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Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (RNA-seq)

ABSTRACT: Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (RNA-seq)

PROVIDER: PRJNA801686 | ENA |

REPOSITORIES: ENA

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Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified

Project description:Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified

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Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified

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

2022-09-06 | GSE199748 | GEO

Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (EPIC850)

Project description:genome-wide profiling of DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls.

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Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (RNA-seq)

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Potential methylation-regulated genes and pathways in hepatocellular neoplasm, not otherwise specified.

Project description:Background and aimsThe molecular basis of hepatocellular neoplasm, not otherwise specified (HCN-NOS) is unknown. We aimed to identify gene expression patterns, potential methylation-regulated genes and pathways that characterize the tumor, and its possible relationship to hepatoblastoma and hepatocellular carcinoma (HCC).Approach & resultsParallel genome-wide profiling of gene expression (RNAseq) and DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls. 2530 significantly differentially expressed genes (DEGs) were identified between tumors and controls. Many of these DEGs were associated with hepatoblastoma and/or HCC. Analysis Match in Ingenuity Pathway Analysis determined that the gene expression profile of HCN-NOS was unique but significantly similar to that of both hepatoblastoma and HCC. A total of 27,195 CpG sites (CpGs) were significantly differentially methylated (DM) between tumors and controls, with a global hypomethylation pattern and predominant CpG island hypermethylation in promotor regions. Aberrant DNA methylation predominated in Developmental Process and Molecular Function Regulator pathways. Embryonic stem cell pathways were significantly enriched. In total, 1055 aberrantly methylated (at CpGs) and differentially expressed genes were identified, including 25 upstream regulators and sixty-one potential CpG island methylation-regulated genes. Eight methylation-regulated genes (TCF3, MYBL2, SRC, HMGA2, PPARGC1A, SLC22A1, COL2A1 and MYCN) had highly consistent gene expression patterns and prognostic value in patients with HCC, based on comparison to publicly available datasets.ConclusionsHCN-NOS has a unique, stem-cell like gene expression and DNA methylation profile related to both hepatoblastoma and HCC but distinct therefrom. Further, 8 methylation-regulated genes associated with prognosis in HCC were identified.

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Identification of multiple subclones in Peripheral T-cell Lymphoma, Not Otherwise Specified with genomic aberrations

Project description:Genomic aberration profiles of Peripheral T-cell Lymphoma, Not Otherwise specified (clinical samples)

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Malignant Fibrous Histiocytoma - Pleomorphic Sarcoma, NOS -Gene expression, Histology and clinical course -A pilot study

Project description:This study was performed to identify gene expression differences in not otherwise specified soft tissue sarcomas (NOS, malignant fibrous histiocytomas) and correlate them to histological findings and the clinical course. RNA was isolated and differential gene expression was analysed by the microarray technique. We used microarrays to detail the global gene expression differences between primary soft tissue sarcoma samples, harvested intraoperatively. Keywords: response to chemotherapeutic agent

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