ArticleCancer medicine2019
In silico DNA methylation analysis identifies potential prognostic biomarkers in type 2 papillary renal cell carcinoma.
Article in Cancer medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
- Identification of prognostic stemness-related genes in kidney renal papillary cell carcinoma.BMC medical genomics · 2024Article
- PTK7: an underestimated contributor to human cancer.Frontiers in oncology · 2024Review
- Biomarkers in renal cell carcinoma and their targeted therapies: a review.Exploration of targeted anti-tumor therapy · 2023Review
- The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments.Cancers · 2021Review
- Article
- Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer.Clinical epigenetics · 2021Article
- In silico DNA methylation analysis identifies potential prognostic biomarkers in type 2 papillary renal cell carcinoma.Cancer medicine · 2019Article
- The Role of MIEF2 in Cisplatin Sensitivity in KIRP Patients: Insights from Four-gene Mitochondrial Fusion RNA Markers.Technology in cancer research & treatmentArticle
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
There are currently no effective treatments for advanced-stage papillary renal cell carcinoma (PRCC). The goal of this study is to define potential DNA methylation-based markers and treatment targets for advanced-stage type 2 PRCC. Progressive DNA methylation changes and copy number variation (CNV) from localized to advanced-stage type 2 PRCC are analyzed by using methylation data generated by TCGA's kidney renal papillary cell carcinoma (TCGA-KIRP, 450k array) project. Survival analyses are performed for the identified biomarkers and genes with CNV. In addition, expression of the corresponding genes is investigated by RNA-seq analysis. Progressive methylation changes in several CpGs from localized to advanced-stage type 2 PRCC are observed. Four CpGs (cg00489401, cg27649239, cg20555674, and cg07196505) in particular are identified as markers for differentiating between localized and advanced-stage type 2 PRCC. Copy number analysis reveals that copy gain of PTK7 mostly occurs in advanced-stage type 2 PRCC. Both the four CpG methylation changes and PTK7 copy number gain are associated with patient survival. RNA-seq analysis demonstrates that PTK7 copy gain leads to higher PTK7 expression relative to tumors without copy number gain. Moreover, PTK7 is significantly upregulated from localized to advanced-stage type 2 PRCC and is linked to cancer cell invasion. In conclusion, DNA methylation markers that differentiate between localized and advanced-stage type 2 PRCC may serve as useful markers for disease staging or outcome, while PTK7 copy gain represents a potential treatment target for advanced-stage type 2 PRCC. Stepwise methylation changes and copy number gain also associate with disease stage in PRCC patients.
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