Dataset Information

Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer.

ABSTRACT: Background: 5-Methylcytidine (m5C) is the most common RNA modification and plays an important role in multiple tumors including cervical cancer (CC). We aimed to develop a novel gene signature by identifying m5C modification subtypes of CC to better predict the prognosis of patients. Methods: We obtained the expression of 13 m5C regulatory factors from The Cancer Genome Atlas (TCGA all set, 257 patients) to determine m5C modification subtypes by the "nonnegative matrix factorization" (NMF). Then the "limma" package was used to identify differentially expressed genes (DEGs) between different subtypes. According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients). We also verified the risk prediction effect of gene signature in TCGA test set (129 patients), TCGA all set (257 patients) and GSE44001 (300 patients). Furthermore, a nomogram including this gene signature and clinicopathological parameters was established to predict the individual survival rate. Finally, the expression and function of these signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, colony formation, migration and invasion assays. Results: Based on consistent clustering of 13 m5C-modified genes, CC was divided into two subtypes (C1 and C2) and the C1 subtype had a worse prognosis. The 4-gene signature comprising FNDC3A, VEGFA, OPN3 and CPE was constructed. In TCGA training set and three validation sets, we found the prognosis of patients in the low-risk group was much better than that in the high-risk group. A nomogram incorporating the gene signature and T stage was constructed, and the calibration plot suggested that it could accurately predict the survival rate. The expression levels of FNDC3A, VEGFA, OPN3 and CPE were all high in cervical cancer tissues. Downregulation of FNDC3A, VEGFA or CPE expression suppressed the proliferation, migration and invasion of SiHa cells. Conclusions: Two m5C modification subtypes of CC were identified and then a 4-gene signature was established, which provide new feasible methods for clinical risk assessment and targeted therapies for CC.

SUBMITTER: Yu J

PROVIDER: S-EPMC8493221 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundHepatocellular carcinoma (HCC) is a malignancy with a bleak prognosis. Although emerging research increasingly supports the involvement of chromatin regulators (CRs) in cancer development, CRs in HCC patients have not received proportionate attention. This study aimed to investigate the role and prognostic significance of CRs in HCC patients, providing new insights for clinical diagnosis and treatment strategies.MethodsWe analyzed 424 samples in The Cancer Genome Atlas-Liver hepatocellular carcinoma (TCGA-LIHC) data to identify key CR genes associated with HCC prognosis by differential expression and univariate Cox regression analyses. LASSO-multivariate Cox regression method was used for construction of a prognostic signature and development of a CR-related prognosis model. The prognosis capacity of the model was evaluated via Kaplan-Meier method. Relationship between the model and tumor microenvironment (TME) was evaluated. Additionally, clinical variables and the model were incorporated to create a nomogram. The role of the prognostic gene MRG-binding protein (MRGBP) in HCC was elucidated by immunohistochemistry and semiquantitative analysis.ResultsA risk score model, comprising B-lymphoma Mo-MLV insertion region 1 (BMI1), chromobox 2 (CBX2), and MRGBP, was constructed. The area under the curve (AUC) of the CR-based signature is 0.698 (P<0.05), exhibiting robust predictive power. Functional and pathway analyses illuminated the biological relevance of these genes. Immune microenvironment analysis suggested potential implications for immunotherapy. Drug sensitivity analysis identified agents for targeted treatment. Clinical samples show that MRGBP is highly expressed in HCC tissues.ConclusionsThis CR-based signature shows promise as a valuable prognostic tool for HCC patients. It demonstrates predictive capabilities, independence from other clinical factors, and potential clinical applicability. In addition, we need more experiments to validate our findings. These findings offer insights into HCC prognosis and treatment, with implications for personalized medicine and improved patient outcomes.

Project description:Lung adenocarcinoma (LUAD) is the most prevalent subtype of non-small cell lung cancer (NSCLC) and is associated with high mortality rates. However, effective methods to guide clinical therapeutic strategies for LUAD are still lacking. The goals of this study were to analyze the relationship between an m5C/m6A-related signature and LUAD and construct a novel model for evaluating prognosis and predicting drug resistance and immunotherapy efficacy. We obtained data from LUAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Based on the differentially expressed m5C/m6A-related genes, we identified distinct m5C/m6A-related modification subtypes in LUAD by unsupervised clustering and compared the differences in functions and pathways between different clusters. In addition, a risk model was constructed using multivariate Cox regression analysis based on prognostic m5C/m6A-related genes to predict prognosis and immunotherapy response. We showed the landscape of 36 m5C/m6A regulators in TCGA-LUAD samples and identified 29 differentially expressed m5C/m6A regulators between the normal and LUAD groups. Two m5C/m6A-related subtypes were identified in 29 genes. Compared to cluster 2, cluster 1 had lower m5C/m6A regulator expression, higher OS (overall survival), higher immune activity, and an abundance of infiltrating immune cells. Four m5C/m6A-related gene signatures consisting of HNRNPA2B1, IGF2BP2, NSUN4, and ALYREF were used to construct a prognostic risk model, and the high-risk group had a worse prognosis, higher immune checkpoint expression, and tumor mutational burden (TMB). In patients treated with immunotherapy, samples with high-risk scores had higher expression of immune checkpoint genes and better immunotherapeutic efficacy than those with low-risk scores. We concluded that the m5C/m6A regulator-related risk model could serve as an effective prognostic biomarker and predict the therapeutic sensitivity of chemotherapy and immunotherapy.

Dataset Information

Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets