Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer [Array]
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PROVIDER: PRJNA1073559 | ENA |
REPOSITORIES: ENA
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Project description:Cancer-associated fibroblasts (CAFs) are critical components of the tumor microenvironment. Several studies demonstrated molecular differences between CAFs and normal tissue-associated fibroblasts (NAFs). In this study, we isolated CAFs and NAFs from liver tumors and analyzed their DNA methylation profiles. A subset of the CAFs exhibited aberrant DNA methylation, which was also reflected on gene expression level. The DNA methylation at liver-CAF-specific CG dinucleotides (CpGs) was associated with survival in liver cancer data. An integrative analysis with public datasets of CAF versus NAF in different cancer types, including lung, prostate, esophagus, and gastric cancer, revealed overlapping epigenetic aberrations. CpGs with common aberrations in DNA methylation included cg09809672 (EDARADD), cg07134930 (HDAC4), and cg05935904 (intergenic). Aberrant DNA methylation at these sites was associated with prognosis in several cancer types. Thus, activation of CAFs by the tumor environment is associated with characteristic epigenetic modifications that could be used as biomarkers for disease stratification.
2025-02-14 | GSE255123 | GEO
Project description:Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer [RNA-seq]
| PRJNA1073556 | ENA
Project description:Cancer-associated fibroblasts (CAFs) are critical components of the tumor microenvironment. Several studies demonstrated molecular differences between CAFs and normal tissue-associated fibroblasts (NAFs). In this study, we isolated CAFs and NAFs from liver tumors and analyzed their DNA methylation profiles. A subset of the CAFs exhibited aberrant DNA methylation, which was also reflected on gene expression level. The DNA methylation at liver-CAF-specific CG dinucleotides (CpGs) was associated with survival in liver cancer data. An integrative analysis with public datasets of CAF versus NAF in different cancer types, including lung, prostate, esophagus, and gastric cancer, revealed overlapping epigenetic aberrations. CpGs with common aberrations in DNA methylation included cg09809672 (EDARADD), cg07134930 (HDAC4), and cg05935904 (intergenic). Aberrant DNA methylation at these sites was associated with prognosis in several cancer types. Thus, activation of CAFs by the tumor environment is associated with characteristic epigenetic modifications that could be used as biomarkers for disease stratification.
2025-02-14 | GSE255122 | GEO
Project description:BackgroundCancer-associated fibroblasts (CAFs) are essential components of the tumor microenvironment and play a critical role in cancer progression. Numerous studies have identified significant molecular differences between CAFs and normal tissue-associated fibroblasts (NAFs). In this study, we isolated CAFs and NAFs from liver tumors and conducted a comprehensive analysis of their DNA methylation profiles, integrating our finding with data from studies on other cancer types.ResultsOur analysis revealed that several CAF samples exhibited aberrant DNA methylation patterns, which corresponded with altered gene expression levels. Notably, DNA methylation at liver CAF-specific CpG sites was linked to survival outcomes in liver cancer datasets. An integrative analysis using publicly available datasets from various cancer types, including lung, prostate, esophageal, and gastric cancers, uncovered common epigenetic abnormalities across these cancers. Among the consistently altered CpGs were cg09809672 (EDARADD), cg07134930 (HDAC4), and cg05935904 (intergenic). These methylation changes were associated with prognosis across multiple cancer types.ConclusionThe activation of CAFs by the tumor microenvironment seems to be associated with distinct epigenetic modifications. Remarkably, similar genomic regions tend to undergo hypomethylation in CAFs across different studies and cancer types. Our findings suggest that CAF-associated DNA methylation changes hold potential as prognostic biomarkers. However, further research and validation are necessary to develop and apply such signatures in a clinical setting.
| S-EPMC11580436 | biostudies-literature
Project description:The goal of this study was to map DNaseI sensitivity and DNaseI hypersensitive sites over the ENCODE regions in multiple human cell types (GM06990, CACO2, HepG2). Keywords: DNase/Array
2007-06-22 | GSE8177 | GEO
Project description:Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other. We therefore hypothesized that these colon cDMRs might also be cDMRs for other cancer types. For colon, lung, breast, thyroid, and Wilms tumors, we show stochastic variation in methylation within each tumor type, but involving the same loci across tumor types, with intermediate values of variation for premalignant adenomas. Seeking to increase the precision of DNA methylation measurements over our previous tiling array-based approach, termed CHARM (Comprehensive High-throughput Array for Relative Methylation), we designed a custom nucleotide-specific bead array on the Illumina GoldenGate platform to analyze 151 colon cDMRs from Irizarry et al. (PMID 19151715). The resulting 384 probes covered 139 regions, with 1-7 probes per region. We studied 290 samples, including cancers from colon (10), lung (24), breast (27), thyroid (36), and kidney (Wilms) (25), with matched normal tissues to 111 of these 122 cancers, along with 30 colon premalignant adenomas, 18 normal colon, and 9 normal breast samples.
2011-06-01 | E-GEOD-29505 | biostudies-arrayexpress
Project description:A powerful way to discover key genes playing causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. We have reported high-resolution analyses of somatic copy-number alterations (SCNAs) from 3131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across multiple cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several candidate genes and families are enriched among these regions of focal SCNA, including members of the BCL2 family of apoptosis regulators and the NF-κΒ pathway. We show that cancer cells harboring amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend upon expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in multiple cancer types.
2010-02-18 | GSE19399 | GEO
Project description:In vitro methylation studies in multiple human cell types [HumanMethylation450 array]
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Project description:In vitro methylation studies in multiple human cell types [HumanMethylation850 array]
| PRJNA811635 | ENA
Project description:Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other. We therefore hypothesized that these colon cDMRs might also be cDMRs for other cancer types. For colon, lung, breast, thyroid, and Wilms tumors, we show stochastic variation in methylation within each tumor type, but involving the same loci across tumor types, with intermediate values of variation for premalignant adenomas.
2011-06-01 | GSE29505 | GEO