Assessing the clear cell Renal Cell Carcinoma (ccRCC) DNA-methylome by MethylCapSeq
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE33954 | GEO | 2017/04/04
SECONDARY ACCESSION(S): PRJNA150547
REPOSITORIES: GEO
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Project description:Clear cell renal cell carcinoma (ccRCC) is the most common adult renal cancer. Although the molecular characteristics of ccRCC are currently being studied, the biologically and clinically relevant ccRCC methylome remains to be elucidated. To explore the RCC hypermethylome we employed massive sequencing of methyl-binding protein enriched DNA and validated the biological relevance of the identified hypermethylated sites by pharmacological inhibition of DNA methylation. We identified four candidate tumor suppressor genes (GREM1, LAD1, NEFH, and NEURL) of which promoter CpG island hypermethylation was strongly predictive for ccRCC survival in two independent series (n=150 and n=185) of ccRCC primary samples. The four markers combined are strongly associated with risk for cancer-related death in the test series (HR 3.64, 95% CI 1.02-13.01) as well as, independently of other clinicopathological characteristics, in the validation series (HR 7.54, 95% CI 2.68-21.19) using Cox proportional hazard models. According to Harrell’s C statistics and the Akaike Information Criterion (AIC) the four marker panel provides the best predictive capacity with the best fit of the model as assessed for the tested markers. These results provide novel insights into the ccRCC hypermethylome and identify a strong methylation marker panel to potentially guide personalized ccRCC patient management. Preliminary to implementation of this marker panel into clinical practice, enrollment of these patients in a Phase-III trial to study adjuvant treatment efficacy is essential. 4 independant clear cell renal cancer cell lines were used before and after treatment with the DNA methylation inhibitor AZA or the HAZA inhibitor TSA.
2013-11-22 | E-GEOD-33916 | biostudies-arrayexpress
Project description:Clear cell renal cell carcinoma (ccRCC) is the most common adult renal cancer. Although the molecular characteristics of ccRCC are currently being studied, the biologically and clinically relevant ccRCC methylome remains to be elucidated. To explore the RCC hypermethylome we employed massive sequencing of methyl-binding protein enriched DNA and validated the biological relevance of the identified hypermethylated sites by pharmacological inhibition of DNA methylation. We identified four candidate tumor suppressor genes (GREM1, LAD1, NEFH, and NEURL) of which promoter CpG island hypermethylation was strongly predictive for ccRCC survival in two independent series (n=150 and n=185) of ccRCC primary samples. The four markers combined are strongly associated with risk for cancer-related death in the test series (HR 3.64, 95% CI 1.02-13.01) as well as, independently of other clinicopathological characteristics, in the validation series (HR 7.54, 95% CI 2.68-21.19) using Cox proportional hazard models. According to Harrell’s C statistics and the Akaike Information Criterion (AIC) the four marker panel provides the best predictive capacity with the best fit of the model as assessed for the tested markers. These results provide novel insights into the ccRCC hypermethylome and identify a strong methylation marker panel to potentially guide personalized ccRCC patient management. Preliminary to implementation of this marker panel into clinical practice, enrollment of these patients in a Phase-III trial to study adjuvant treatment efficacy is essential.
2013-11-22 | GSE33916 | GEO
Project description:Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. We analyzed frequent ccRCC-specific peptides by MS-based HLA ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate target genes with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from the Cancer Genome Atlas (TCGA KIRC, n=452), yielding 113 candidate genes. DNA methylation (TCGA KIRC, n=273), and somatic mutations (TCGA KIRC, n=392), as well as correlations with tumor metabolites (cohort 1, n=30) and immune-oncological markers (cohort 1, n=37) were analyzed to refine regulatory and functional involvements of candidates. Immunogenicity analysis identified candidate epitopes able to activate native CD8+ T cells. Functional analysis of EGLN3, a candidate with frequent ccRCC-specific immunogenic peptides, revealed possible tumor-promoting functions. Integration of HLA ligandomics, transcriptomics, genetic and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is now mandatory to expand the treatment landscape of ccRCC.
2020-04-03 | PXD017149 | Pride
Project description:To identify a therapeutic candidate target molecule for ccRCC, we analyzed the microRNA (miRNA) expression signatures in ccRCC clinical specimens. 9 matched pair (normal tissue and ccRCC tissue) plus 7 ccRCC tissue were analyzed for miRNA-microarray
2014-02-20 | E-GEOD-55138 | biostudies-arrayexpress
Project description:Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain–containing 2 (SETD2) has been identified as an important tumor suppressor gene in ccRCC. However, the role of SETD2 in tumorigenesis during the transition from PKD to ccRCC remains largely unexplored. Herein, we performed metabolomics, lipidomics, transcriptomics and proteomics with SETD2 loss induced PKD-ccRCC transition mouse model. To characterize biological responses triggered by SETD2 deletion during PKD-ccRCC transition at the protein level, we conducted global proteomics studies.
2023-10-31 | PXD038966 | Pride
Project description:Purpose: To establish pancreatic cancer-related aberrnat DNA methylation patterns, especially in CGI, CGI shore, orphan CGI and non-CGI promoter region and provide diagnosis or prognosis biomarker for pancreatic cancer dignosis or prognosis prediction Methods:MBD methylCap/seq was carried out to screen differentially methylated CpG islands in 3 libraries which includes 1 pancreatic cancer mix library, 1 adjacent normal tissue mix library and 1 normal pancreas tissue. MSP and multiplex-BSP validation was performed in independent tumor and adjacent tissues. Results: 66807 Hypermethylation DMR and 46815 Hypomethylation DMR were discovered in whole pancreatic cancer genome. 5280 Hypermethylation and 3488 Hypomethylation CpGI region were related gene promoter or gene body. Gene expression of 10 aberrant DMR were related with their methylation status validated by MSRE-qPCR and RT-PCR in 5-aza’ treated pancreatic cancer cell line. 40 DMR were validated in pancreatic cancer and adjacent tissues with MSP and gene ontology analysis showed seven of them were related with regulation of transcription(GO:0006355) which included DLX4,ELAVL2,IRX1,PITX2,SIM2,TBX5,TFAP2C. Conclusions: Methylcap-seq identified hundreds of DMR genes and regions which might involve with gene expression regulation and could be used as biological markers of pancreatic cancer therapy target or diagnosis.
2014-07-08 | GSE54854 | GEO
Project description:To identify a therapeutic candidate target molecule for ccRCC, we analyzed the microRNA (miRNA) expression signatures in ccRCC clinical specimens.
2014-02-20 | GSE55138 | GEO
Project description:Renal cell carcinoma (RCC) is the most common and lethal cancer of the adult kidney. Its incidence is increasing and outcomes remain poor. Accurate discrimination of RCC patients with poor prognosis was very important for the appropriate and effective patient management. ccRCC originated from dysregulation of different gene expression. To screen novel prognosis markers, a dysregulated mRNA expression profile was identified by microarray in some pairs of different stages ccRCC.
2017-12-31 | GSE100666 | GEO
Project description:Renal cell carcinoma (RCC), particularly clear cell RCC (ccRCC), is the most common type of kidney tumors characterized by the highest mortality rate of the genitourinary cancers. Lack of symptoms leads to late detection of the disease using conventional imagining procedures. There is an urgent need for new diagnostic biomarkers with the potential for early detection and prediction of high risk of progression. In the present study, based on microarray profiling of DNA methylation in 11 pairs of ccRCC and noncancerous renal tissues (NRT), the methylation at regulatory regions of six putative ccRCC biomarkers was further analyzed in 123 ccRCC and 45 NRT samples by means of methylation specific PCR (MSP). Thereafter, the quantitative MSP was applied for the methylation analysis in the urine samples of 123 ccRCC patients and 93 asymptomatic controls (ASC). The comparison of ccRCC and NRT samples revealed significant methylation differences in 1319 genes, of which 191 were hypermethylated and 1128 were hypomethylated. DNA methylation of selected genes were validated by means of MSP and significantly higher methylation frequencies for all genes was found in ccRCC tissues compared to NRT (33-60% vs. 0-11%). Methylated status of at least one gene was significantly related with various adverse clinical-pathological parameters of the patients, including larger tumor size, higher tumor pathological stage, grade, intravascular and fat invasion as welll as tumor necrosis. The multivariate Cox regression model revealed the methylation in a panel of selected three genes as independent prognostic biomarker of ccRCC. Moreover, five genes were characterised by higher methylation intensity in the urine samples of ccRCC patients, as compared to ASC, and various combination of these biomarkers revealed moderate-to-high sensitivity and specificity values for the diagnosis of ccRCC.
2021-02-15 | GSE166734 | GEO