand, the C2 subtype exhibits cell cycle activation, enhanced lipid metabolic activity, and stronger fibrosis accompanied by a high infiltration of CD8+ T cells and NK cells. CD8+ T cells may promote value-added and differentiation through signaling pathways such as CD99, CLEC, and ITGB2, further leading to fibrosis. Conclusion: In conclusion, we have defined two novel inflammatory subtypes and offered the possibility to identify and treat them. The role of neutrophils, CD8+ T cells, and CD16+ NK cells in BA deserve to be further explored.