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

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

PROVIDER: PRJNA821432 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17809038_1.fastq.gz	Fastqsanger.gz
	SRR17809038_2.fastq.gz	Fastqsanger.gz
	SRR17809039_1.fastq.gz	Fastqsanger.gz
	SRR17809039_2.fastq.gz	Fastqsanger.gz
	SRR17809040_1.fastq.gz	Fastqsanger.gz

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

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

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Malignant hepatocellular carcinoma cells enrich translation regulatory proteins in exosomes

Project description:It is known that exosomes (endosome derived vesicles) play important roles in the formation of the tumor microenvironment. Hepatocellular carcinoma (HCC) is a highly malignant cancer, whose malignancy is largely influenced by the tumor microenvironment. The possible role and the specific content of the HCC derived exosomes are however largely unknown. We performed super-SILAC-based mass spectrometry (MS) analyses to interrogate the differential proteins in the exosome of three human HCC cell lines, MHCC97H, MHCCLM3 and Hep3B cells. Exosomal proteins were systematically compared with multi-omics strategies, considering both proteomics and translatomics. With stringent data quality control (quantified unique peptides ≥ 2, FDR ≤ 0.01 at both protein and peptide level), 1907 exosomal proteins were confidently identified from the three HCC cell lines, out of which 469 and 443 exosomal proteins significantly altered in the highly malignant cell lines (MHCC97H/Hep3B and MHCCLM3/Hep3B), respectively. ClueGo and IPA analyses on the differentially expressed proteins (DEPs) revealed that translation and ubiquitination biological processes pathways were significantly more encapsulated in the exosome of higher malignant cell lines. We further observed significantly negative correlation of exosomal protein to cellular protein and translating mRNA in terms of relative abundances comparing the higher malignant cell lines with the low malignant cell line. The negatively correlated genes are also translation regulation-centric. In conclusion, we demonstrated that the exosomal enrichment of translation regulatory proteins is related to the malignant level of HCC cells.

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

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