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Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium Methylation450K)

ABSTRACT: Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium Methylation450K)

PROVIDER: PRJNA900237 | ENA |

REPOSITORIES: ENA

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Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium MethylationEPIC)

Project description:Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium MethylationEPIC)

| PRJNA900238 | ENA

Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium MethylationEPIC)

Project description:Comprehensive DNA methylation analysis of each histological LUAD subtype. Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across 850,000 CpG sites. Samples included 4 Micropapillary subtype, 5 Acinar subtype, 5 Solid subype.

2023-09-11 | GSE217731 | GEO

Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium Methylation450K)

Project description:Comprehensive DNA methylation analysis of each histological LUAD subtype. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 6 Micropapillary subtype, 5 Papillary subtype, 5 Lepidic subype and 3 normal lung tissues.

2023-09-11 | GSE217732 | GEO

Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma

Project description:Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma

| PRJNA900234 | ENA

Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma.

Project description:Lung adenocarcinoma is classified morphologically into five histological subtypes according to the WHO classification. While each histological subtype correlates with a distinct prognosis, the molecular basis has not been fully elucidated. Here we conducted DNA methylation analysis of 30 lung adenocarcinoma cases annotated with the predominant histological subtypes and three normal lung cases using the Infinium BeadChip. Unsupervised hierarchical clustering analysis revealed three subgroups with different methylation levels: high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME). Micropapillary pattern (MPP)-predominant cases and those with MPP components were significantly enriched in HME (p = 0.02 and p = 0.03, respectively). HME cases showed a significantly poor prognosis for recurrence-free survival (p < 0.001) and overall survival (p = 0.006). We identified 365 HME marker genes specifically hypermethylated in HME cases with enrichment of "cell morphogenesis" related genes; 305 IME marker genes hypermethylated in HME and IME, but not in LME, with enrichment "embryonic organ morphogenesis"-related genes; 257 Common marker genes hypermethylated commonly in all cancer cases, with enrichment of "regionalization"-related genes. We extracted surrogate markers for each epigenotype and designed pyrosequencing primers for five HME markers (TCERG1L, CXCL12, FAM181B, HOXA11, GAD2), three IME markers (TBX18, ZNF154, NWD2) and three Common markers (SCT, GJD2, BARHL2). DNA methylation profiling using Infinium data was validated by pyrosequencing, and HME cases defined by pyrosequencing results also showed the worse recurrence-free survival. In conclusion, lung adenocarcinomas are stratified into subtypes with distinct DNA methylation levels, and the high-methylation subtype correlated with MPP-predominant cases and those with MPP components and showed a poor prognosis.

| S-EPMC10323093 | biostudies-literature

Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-09-11 | GSE217733 | GEO

DNA Methylation Profile in Human Cord Blood Mononuclear Leukocytes from Term Neonates: Effects of Histological Chorioamnionitis

Project description:Genome wide DNA methylation profiling of human cord blood mononuclear leokocytes (CBML) from neonates exposed to histological chorioamnionitis (HCA) compared to healthy neonates. The Infinium HumanMethylationEPIC BeadChip array was used to obtain DNA methylation profiles across 866,836 CpGs in five HCA and five control samples.

2020-07-31 | GSE153668 | GEO

Histological heterogeneity in primary prostate

Project description:Histological heterogeneity in primary prostate

| PRJNA1028110 | ENA

SPOP mutations derived from prostate cancer establish a DNA hypermethylation epigenome through stabilizing GLP histone methyltransferase [methylation array]

Project description:Abnormal DNA methylation is one of the major factors driving oncogenesis and therapy resistance in cancer. The CULLIN3-RBX1 E3 ubiquitin ligase adaptor gene SPOP is the most frequently mutated gene in primary prostate cancers (PCa). SPOP-mutated prostate tumors strikingly associate with strongly elevated levels of genome-wide DNA hypermethylation, although the underlying mechanism remains elusive.We use Illumina Infinium MethylationEPIC BeadChip to depict DNA methylation in control and SPOP F102C stabily expressed 22Rv1 cells. Genomic DNA of cells are extracted and quantified by PicoGreen, followed by Illumina Infinium arrays. We find that SPOP mutant expression increases not only the overall cellular level of DNA methylation, but also specifically at loci of a subset of tumor suppressor genes (TSG) including FOXO3 and NDRG1, and this effect is mediated by GLP/G9a binding with DNMT proteins.These findings reveal a previously uncharacterized mechanism by which SPOP mutations promote DNA hypermethylation through stabilization GLP as a chromatin recruiter of DNMT. Our results also suggest that targeting DNA hypermethylation is a viable strategy for effective management of SPOP mutated PCa.

2021-08-01 | GSE179234 | GEO

MiRNA profiling of meningioma of different grades and histological subtypes

Project description:Although meningiomas are one of the most frequent primary intracranial tumors, there are only a few studies dealing with gene regulation processes in meningiomas. MiRNAs are key regulators of gene expression and regulation and miRNA profiles offer themselves as biomarkers for cancer development and progression. To investigate the role of miRNAs during meningioma growth and progression, we compared expression of 1205 miRNAs in 55 meningioma samples of different tumor grades and histological subtypes. We were able to classify histological subtypes in WHO grade I meningiomas with up to 97% accuracy (meningothelial versus fibroblastic) and different WHO grades with up to 93% accuracy (WHO I versus WHO III). We found significant downregulation of miRNAs on chromosome 1p36 and within two large miRNA clusters on 14q32 in high grade meningiomas, two regions that are yet associated with meningioma progression. We also identified several miRNAs associated with epithelial to mesenchymal transition differentially expressed in meningothelial meningioma compared to fibroblastic meningioma. Combined, our data show that meningiomas of different WHO grades and histological subtypes show a specific miRNA expression profile. Some individual miRNAs can also serve as potential biomarkers for meningioma progression.

2014-12-31 | GSE50641 | GEO

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