Integrative Analysis of DNA Methylation Identified 12 Signature Genes Specific to Metastatic ccRCC

  title={Integrative Analysis of DNA Methylation Identified 12 Signature Genes Specific to Metastatic ccRCC},
  author={Siwei Qian and Si Sun and Lei Zhang and Shengwei Tian and Kaiqiang Xu and Guangyuan Zhang and Ming Chen},
  journal={Frontiers in Oncology},
Background: Abnormal epigenetic alterations can contribute to the development of human malignancies. Identification of these alterations for early screening and prognosis of clear cell renal cell carcinoma (ccRCC) has been a highly sought-after goal. Bioinformatic analysis of DNA methylation data provides broad prospects for discovery of epigenetic biomarkers. However, there is short of exploration of methylation-driven genes of ccRCC. Methods: Gene expression data and DNA methylation data in… 

Figures and Tables from this paper

Identification of Prognostic Metabolism-Related Genes in Clear Cell Renal Cell Carcinoma
The analysis found that the Riskscore model was associated with most of the metabolic processes, immune infiltration of cells such as plasma cells, immune checkpoints such as PD-1, and clinical characteristics such as M stage.
Epigenetic inactivation of ACAT1 promotes epithelial-mesenchymal transition of clear cell renal cell carcinoma.
The methylation level of the ACAT1 promoter region in KIRC was significantly higher than that in the normal kidney tissues and patients with high miR-21-5p expression tended to have lower overall survival, suggesting that miR+5p could serve as a potentially valuable diagnostic biomarker for KIRC.
Integrative 5-Methylcytosine Modification Immunologically Reprograms Tumor Microenvironment Characterizations and Phenotypes of Clear Cell Renal Cell Carcinoma
Assessment of tumor m5C modification patterns may enhance understanding of TME cell-infiltrating characterizations and help establish precision immunotherapy strategies for individual ccRCC patients and provide insights into the regulation mechanisms of DNAm5C methylation modification patterns on the tumor immune microenvironment.
STARD5 as a potential clinical target of hepatocellular carcinoma
STARD5 had strong diagnostic accuracy for HCC patients and it could be an independent prognostic predictor, and the TIMER1.0 and TISIDB databases found a negative correlation between STARD5 and tumor immune infiltrating cells.
Heterogeneous nuclear ribonucleoprotein A/B: an emerging group of cancer biomarkers and therapeutic targets
This review focuses on the clinical significance of hnRNPA/B in various cancers and systematically summarizes its biological function and molecular mechanisms.
hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease
There are critical gaps in the grasp of A/B proteins’ alternative splice isoforms, structures, regulation, and tissue and cell-type-specific functions, and it is proposed that future mechanistic research integrating multiple A/ B proteins will significantly improve the understanding of how this essential protein family contributes to cell homeostasis and disease.


Comprehensive analysis of DNA methylation and gene expression profiles in cholangiocarcinoma
This study identified novel methylation-regulated differentially expressed genes (MeDEGs) and explored their related pathways and functions in CCA, which may provide novel insights into a further understanding ofmethylation-mediated regulatory mechanisms in C CA.
Integrative Analysis of DNA Methylation and Gene Expression Identify a Three-Gene Signature for Predicting Prognosis in Lower-Grade Gliomas
An integrated analysis of genome-wide methylation and gene expression data to find novel prognostic genes for lower-grade gliomas found a three-gene prognostic signature by integrating multidimensional genomic data from the TCGA and CGGA datasets, which may help in fine-tuning the current histology-based tumors classification system and providing better stratification for future clinical trials.
Identification of core differentially methylated genes in glioma
Differentially methylated genes (DMGs) serve a crucial role in the pathogenesis of glioma via the regulation of the cell cycle, proliferation, apoptosis, migration, infiltration, DNA repair and signaling pathways and may provide potential methylation-based biomarkers for the precise diagnosis and targeted treatment ofglioma.
Construction of Novel DNA Methylation-Based Prognostic Model to Predict Survival in Glioblastoma
A novel prognostic model for survival prediction of GBMs was constructed and five genes with abnormal methylation level were significantly correlated with prognosis according to survival analysis, such as ALX1, KANK1, NUDT12, SNED1, and SVOP.
Identification of potential biomarkers and pivotal biological pathways for prostate cancer using bioinformatics analysis methods
This study excavated the key genes and pathways in PCa, which might be biomarkers for diagnosis, prognosis, and potential therapeutic targets, and two additional top DEGs were found to be associated with the prognosis of PCa patients.
Systematic investigation of the prognostic value of cell division cycle-associated proteins for clear cell renal cell carcinoma patients.
The aberrant expression of CDCA gene family members plays an indispensable role in tumorigenesis and was significantly increased in clear cell renal cell carcinoma patients.
Molecular differences in IDH wildtype glioblastoma according to MGMT promoter methylation
MGMT promoter methylation status does not define a molecularly distinct glioblastoma subpopulation among untreated tumors, and Progressive mMGMT glooblastomas and m MGMT tumors of patients with short survival tend to have more unfavorable molecular profiles.
Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment
This comprehensive genome-wide analysis of the AS landscape in HNSC revealed novel AS events related to carcinogenesis and immune microenvironment, with implications for prognosis and therapeutic responses.
Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways
The DEGs, associated pathways and hub genes identified in the present study help elucidate the underlying molecular mechanisms of ES carcinogenesis and progression, and provide potential molecular targets and biomarkers for ES.
Development and validation of a prognostic immune-associated gene signature in clear cell renal cell carcinoma.