Promoter methylation of DNA damage repair (DDR) genes in human tumor entities: RBBP8/CtIP is almost exclusively methylated in bladder cancer

Abstract

BackgroundGenome-wide studies identified pan-cancer genes and shared biological networks affected by epigenetic dysregulation among diverse tumor entities. Here, we systematically screened for hypermethylation of DNA damage repair (DDR) genes in a comprehensive candidate-approach and exemplarily identify and validate candidate DDR genes as targets of epigenetic inactivation unique to bladder cancer (BLCA), which may serve as non-invasive biomarkers.MethodsGenome-wide DNA methylation datasets (2755 CpG probes of n = 7819 tumor and n = 659 normal samples) of the TCGA network covering 32 tumor entities were analyzed in silico for 177 DDR genes. Genes of interest were defined as differentially methylated between normal and cancerous tissues proximal to transcription start sites. The lead candidate gene was validated by methylation-specific PCR (MSP) and/or bisulfite-pyrosequencing in different human cell lines (n = 36), in primary BLCA tissues (n = 43), and in voided urine samples (n = 74) of BLCA patients. Urines from healthy donors and patients with urological benign and malignant diseases were included as controls (n = 78). mRNA expression was determined using qRT-PCR in vitro before (n = 5) and after decitabine treatment (n = 2). Protein expression was assessed by immunohistochemistry (n = 42). R 3.2.0. was used for statistical data acquisition and SPSS 21.0 for statistical analysis.ResultsOverall, 39 DDR genes were hypermethylated in human cancers. Most exclusively and frequently methylated (37%) in primary BLCA was RBBP8, encoding endonuclease CtIP. RBBP8 hypermethylation predicted longer overall survival (OS) and was found in 2/4 bladder cancer cell lines but not in any of 33 cancer cell lines from entities with another origin like prostate. RBBP8 methylation was inversely correlated with RBBP8 mRNA and nuclear protein expression while RBBP8 was re-expressed after in vitro demethylation. RBBP8 methylation was associated with histological grade in primary BLCA and urine samples. RBBP8 methylation was detectable in urine samples of bladder cancer patients achieving a sensitivity of 52%, at 91% specificity.ConclusionsRBBP8 was identified as almost exclusively hypermethylated in BLCA. RBBP8/CtIP has a proven role in homologous recombination-mediated DNA double-strand break repair known to sensitize cancer cells for PARP1 inhibitors. Since RBBP8 methylation was detectable in urines, it may be a complementary marker of high specificity in urine for BLCA detection.Electronic supplementary materialThe online version of this article (10.1186/s13148-018-0447-6) contains supplementary material, which is available to authorized users.

Integrative Bioinformatics Approaches to Map Potential Novel Genes and Pathways Involved in Ovarian Cancer

“…Soria-Bretones et al (2013) observed decreased or no expression of RBBP8 in paraffinembedded breast cancer biopsy tissues from high-grade breast cancer and nodal metastases that were acquired during tumor removal surgery (Soria-Bretones et al, 2013). The research group led by Rose et al suggested that RBBP8 was significantly hypermethylated in bladder cancer (BLCA) and was associated with more prolonged overall survival, and they indicated that it may be used as a complementary marker for the detection of BLCA in urine (Mijnes et al, 2018). Miao et al (2019) reported that the downregulation of the long noncoding RNA (lncRNA) cancer susceptibility candidate 2 (CASC2, enhanced tumor development, increased miR-18a-5p levels, and reduced the expression of RBBP8 in nasopharyngeal carcinoma (NPC).…”

ITIH5 and ECRG4 DNA Methylation Biomarker Test (EI-BLA) for Urine-Based Non-Invasive Detection of Bladder Cancer

“…Infinium HumanMethylation450 BeadChip data (level 2) and RNASeqV2 data (level 3) of the tumor and normal tissue samples were obtained from the TCGA data portal [30] and analyzed, as previously described [43].…”

“…OS was measured from surgery until death and it was censored for patients alive without evidence of death at the last follow-up date. The receiver operating characteristics (ROC) curves and AUC values were calculated to assess the biomarker performance of ECRG4 and ITIH5 methylation similar to our previous report [43]. The ROC curves of combined biomarkers were based on the binary logistic regression model using the probability as test variable.…”

Prognosis value of RBBP8 expression in plasma cell myeloma

“…Investigation found RBBP8 genes was associated with sporadic brain arteriovenous malformations [19]. Advanced invasive bladder cancer was associated with the deletion of nuclear RBBP8 protein [20]. Deletion of the RBBP8 gene was associated with significantly worse prognosis in ovarian cancer [21].…”