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DNA methylation profiling reveals new potential subtype-specific gene markers for early-stage renal cell carcinoma in Caucasian population

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Quantitative Biology 2022年第1期10卷 79-93页

作者： Alvaro Filbert Liko Edward Ciputra nathaniel alvin sanjaya Priskila Cherisca Then aka David Agustriawan Department of Biomedicine School of Life SciencesIndonesia International Institute for Life SciencesJakarta 13210Indonesia Department of Bioinformatics School of Life SciencesIndonesia International Institute for Life SciencesJakarta 13210Indonesia

Background:Renal cell carcinoma(RCC)is among the top adult cancers worldwide,with a challenging management due to lack of early diagnosis,therapy resistance,and diverse molecular *** DNA methylation has been associated with RCC development due to transcription *** discovered potential DNA methylation-based biomarkers for stage I RCC in Caucasian population from The Cancer Genome Atlas(TCGA)***:Patients’clinical,methylation beta-value,and mRNA expression data were *** methylation and expression analysis were conducted to obtain differentially methylated CpG-gene *** correlated CpG-gene pairs between their expression and methylation levels were selected using Pearson’s correlation test and then screened for any recorded somatic *** biomarker capacities were analyzed’using the Kaplan-Meier and receiver operating characteristic analysis,followed by protein network and functional enrichment ***:We obtained differentially methylated CpGs in clear cell(KIRC)and papillary RCC(KIRP)but not chromophobe RCC(KICH).Six inversely correlated CpG-gene pairs with no reported cancer-associated mutations were *** values were found in ATXN1 and RFTN1 for KIRC,along with GRAMD1B and TM4SF19 for KIRP,while diagnostic values were found in VIM and RFTN1 for KIRC,along with TNFAIP6 and TM4SF19 for *** subtypes showed enrichment of immune and metabolism-related ***:We discovered novel potential DNA methylation-based prognostic and diagnostic markers for early-stage RCC in Caucasian *** by wet laboratory analysis and adjustments for confounding variables might be needed,considering our study limitation to specific race.

关键词： biomarker chromophobe renal cell carcinoma clear cell renal cell carcinoma DNA methylation papillary renal cell carcinoma TCGA

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