Combined identification of ARID1A, CSMD1, and SENP3 as effective prognostic biomarkers for hepatocellular carcinoma

Zhao, Yuanyuan; Yang, Bo; Chen, Dong; Zhou, Xiaojun; Wang, Meixi; Jiang, Jianzhong; Wei, Lai; Chen, Zhishui

doi:10.18632/aging.202586

Cited by 8 publications

(7 citation statements)

References 32 publications

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“…The process subsequently leads to the upregulation of c-Myc and epithelial-mesenchymal transition markers ( Chen et al, 2019 ). It has also been reported that combined identification of ARID1A, SENP3, and CSMD1 are effective prognostic biomarkers for HCC patients ( Zhao et al, 2021 ). The third gene RoBo2 can suppress cancer development through TGF-β signalling and stroma activation ( Pinho et al, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of DNA 5-Methylcytosine and N6-Adenine Methylation by Nanopore Sequencing in Hepatocellular Carcinoma

Zhang

Rong

et al. 2022

Front. Cell Dev. Biol.

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DNA methylation is a widespread epigenetic signal in human genome. With Nanopore technology, differential methylation modifications including 5-methylcytosine (5mC) and 6-methyladenine (6mA) can be identified. 5mC is the most important modification in mammals, although 6mA may also function in growth and development as well as in pathogenesis. While the role of 5mC at CpG islands in promoter regions associated with transcriptional regulation has been well studied, but the relationship between 6mA and transcription is still unclear. Thus, we collected two pairs of tumor tissues and adjacent normal tissues from hepatocellular carcinoma (HCC) surgical samples for Nanopore sequencing and transcriptome sequencing. It was found that 2,373 genes had both 5mC and 6mA, along with up- and down-regulated methylation sites. These genes were regarded as unstable methylation genes. Compared with 6mA, 5mC had more inclined distribution of unstable methylation sites. Chi-square test showed that the levels of 5mC were consistent with both up- and down-regulated genes, but 6mA was not significant. Moreover, the top three unstable methylation genes, TBC1D3H, CSMD1, and ROBO2, were all related to cancer. Transcriptome and survival analyses revealed four potential tumor suppressor genes including KCNIP4, CACNA1C, PACRG, and ST6GALNAC3. In this study, we firstly proposed to combine 5mC and 6mA methylation sites to explore functional genes, and further research found top of these unstable methylation genes might be functional and some of them could serve as potential tumor suppressor genes. Our study provided a new solution for epigenetic regulation research and therapy of HCC.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of DNA 5-Methylcytosine and N6-Adenine Methylation by Nanopore Sequencing in Hepatocellular Carcinoma

Zhang

Rong

et al. 2022

Front. Cell Dev. Biol.

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“…For instance, several genes that are mutated in human hepatocellular carcinoma were not observed in this pilot analysis. These genes include the telomerase reverse transcriptase gene, TERT [ 38 ], CSMD1 , a putative tumor suppressor that is frequently mutated in human hepatocellular carcinoma associated with HBV infection [ 40 ], FRAS1 and the mitochondrial encoded gene ND5 . TERT , CSMD1 , FRAS1 and ND5 are mutated in 28.6%, 5.7%, 5.2% and 5.3% of human hepatocellular carcinomas.…”

Section: Resultsmentioning

confidence: 99%

Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study

Gunady

Ware

Plumlee

et al. 2022

Evolution, Medicine, and Public Health

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Background and objectives Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers in this group is unknown. Characterizing the genetic changes associated with hepatocellular carcinoma in prosimians may point to possible causes, treatments, and methods of prevention, aiding conservation efforts that are particularly crucial to the survival of endangered lemurs. Although genomic studies of cancer in non-human primates have been hampered by a lack of tools, recent studies have demonstrated the efficacy of using human exome capture reagents across primates. Methodology In this proof-of-principle study, we applied human exome capture reagents to tumor-normal pairs from five lemurs with hepatocellular carcinoma to characterize the mutational landscape of this disease in lemurs. Results Several genes implicated in human hepatocellular carcinoma, including ARID1A, TP53, and CTNNB1, were mutated in multiple lemurs, and analysis of cancer driver genes mutated in these samples identified enrichment of genes involved with TP53 degradation and regulation. In addition to these similarities with human hepatocellular carcinoma, we also noted unique features, including six genes that contain mutations in all five lemurs. Interestingly, these genes are infrequently mutated in human hepatocellular carcinoma, suggesting potential differences in the etiology and/or progression of this cancer in lemurs and humans. Conclusions and implications Collectively, this pilot study suggests that human exome capture reagents are a promising tool for genomic studies of cancer in lemurs and other non-human primates. LAY SUMMARY Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers is unknown. In this proof-of-principle study, we applied human DNA sequencing tools to tumor-normal pairs from five lemurs with hepatocellular carcinoma and compared the lemur mutation profiles to those of human hepatocellular carcinomas.

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“…Elucidating the relationship of CSMD1 with the aforementioned diseases in this review may be important in terms of both treatment and diagnosis in the future. Recent studies have revealed a possible role for CSMD1 in immunotherapy for some cancer types [ 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 ]. The determination of the factors affecting the expression of CSMD1 and the clarification of the signalling pathways it affects will increase the clinical utility of CSMD1.…”

Section: Discussionmentioning

confidence: 99%

“…As a result, it was speculated that lncCSMD1 could be a novel and reproducible prognostic biomarker for HCC patients, as well as playing an important role in HCC progression [ 76 ]. Using the GEO and TCGA databases, a study identified several novel driver genes including CSMD1 associated with HCC and demonstrated that this gene was strongly related to the prognosis of early recurrence and an effective prognostic marker for HCC [ 77 ].…”

Section: Csmd1 Functionmentioning

confidence: 99%

The Diverse Role of CUB and Sushi Multiple Domains 1 (CSMD1) in Human Diseases

Ermis

Bell

2022

Genes

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CUB and Sushi Multiple Domains 1 (CSMD1), a tumour suppressor gene, encodes a large membrane-bound protein including a single transmembrane domain. This transmembrane region has a potential tyrosine phosphorylation site, suggesting that CSMD1 is involved in controlling cellular functions. Although the specific mechanisms of action for CSMD1 have not yet been uncovered, it has been linked to a number of processes including development, complement control, neurodevelopment, and cancer progression. In this review, we summarise CSMD1 functions in the cellular processes involved in the complement system, metastasis, and Epithelial mesenchymal transition (EMT) and also in the diseases schizophrenia, Parkinson’s disease, and cancer. Clarifying the association between CSMD1 and the aforementioned diseases will contribute to the development of new diagnosis and treatment methods for these diseases. Recent studies in certain cancer types, e.g., gastric cancer, oesophageal cancer, and head and neck squamous cell carcinomas, have indicated the involvement of CSMD1 in response to immunotherapy.

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Combined identification of ARID1A, CSMD1, and SENP3 as effective prognostic biomarkers for hepatocellular carcinoma

Cited by 8 publications

References 32 publications

Comprehensive Analysis of DNA 5-Methylcytosine and N6-Adenine Methylation by Nanopore Sequencing in Hepatocellular Carcinoma

Comprehensive Analysis of DNA 5-Methylcytosine and N6-Adenine Methylation by Nanopore Sequencing in Hepatocellular Carcinoma

Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study

The Diverse Role of CUB and Sushi Multiple Domains 1 (CSMD1) in Human Diseases

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