1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Identification of hub genes and pathways connect gut microbiome to hepatocellular carcinoma using bioinformatics analysis in mus musculus
Paper ID : 1133-ICB10
Authors:
Mohammad Amin Malekraeisi *
دانشگاه علوم پزشکی ایران
Abstract:
Background
Liver cancer was the sixth common cancer and the third fatal cancer in 2020. Hepatocellular carcinoma (HCC) included 75%-85% of liver cancer cases. Gut microbiome-induced inflammation and elevated deoxycholic acid, secondary bile acid, were associated with HCC. In a study on mice, deoxycholic acid increased development to HCC in mice receiving STHD-01. The current study used bioinformatics approaches to reveal pathways and hub genes related to HCC and the gut microbiome.

Materials and methods
GSE114400 and GSE71628 for liver transcriptome related to gut microbiome changes, and GSE23680 and GSE104627 for HCC in mus musculus were chosen from the GEO. GEO2R, edgeR, and limma packages of R software were used to identify differentially expressed genes (DEGs) with Adjusted.P.value<0.05 and |logFC|>0. Shared genes of the up-regulated gut microbiome and down-regulated genes of HCC (up microbiome&down HCC) and the intersection of down-regulated genes of the gut microbiome and up-regulated genes of HCC (down microbiome&up HCC) were determined distinctly. Genes entered Enrichr, and BioPlanet identified enriched pathways. STRING and Cytoscape were used for network construction and analysis of protein-protein interaction (PPI) networks.

Results
Up microbiome&down HCC had 44 genes. The number of genes was 51 for down microbiome&up HCC. Pathway analysis using BioPlanet detected amino acid metabolism, pyrimidine nucleotides metabolism, urea cycle, and drug metabolism as significant pathways which involved up microbiome& down HCC genes. The unwinding of DNA, DNA strand elongation, cell cycle, DNA replication, and CDK regulation of DNA replication were significant pathways for the other intersection. Analysis of PPI network suggested Csp1, Fah, Upb1, Kynu for up microbiome&down HCC genes. Aurka, Incenp, Trip13 were hub genes for the other network.

Conclusion
Understanding pathways and hub genes related to the gut microbiome and HCC interaction would help provide more efficient treatments targeting HCC based on the gut microbiome.
Keywords:
bioinformatics; gut microbiome; hepatocellular carcinoma; hub gene; pathway
Status : Paper Accepted (Poster Presentation)