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A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
Published on: December 5, 2016
Integrative analysis of bulk and single-cell RNA sequencing data reveals distinct subtypes of MAFLD based on
Jinyong He1,2,3, Cuicui Xiao3,4, Cuiping Li1,2
1Cell-gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
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 non-parenchymal cells was extremely sophisticated and changed significantly in MAFLD.
Conclusions:
In summary, these findings demonstrate the involvement of m1A in MAFLD heterogeneity and emphasize the crucial role of m1A modulation of immune cells in regulating inflammation in MAFLD. These results may suggest potential therapeutic strategies for MAFLD.
Insights
RNA N1-methyladenosine (m1A) modification in immune cells contributes to metabolic dysfunction-associated fatty liver disease (MAFLD) heterogeneity. This study identifies m1A regulators and immune cell differences, suggesting potential therapeutic targets for MAFLD.
Area of Science:
- Hepatology
- Immunology
- Molecular Biology
- Bioinformatics
Background:
- Metabolic dysfunction-associated fatty liver disease (MAFLD) is the leading cause of chronic liver disease globally, exhibiting significant heterogeneity.
- RNA methylation, specifically m1A modification, is implicated in liver disease pathogenesis, but its role in MAFLD immune cell involvement is unclear.
Purpose of the Study:
- To investigate the role of RNA N1-methyladenosine (m1A) modification in immune cells in the pathogenesis and heterogeneity of MAFLD.
- To identify key m1A regulators and their association with immune cell infiltration and inflammation in MAFLD.
Main Methods:
- Integrated bioinformatics analysis of MAFLD bulk and single-cell RNA sequencing (scRNA-seq) data.
- Identification of m1A regulators, molecular subtyping, pathway enrichment analysis, and WGCNA.
- Analysis of immune cell infiltration and cell-cell communication networks.
Main Results:
- MAFLD patients were stratified into two molecular subtypes (Cluster 1 and Cluster 2) based on m1A regulatory gene expression, with distinct immune profiles.
- Cluster 2 showed a pro-inflammatory phenotype, suggesting a higher risk for disease progression.
- Three hub genes (ALKBH1, YTHDC1, YTHDF3) correlated with immune cell infiltration were identified. Endothelial cells, macrophages, and monocytes showed significant differences in MAFLD.
- Complex alterations in cell-cell communication networks between immune and non-parenchymal cells were observed in MAFLD.
Conclusions:
- m1A modification plays a critical role in MAFLD heterogeneity and immune-inflammatory responses.
- The identified m1A regulators and immune cell signatures offer potential therapeutic targets for MAFLD.
- Understanding m1A's role in immune cells provides insights into MAFLD pathogenesis and potential treatment strategies.
