Comprehensive analysis of Mendelian randomization and single-cell sequencing reveals the causal relationship between intrahepatic cholangiocarcinoma and chronotype-related genes

Abstract

Background The tumor development is related to disruption of circadian rhythms. However, the causal relationship between chronotype and intrahepatic cholangiocarcinoma (ICC) and molecular mechanism of chronotype-related genes (CRGs) are vague. Methods Genetic summary statistics were obtained from the Integrative Epidemiology Unit (IEU) OpenGWAS and genome-wide association studies (GWAS) Catalog. Univariate Mendelian randomization (MR) analysis and sensitivity analysis were then performed. Subsequently, the CRGs were obtained based on the single nucleotide polymorphisms (SNPs) of chronotype for differential expression analysis between disease and control groups based on University of California, Santa Cruz (UCSC) Xena database, and the identification of hub genes via STRING database and immune infiltration analysis. Finally, the single-cell transcriptome dataset GSE138709 downloaded from Gene Expression Omnibus (GEO) database was used to analyze the relationship between hub genes and annotated cell types. The functional enrichment analysis, pseudotime analysis and cell communication analysis were also explored. Results The MR results revealed that chronotype was a protective factor causally related to ICC, and the reliability was illustrated by the sensitivity analysis. A total of 180 differentially expressed CRGs were acquired, including 101 up-regulated and 79 down-regulated in ICC. Of which, four genes were marked as hub genes based on protein-protein interaction network, namely IDH1, PEX13, DECR2 and PEX12. Moreover, a total of ten cell types were annotated in GSE138709, including T cells, malignant cells, macrophages, NK cells, dendritic cells, B cells, endothelial cells, cholangiocytes, hepatocytes and fibroblasts. Thereinto, NK cells and hepatocytes as key cells were remarkably discrepant between ICC and control samples. The expression of DECR2 and IDH1 in hepatocytes was higher in control group than in ICC group. Furthermore, hepatocytes might transform into cholangiocytes and malignant cells, and both hepatocytes and NK cells interacted strongly with macrophages. Conclusion Our study supported a causal relationship between chronotype and ICC, and provided the theoretical basis and reference value for research on MR.