Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma

• DOI: 10.3389/fgene.2022.944681
• Publication Date: 2022-11-10T10:13:35Z
• Authors: Zhipeng Jin; Mengying Song; Jianping Wang; Wenjing Zhu; Dongxu Sun; Huayuan Liu; Guangjun Shi
• Keywords: Fold change; Human Protein Atlas

Background: The pseudouridine synthases (PUSs) have been reported to be associated with cancers. However, their involvement in hepatocellular carcinoma (HCC) has not well documented. Here, we assess the roles of PUSs HCC. Methods: RNA sequencing data TCGA-LIHC and LIRI-JP were downloaded from Cancer Genome Atlas (TCGA) International Consortium (ICGC), respectively. GSE36376 gene expression microarray was Gene Expression Omnibus (GEO). Proteomics for an HBV-related HCC cohort obtained CPTAC Data Portal. RT-qPCR assay performed measure relative mRNA genes clinical tissues cell lines. Diagnostic efficiency evaluated by ROC curve. Prognostic value assessed using Kaplan-Meier curve, Cox regression model, time-dependent Copy number variation (CNV) analyzed GSCA database. Functional analysis carried out GSEA, GSVA, clusterProfiler package. tumor microenvironment (TME) related ssGSEA ESTIMATE algorithm. Results: We identified 7 that significantly upregulated HCC, 5 them ( DKC1 , PUS1 PUS7 PUSL1 RPUSD3 ) independent risk factors patients’ OS. Meanwhile, protein DKC1, PUS1, also poor survival. Both these highly diagnostic Moreover, CNV PUS7L RPUSD2 prognosis. Further functional revealed mainly involved pathways such as genetic information processing, substance metabolism, cycle, immune regulation. Conclusion: may play crucial could used potential biomarkers diagnosis prognosis patients.