Background:Metabolic dysfunction-associated fatty liver disease(MAFLD)is now the most prevalent chronic liver disease worldwide,with an increasing incidence rate.MAFLD is a heterogeneous disease that can have a low or...Background:Metabolic dysfunction-associated fatty liver disease(MAFLD)is now the most prevalent chronic liver disease worldwide,with an increasing incidence rate.MAFLD is a heterogeneous disease that can have a low or high-risk profile for developing severe liver disease in its natural course.Recent evidence has highlighted the critical role of RNA methylation modification in the pathogenesis of various liver diseases.However,it remains unclear whether the RNA N1-methyladenosine(m1A)modification of immune cells could potentially contribute to the pathogenesis and heterogeneity of MAFLD.Materials and methods:To address this issue,we conducted an integrated bioinformatics analysis of MAFLD bulk and single-cell RNA sequencing(scRNA-seq)data to pinpoint m1A regulators in the network.This was followed by a description of the immune landscape,pathway enrichment analysis,and molecular subtyping.Results:The expression patterns of m1A regulatory genes stratify MAFLD into two molecular subtypes,Cluster 1 and Cluster 2.These subtypes demonstrate different immune cell infiltration with distinct inflammation characteristics,which suggest different immune-inflammatory responses in the liver.Notably,Cluster 2 is associated with pro-inflammation and may be more likely to lead to progressive stages of MAFLD.Through intersection analysis of weighted gene co-expression network analysis(WGCNA)and m1A regulatory genes,three true hub genes(ALKBH1,YTHDC1,and YTHDF3)were identified,all of which were strongly correlated with infiltrating immune cells.The specific signaling pathways involved in the three core genes were derived from genomic variation analysis.Furthermore,scRNA-seq data from 33,168 cells from six liver samples identified 26 cell clusters and eight cell types,with endothelial cells,macrophages,and monocytes showing the most significant differences between MAFLD and normal controls.The cell-cell communication network between immune cells and nonparenchymal cells was extremely sophisticated and changed significantly in MAFLD.展开更多
基金This work was funded by the National Natural Science Foundation of China(82000620,81870449)GuangDong Basic and Applied Basic Research Foundation(2023A1515010583)+1 种基金China Postdoctoral Science Foundation(2022M723610)Natural Science Foundation of Xinjiang Uyghur Autonomous Region(2020D01C006).
文摘Background:Metabolic dysfunction-associated fatty liver disease(MAFLD)is now the most prevalent chronic liver disease worldwide,with an increasing incidence rate.MAFLD is a heterogeneous disease that can have a low or high-risk profile for developing severe liver disease in its natural course.Recent evidence has highlighted the critical role of RNA methylation modification in the pathogenesis of various liver diseases.However,it remains unclear whether the RNA N1-methyladenosine(m1A)modification of immune cells could potentially contribute to the pathogenesis and heterogeneity of MAFLD.Materials and methods:To address this issue,we conducted an integrated bioinformatics analysis of MAFLD bulk and single-cell RNA sequencing(scRNA-seq)data to pinpoint m1A regulators in the network.This was followed by a description of the immune landscape,pathway enrichment analysis,and molecular subtyping.Results:The expression patterns of m1A regulatory genes stratify MAFLD into two molecular subtypes,Cluster 1 and Cluster 2.These subtypes demonstrate different immune cell infiltration with distinct inflammation characteristics,which suggest different immune-inflammatory responses in the liver.Notably,Cluster 2 is associated with pro-inflammation and may be more likely to lead to progressive stages of MAFLD.Through intersection analysis of weighted gene co-expression network analysis(WGCNA)and m1A regulatory genes,three true hub genes(ALKBH1,YTHDC1,and YTHDF3)were identified,all of which were strongly correlated with infiltrating immune cells.The specific signaling pathways involved in the three core genes were derived from genomic variation analysis.Furthermore,scRNA-seq data from 33,168 cells from six liver samples identified 26 cell clusters and eight cell types,with endothelial cells,macrophages,and monocytes showing the most significant differences between MAFLD and normal controls.The cell-cell communication network between immune cells and nonparenchymal cells was extremely sophisticated and changed significantly in MAFLD.
