Pancreas · 2025
scRNA-Seq and Bulk-Seq Identify Novel Markers Associated With Calcium Regulation and Immunomodulation in Acute Pancreatitis.
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Sun Zefang, Zhou Rui, Ning Caihong, Zhu Shuai, Li Xueguang, He Quanyuan, Huang Gengwen
Аннотация
BACKGROUND: The exact pathogenesis of acute pancreatitis (AP) remains unclear. A ceRNA profile based on single-cell RNA-seq (scRNA-seq) and bulk RNA-seq analysis will deepen our understanding of the mechanisms in AP and identify new potential biomarkers.
MATERIALS AND METHODS: The differentially expressed lncRNA (DElncRNA) and mRNA (DEmRNA) were identified using bulk RNA-seq data. The interactions across miRNA and lncRNA/mRNA were integrated to construct a ceRNA network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to analyze the function and pathways. Meanwhile, scRNA-seq analysis was used to evaluate the expression of genes. In addition, immune cell infiltration was also evaluated and the correlation analysis was used to assess the relationship between candidate lncRNAs and immune-related genes.
RESULTS: A ceRNA network that contains 6 DElncRNAs, 38 miRNAs, and 215 DEmRNAs was constructed. A total of 5 candidate mRNAs and 5 candidate lncRNAs were identified. Pathway analysis suggested the candidate genes are associated with calcium-related regulation. scRNA-seq analysis indicated that 5 candidate mRNAs (Afdn, Pik3r1, Ap1s1, Cryab, and Sel1l) may be involved in the pathogenesis of AP by influencing calcium signaling. Immune infiltration analysis found that mice with AP are highly infiltrated with M1 macrophage, monocyte, and CD4+ memory T cells. In quantitative real-time PCR (qRT-PCR) validation, all candidate mRNAs and most candidate lncRNAs displayed consistent expression trends.
CONCLUSIONS: The comprehensive analysis of the ceRNA network identified novel genes may regulate calcium-related pathways and participate in the immunomodulation in AP.Trial registration: Not applicable.
MATERIALS AND METHODS: The differentially expressed lncRNA (DElncRNA) and mRNA (DEmRNA) were identified using bulk RNA-seq data. The interactions across miRNA and lncRNA/mRNA were integrated to construct a ceRNA network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to analyze the function and pathways. Meanwhile, scRNA-seq analysis was used to evaluate the expression of genes. In addition, immune cell infiltration was also evaluated and the correlation analysis was used to assess the relationship between candidate lncRNAs and immune-related genes.
RESULTS: A ceRNA network that contains 6 DElncRNAs, 38 miRNAs, and 215 DEmRNAs was constructed. A total of 5 candidate mRNAs and 5 candidate lncRNAs were identified. Pathway analysis suggested the candidate genes are associated with calcium-related regulation. scRNA-seq analysis indicated that 5 candidate mRNAs (Afdn, Pik3r1, Ap1s1, Cryab, and Sel1l) may be involved in the pathogenesis of AP by influencing calcium signaling. Immune infiltration analysis found that mice with AP are highly infiltrated with M1 macrophage, monocyte, and CD4+ memory T cells. In quantitative real-time PCR (qRT-PCR) validation, all candidate mRNAs and most candidate lncRNAs displayed consistent expression trends.
CONCLUSIONS: The comprehensive analysis of the ceRNA network identified novel genes may regulate calcium-related pathways and participate in the immunomodulation in AP.Trial registration: Not applicable.