Renal clear cell carcinoma (RCCC) is the most common subtype of kidney tumors, accounting for the majority of deaths from genitourinary cancers. Due to widespread use of ultrasound imaging, the majority of kidney tumors are detected at an early stage simultaneously resulting the increase of patient overtreatment. On the other hand, up to 30% of patients will develop the distant disease even after surgical tumor excision. Thus, there is a vital need for new, and non-invasive biomarkers providing valuable information about the disease presence, aggressiveness, and prognosis. The present study aimed at developing a gene-specific methylated DNA-based tool for the early non-invasive RCCC diagnosis and follow-up.
Genome-wide DNA methylation and gene expression profiling in 11 RCCC and paired non-cancerous renal tissues (NRT) was performed using Human DNA Methylation 1×244K and Gene Expression 8×60K Microarrays. Qualitative and quantitative methylation-specific PCR was applied for the validation of DNA methylation changes in 168 renal tissues and 307 urine samples.
Abundant changes in DNA methylation and gene expression were observed in RCCC. Deregulated genes were enriched among biological processes related to tumor development and progression and ten such protein-coding genes were selected for further DNA methylation analysis. Significantly higher methylation frequencies for all genes were found in RCCC tissues compared to NRT (17-60% vs. 0-11%). The best diagnostic performance was demonstrated for a panel of six genes showing 85% sensitivity and 96% specificity. Moreover, higher methylation levels of selected six genes were detected in the urine of RCCC cases as compared to controls and the highest diagnostic power (AUC=0.78) was calculated for the panel of ZNF677 & PCDH8 with 78% sensitivity and 69% specificity. Moreover, the methylated status of ZNF677 & PCDH8 was identified as an independent highly prognostic tool for RCCC patients' overall survival with HR of 12.5.
To sum up, during this study a novel non-invasive and highly promising DNA methylation-based tool was developed for the detection of RCCC and patients‘ follow-up, which after further validation steps has a high potential for translation into clinical practice.
The authors.
This work was funded by the 2014-2020 European Union Structural Funds according to the activity “Intelligence. Joint science-business projects” grant No. J05-LVPA-K-04–0029.
All authors have declared no conflicts of interest.