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The gene expression profiling array of mRNAs and LncRNA between portal vein tumor thrombus tissues and paired tumor tissues in hapatocellular carcinoma

ABSTRACT: Investigation of whole genome gene expression level changes of mRNAs and LncRNAs in portal vein tumor thrombus tissues and paired tumor tissues in hapatocellular carcinoma. The different expression genes were further analyzed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE43630 | GEO | 2013/01/19

SECONDARY ACCESSION(S): PRJNA186865

REPOSITORIES: GEO

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The gene expression profiling array of mRNAs between portal vein tumor thrombus tissues and paired tumor tissues in hapatocellular carcinoma.

Project description:Investigation of whole genome gene expression level changes of mRNAs in portal vein tumor thrombus tissues and paired tumor tissues in hapatocellular carcinoma. The different expression genes were further analyzed. The human mRNA microarray analysis of the 6 samples (3 portal vein tumor thrombus tissues and 3 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples. .

2013-01-19 | E-GEOD-43630 | biostudies-arrayexpress

The gene expression profiling array of mRNAs between portal vein tumor thrombus tissues and paired tumor tissues in hapatocellular carcinoma.

Project description: Not available

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CNV analysis of hepatocellular carcinoma with portal vein tumor thrombosis

Project description:Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular alterations of these metastatic HCCs is important for understanding the molecular mechanisms during HCC progression and metastasis. Previous genomic studies mainly focus on single molecular layer, such as gene expressions or exonic mutations. In this study, we systematically examined the copy number variation (CNV), DNA methylation, miRNA and transcriptome of matched adjacent normal tissues, primary tumors and PVTTs from 19 HCC patients. Based on the integrative multi-omics profiles, we established the molecular landscape of the metastatic HCCs and identified a set of the recurrent genomic alterations and candidate driver genes.

2017-02-17 | GSE77275 | GEO

RNA-seq analysis of hepatocellular carcinoma with portal vein tumor thrombosis

2017-02-17 | GSE77509 | GEO

DNA methylation analysis of hepatocellular carcinoma with portal vein tumor thrombosis

2017-02-17 | GSE77269 | GEO

miRNA-seq analysis of hepatocellular carcinoma with portal vein tumor thrombosis

2017-02-17 | GSE76903 | GEO

RNA sequencing for cancer tissues and adjacent tissues of third-stage rectal cancer patients with and without blood vascular thrombus

Project description:The Agilent Human Gene Expression(8*60K，Design ID：039494) was used in this experiment of sequencing of the 12 samples. A total of 12 tissues were sequenced from adjacent and cancerous tissues of 6 patients with TNM stage 3 colon cancer. Three patients had cancer thrombus and three patients had no cancer thrombus.

2021-02-23 | GSE127069 | GEO

The molecular landscape of hepatocellular carcinoma with portal vein tumor thrombosis

Project description:The molecular landscape of hepatocellular carcinoma with portal vein tumor thrombosis

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Is multidisciplinary treatment effective for hepatocellular carcinoma with portal vein tumor thrombus?

Project description: Not available

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Transarterial chemoembolization for hepatocellular carcinoma with portal vein tumor thrombus: a meta-analysis.

Project description:BackgroundAlthough transarterial chemoembolization (TACE) has been used extensively for advanced hepatocellular carcinoma (HCC) with portal vein tumor thrombus (PVTT), no consensus has been reached and an evidence base for practice is lacking. This meta-analysis evaluated the efficacy and safety of TACE for treatment of HCC with PVTT.MethodsOvid Medline, EMBASE, Web of Knowledge, and Cochrane library databases were searched up to August 2012 for controlled trials assessing TACE in patients with PVTT. Data concerning the study design, characteristics of trials, and outcomes were extracted. Hazard ratio (HR) and 95% confidence interval (CI) were calculated using random effects models.ResultsEight controlled trials involving 1601 HCC patients were included. TACE significantly improved the 6-month (HR, 0.41; 95% CI: 0.32-0.53; z, 6.28; p = 0.000) and 1-year (HR, 0.44; 95% CI: 0.34-0.57; z, 6.22; p = 0.000) overall survival of patients with PVTT compared with conservative treatment. Subgroup analyses showed that TACE was significantly effective in HCC patients whether with main portal vein (MPV) obstruction or with segmental PVTT. Fatal complications were rare, even in patients with MPV obstruction. Temporary liver decompensation and postembolization syndrome occurred frequently. However, they could be treated successfully with conservative treatment.ConclusionsTACE, as a safe treatment, has potential for incurring a survival benefit for advanced HCC with PVTT, even with MPV obstruction. Further large randomized controlled trials may be needed to confirm this result.

| S-EPMC3626696 | biostudies-literature

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