Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types

Liu, Taisheng; Zhang, Jian; Lin, Chunxuan; Liu, Guihong; Xie, Gaoqiang; Dai, Zili; Yu, Peng; Wang, Jian; Guo, Liyi

doi:10.3389/fcell.2022.839136

Cited by 6 publications

(4 citation statements)

References 46 publications

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“…We performed PCA analysis on the corrected datasets from GEO and TCGA, the results suggested a good correction effect ( Figures 1A,B ). Referring to Cui et al's study ( Cui et al, 2021 ; Wang et al, 2021 ; Liu et al, 2022a ), we selected the seven most common m5C regulator genes (NOP2, NSUN2, TET3, NSUN6, TET1, YBX1, and DNMT3B) as the subjects. In the GEO dataset, four of the seven m5C regulator genes (TET3, NSUN6, TET1, and YBX1) were differentially expressed ( Figure 1C ), while all seven m5C regulator genes had significant differential expression in the TCGA dataset ( Figure 1D ).…”

Section: Resultsmentioning

confidence: 99%

“…The TCGA database contains expression data ( Table 1 ), copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and relevant clinicopathological features for 374 HCC samples and 50 paraneoplastic samples. The microarray platform for GSE76427 (sample size: disease group 115/control group 52) ( Table 1 ) dataset is Illumina HumanHT-12 V4.0 expression beadchip, and gene set related to m5C regulators was obtained by Cui et al's study ( Cui et al, 2021 ; Wang et al, 2021 ; Liu et al, 2022a ). We first used “sva” package ( Leek et al, 2012 ) to preprocess the downloaded TCGA and GEO dataset expression matrices, including: data background adjustment and normalization, and output the expression of intersecting genes in the two datasets separately.…”

Section: Methodsmentioning

confidence: 99%

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Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Yang

Lan

et al. 2022

Front. Genet.

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Background: A high mortality rate makes hepatocellular carcinoma (HCC) one of the most common types of cancer globally. 5-methylcytosine (m5C) is an epigenetic modification that contributes to the prognosis of several cancers, but its relevance to HCC remains unknown. We sought to determine if the m5C-related regulators had any diagnostic or prognostic value in HCC.Methods: M5C regulatory genes were screened and compared between HCC and normal tissue from The Cancer Genome Atlas (TCGA)and Gene Expression Omnibus (GEO) databases. Least absolute shrinkage and selection operator method (LASSO) and univariate Cox regression analysis of differentially expressed genes were then performed to identify diagnostic markers. A LASSO prognostic model was constructed using M5C regulatory genes with prognostic values screened by TCGA expression data. HCC patients were stratified based on risk score, then clinical characteristics analysis and immune correlation analysis were performed for each subgroup, and the molecular functions of different subgroups were analyzed using both Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA). The prognostic model was evaluated using univariate and multivariate Cox analyses as well as a nomogram. Molecular typing was performed according to m5C regulatory genes and immune checkpoint genes expression respectively, and clinical characterization and immune correlation analysis were performed for each subgroup.Results: M5C regulatory genes are expressed differently in HCC patients with different clinical and pathological characteristics, and mutations in these genes are frequent. Based on five m5C regulators (NOP2, NSUN2, TET1, YBX1, and DNMT3B), we constructed a prognostic model with high predictive ability. The risk score was found to be an independent prognostic indicator. Additionally, risk scores can also be applied in subgroups with different clinical characteristics as prognostic indicators.Conclusion: The study combined data from TCGA and GEO for the first time to reveal the genetic and prognostic significance of m5C-related regulators in HCC, which provides new directions for identifying predictive biomarkers and developing molecularly targeted therapies for HCC.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Yang

Lan

et al. 2022

Front. Genet.

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“…The complexity of ascites determines the multi-origin of ovarian cancer exosomes. Indeed, the source cells of ovarian cancer exosomes may include T cells, B cells, DCs, and ovarian cancer cells ( 32 ). Meanwhile, exosomes play crucial roles in tumor immune escape by inducing apoptosis of immune cells ( 33 , 34 ).…”

Section: Exosomes In Tumor Diagnosismentioning

confidence: 99%

Exosomes: A potential tool for immunotherapy of ovarian cancer

et al. 2023

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Ovarian cancer is a malignant tumor of the female reproductive system, with a very poor prognosis and high mortality rates. Chemotherapy and radiotherapy are the most common treatments for ovarian cancer, with unsatisfactory results. Exosomes are a subpopulation of extracellular vesicles, which have a diameter of approximately 30–100 nm and are secreted by many different types of cells in various body fluids. Exosomes are highly stable and are effective carriers of immunotherapeutic drugs. Recent studies have shown that exosomes are involved in various cellular responses in the tumor microenvironment, influencing the development and therapeutic efficacy of ovarian cancer, and exhibiting dual roles in inhibiting and promoting tumor development. Exosomes also contain a variety of genes related to ovarian cancer immunotherapy that could be potential biomarkers for ovarian cancer diagnosis and prognosis. Undoubtedly, exosomes have great therapeutic potential in the field of ovarian cancer immunotherapy. However, translation of this idea to the clinic has not occurred. Therefore, it is important to understand how exosomes could be used in ovarian cancer immunotherapy to regulate tumor progression. In this review, we summarize the biomarkers of exosomes in different body fluids related to immunotherapy in ovarian cancer and the potential mechanisms by which exosomes influence immunotherapeutic response. We also discuss the prospects for clinical application of exosome-based immunotherapy in ovarian cancer.

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“… 113 In addition to m 6 A, METTL1 and the m 5 C modulator-NOP2 are associated with immune invasion in many tumor subtypes. 114 , 115 As a piece of evidence, upregulation of METTL1 enhances TGF-β2 translation by inducing myeloid-derived suppressor cells to form an immunosuppressive environment, thereby leading to HCC recurrence. 116 Also, the NSUN2 promotes the progression of NPC by regulating immune infiltration.…”

Section: Rna Modifications In the Tumor Microenvironmentmentioning

confidence: 99%

RNA Modifications Meet Tumors

Yang¹,

Zhang²,

Xia³

et al. 2022

CMAR

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RNA modifications occur through the whole process of gene expression regulation, including transcription, translation, and post-translational processes. They are closely associated with gene expression, RNA stability, and cell cycle. RNA modifications in tumor cells play a vital role in tumor development and metastasis, changes in the tumor microenvironment, drug resistance in tumors, construction of tumor cell-cell “internet”, etc. Several types of RNA modifications have been identified to date and have various effects on the biological characteristics of different tumors. In this review, we discussed the function of RNA modifications, including N 6 -methyladenine (m 6 A), 5-methylcytosine (m 5 C), N 7 -methyladenosine (m 7 G), N 1 -methyladenosine (m 1 A), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I), in the microenvironment and therapy of solid and liquid tumors.

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Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types

Cited by 6 publications

References 46 publications

Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Exosomes: A potential tool for immunotherapy of ovarian cancer

RNA Modifications Meet Tumors

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