Table9_Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma.XLSX

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

背景：伪尿苷合成酶（PUSs）已被报道与癌症相关。然而，其在肝细胞癌（HCC）中的参与尚无充分文献记载。本研究旨在评估PUSs在HCC中的作用。
方法：从癌症基因组图谱（TCGA）和国际癌症基因组联盟（ICGC）分别下载了TCGA-LIHC和LIRI-JP的RNA测序数据。从基因表达综合数据库（GEO）下载了GSE36376基因表达微阵列数据。通过CPTAC数据门户获取了与乙型肝炎病毒相关HCC队列的蛋白质组学数据。采用RT-qPCR技术检测临床组织和细胞系中基因的相对mRNA表达。通过ROC曲线评估诊断效率。使用Kaplan-Meier曲线、Cox回归模型和时间依赖性ROC曲线评估预后价值。利用GSCA数据库分析拷贝数变异（CNV）。通过GSEA、GSVA和clusterProfiler包进行功能分析。利用ssGSEA和ESTIMATE算法进行肿瘤微环境（TME）相关分析。
结果：我们鉴定出7种在HCC中显著上调的PUSs，其中5种（DKC1、PUS1、PUS7、PUSL1和RPUSD3）是患者总生存期（OS）的独立风险因素。同时，DKC1、PUS1和PUS7的蛋白质表达上调，且与不良预后相关。这些PUSs的mRNA和蛋白质表达对HCC具有较高的诊断价值。此外，PUS1、PUS7、PUS7L和RPUSD2的CNV也与预后相关。进一步的功能分析揭示，PUSs主要参与遗传信息处理、物质代谢、细胞周期和免疫调节等途径。
结论：PUSs可能在HCC中发挥关键作用，并可作为患者诊断和预后的潜在生物标志物。