Exploration of Potential Roles of m5C-Related Regulators in Colon Adenocarcinoma Prognosis

Huang, Yuancheng; Huang, Chao-Yuan; Jiang, Xiaotao; Yan, Yanhua; Zhuang, Kunhai; Liu, Fengbin; Li, Peiwu; Wen, Yi

doi:10.3389/fgene.2022.816173

Cited by 10 publications

(9 citation statements)

References 49 publications

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“…Increasing evidence suggested that m5C modification plays an indispensable role in both physiological and pathological processes, particularly in the development and progression of cancer (42). Many studies have explored the roles of m5C regulatory genes and constructed prognostic models in colon adenocarcinoma, hepatocellular cancer, cervical cancer, and clear cell renal cell carcinoma (43)(44)(45). However, there were a few studies that investigated the biological role of m5C regulatory genes in PCa.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of m5C Methylation Regulatory Genes and Tumor Microenvironment in Prostate Cancer

Bao

Zhan

et al. 2022

Front. Immunol.

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Background5-Methylcytidine (m5C) methylation is an emerging epigenetic modification in recent years, which is associated with the development and progression of various cancers. However, the prognostic value of m5C regulatory genes and the correlation between m5C methylation and the tumor microenvironment (TME) in prostate cancer remain unknown.MethodsIn the current study, the genetic and transcriptional alterations and prognostic value of m5C regulatory genes were investigated in The Cancer Genome Atlas and Gene Expression Omnibus datasets. Then, an m5C prognostic model was established by LASSO Cox regression analysis. Gene set variation analyses (GSVA), gene set enrichment analysis (GSEA), clinical relevance, and TME analyses were conducted to explain the biological functions and quantify the TME scores between high-risk and low-risk subgroups. m5C regulatory gene clusters and m5C immune subtypes were identified using consensus unsupervised clustering analysis. The Cell-type Identification By Estimating Relative Subsets of RNA Transcripts algorithm was used to calculate the contents of immune cells.ResultsTET3 was upregulated at transcriptional levels in PCa compared with normal tissues, and a high TET3 expression was associated with poor prognosis. An m5C prognostic model consisting of 3 genes (NSUN2, TET3, and YBX1) was developed and a nomogram was constructed for improving the clinical applicability of the model. Functional analysis revealed the enrichment of pathways and the biological processes associated with RNA regulation and immune function. Significant differences were also found in the expression levels of m5C regulatory genes, TME scores, and immune cell infiltration levels between different risk subgroups. We identified two distinct m5C gene clusters and found their correlation with patient prognosis and immune cell infiltration characteristics. Naive B cells, CD8+ T cells, M1 macrophages and M2 macrophages were obtained and 2 m5C immune subtypes were identified. CTLA4, NSUN6, TET1, and TET3 were differentially expressed between immune subtypes. The expression of CTLA4 was found to be correlated with the degree of immune cell infiltration.ConclusionsOur comprehensive analysis of m5C regulatory genes in PCa demonstrated their potential roles in the prognosis, clinical features, and TME. These findings may improve our understanding of m5C regulatory genes in the tumor biology of PCa.

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Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of m5C Methylation Regulatory Genes and Tumor Microenvironment in Prostate Cancer

Bao

Zhan

et al. 2022

Front. Immunol.

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“…To determine subgroups of GC, we used the R package “ConsensusClusterPlus” for the consistent clustering based on the expression pattern of prognostic m 6 AIGs as the previous study ( 32 ). Using the K-mean cluster algorithm and the Euclidean squared distance metric, the optimal clustering amount was confirmed by the clustering score.…”

Section: Methodsmentioning

confidence: 99%

N6-methylandenosine-related immune genes correlate with prognosis and immune landscapes in gastric cancer

et al. 2022

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ObjectivesThis study aimed to probe into the significance of N6-methyladenosine (m6A)-related immune genes (m6AIGs) in predicting prognoses and immune landscapes of patients with gastric cancer (GC).MethodsThe clinical data and transcriptomic matrix of GC patients were acquired from The Cancer Genome Atlas database. The clinically meaningful m6AIGs were acquired by univariate Cox regression analysis. GC patients were stratified into different clusters via consensus clustering analysis and different risk subgroups via m6AIGs prognostic signature. The clinicopathological features and tumor microenvironment (TME) in the different clusters and different risk subgroups were explored. The predictive performance was evaluated using the KM method, ROC curves, and univariate and multivariate regression analyses. Moreover, we fabricated a nomogram based on risk scores and clinical risk characteristics. Biological functional analysis was performed based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The connectivity map was used to screen out potential small molecule drugs for GC patients.ResultsA total of 14 prognostic m6AIGs and two clusters based on 14 prognostic m6AIGs were identified. A prognostic signature based on 4 m6AIGs and a nomogram based on independent prognostic factors was constructed and validated. Different clusters and different risk subgroups were significantly correlated with TME scores, the distribution of immune cells, and the expression of immune checkpoint genes. Some malignant and immune biological processes and pathways were correlated with the patients with poor prognosis. Ten small molecular drugs with potential therapeutic effect were screened out.ConclusionsThis study revealed the prognostic role and significant values of m6AIGs in GC, which enhanced the understanding of m6AIGs and paved the way for developing predictive biomarkers and therapeutic targets for GC.

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“…The neoplastic tendency of the pancreas needs to be identified, and specific non-invasive markers discriminating PanCa from CP or other pancreatic precursor lesions such as pancreatic intraepithelial neoplasia (PanIN), intrapapillary mucinous neoplasia (IPMN) and mucinous cystic neoplasm need to be developed[ 28 ]. Luo et al [ 29 ] documented that cg10673833, a circulating tumor DNA (ctDNA) methylation marker was found to be very sensitive (89.7%) and specific (86.8%) for the detection of colorectal cancer and its associated pre-cancerous lesions.…”

Section: Liquid Biopsy and Its Role In Panca Diagnosismentioning

confidence: 99%

Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer

Bararia¹,

Chakraborty²,

Roy³

et al. 2023

World J Gastroenterol

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A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.

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Exploration of Potential Roles of m5C-Related Regulators in Colon Adenocarcinoma Prognosis

Cited by 10 publications

References 49 publications

Comprehensive Analysis of m5C Methylation Regulatory Genes and Tumor Microenvironment in Prostate Cancer

Comprehensive Analysis of m5C Methylation Regulatory Genes and Tumor Microenvironment in Prostate Cancer

N6-methylandenosine-related immune genes correlate with prognosis and immune landscapes in gastric cancer

Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer

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