H/ACA snoRNP Gene Family as Diagnostic and Prognostic Biomarkers for Hepatocellular Carcinoma

Zhang, Mi; Zhao, Wei; Liu, Shanshan; Liu, Haichuan; Liu, Liang; Peng, Qiling; Du, Changsheng; Jiang, Ning

doi:10.2147/pgpm.s333838

Cited by 8 publications

(6 citation statements)

References 43 publications

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“…41 Most pertinent to this report, higher expression of NHP2, as well as other H/ACA snoRNP family genes, has also been correlated with poorer prognoses for HCC patients. 42 Evidence suggests NHP2's role in HCC development involves stimulating the proliferation of hepatoma cells overexpressing HBx, 43 which fascinatingly, independently aligns with our results, as HBV*767693 is an epitope associated with HBx (Table 3). In other words, the assessments in this report did not at first involve NHP2;…”

Section: Discussionsupporting

confidence: 85%

“…This latter function accounts for the gene's oncogenicity with increased expression having been observed in numerous cancers, such as endometrial cancer, 38 colorectal cancer, 39,40 and squamous cell lung cancer 41 . Most pertinent to this report, higher expression of NHP2, as well as other H/ACA snoRNP family genes, has also been correlated with poorer prognoses for HCC patients 42 . Evidence suggests NHP2's role in HCC development involves stimulating the proliferation of hepatoma cells overexpressing HBx, 43 which fascinatingly, independently aligns with our results, as HBV*767693 is an epitope associated with HBx (Table 3).…”

Section: Discussionmentioning

confidence: 60%

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TRB CDR3 chemical complementarity with HBV epitopes correlates with increased hepatocellular carcinoma, disease‐free survival

Song,

Chobrutskiy,

Chobrutskiy

et al. 2023

Journal of Medical Virology

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The liver is a site of immune privilege, compared with the bladder and skin, for example. To study this attenuation of the immune response in the cancer setting, we compared quantities and features of adaptive immune receptor (IR) recombination reads obtained from hepatocellular carcinoma (HCC) and six other cancers. Of these cancers, HCC had the lowest numbers of IR recombination reads and was the only cancer with a greater number immunoglobulin rather than T‐cell receptor recombination reads. To better understand the role of adaptive IRs obtained from the tumor microenvironment in shaping the outcome of HCC cases, we quantified the chemical complementarity between HCC tumor TRB and IGH complementarity determining region‐3 (CDR3) amino acid (AA) sequences, and known hepatitis B virus (HBV) epitopes. High chemical complementarity between HCC‐resident CDR3s and three HBV epitopes correlated with increased survival probabilities, for two sources of CDR3s representing different CDR3 recovery algorithms. These results suggest the potential of CDR3 AA sequences as biomarkers for HCC patient stratification and as guides for future development of therapeutics.

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Section: Discussionsupporting

confidence: 85%

Section: Discussionmentioning

confidence: 60%

TRB CDR3 chemical complementarity with HBV epitopes correlates with increased hepatocellular carcinoma, disease‐free survival

Song,

Chobrutskiy,

Chobrutskiy

et al. 2023

Journal of Medical Virology

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“…Previous studies have found that both protein and mRNA expression of DKC1 was higher in HCC than in non-cancerous liver tissues and was associated with advanced clinical stage and poor prognosis (Liu et al, 2012;Ko et al, 2018;Zhang et al, 2021b;Li et al, 2022a). As for RNA-independent PUSs, their roles in HCC have rarely been explored.…”

Section: Discussionmentioning

confidence: 96%

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

et al. 2022

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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.

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“…Another study used bioinformatics to analyze the expression and role of the H/ACA snoRNP gene family in HCC. The expression of the H/ACA snoRNP gene family was higher in HCC tissues than in normal or adjacent tissues, and their differential expression was strongly associated with poor prognosis and multiple immune cell infiltration in HCC patients and could be considered as biomarkers for the treatment of HCC (Zhang et al, 2021b). It has also been shown that overexpression of DKC1 can serve as a marker of the proliferative potential of HCC cells and is an unfavorable prognostic factor for HCC (Liu et al, 2012).…”

Section: Role Of Pseudouridine In Hepatocellular Carcinomamentioning

confidence: 99%

The role of RNA modification in hepatocellular carcinoma

et al. 2022

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Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.

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H/ACA snoRNP Gene Family as Diagnostic and Prognostic Biomarkers for Hepatocellular Carcinoma

Cited by 8 publications

References 43 publications

TRB CDR3 chemical complementarity with HBV epitopes correlates with increased hepatocellular carcinoma, disease‐free survival

TRB CDR3 chemical complementarity with HBV epitopes correlates with increased hepatocellular carcinoma, disease‐free survival

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

The role of RNA modification in hepatocellular carcinoma

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