Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Array-based comparative genomic hybridization (aCGH) analysis of human hepatocarcinomas of different histological grades and tumor-adjacent non-tumorous liver tissues

ABSTRACT: Human hepatocarcinomas (HCCs) of different histological grades and tumour-adjacent non-neoplastic liver tissues (FFPE samples of surgical specimens) were analysed by array-based comparative genomic hybridization (aCGH) versus human male genomic DNA to identify high-frequency chromosomal aberrations in the tumors and initial chromosomal imbalances in the tumor-adjacent non-neoplastic liver tissues.

ORGANISM(S): Homo sapiens

SUBMITTER: Tatiana Meier

PROVIDER: E-MTAB-8886 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene networks and transcriptional regulators associated with liver cancer development and progression.

Meier Tatiana T Timm Max M Montani Matteo M Wilkens Ludwig L

BMC medical genomics 20210204 1

<h4>Background</h4>Treatment options for hepatocellular carcinoma (HCC) are limited, and overall survival is poor. Despite the high frequency of this malignoma, its basic disease mechanisms are poorly understood. Therefore, the aim of this study was to use different methodological approaches and combine the results to improve our knowledge on the development and progression of HCC.<h4>Methods</h4>Twenty-three HCC samples were characterized by histological, morphometric and cytogenetic analyses, ...[more]

PMID: 33541355

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Project description:Background: CrohnM-bM-^@M-^Ys disease is presently an incurable inflammatory bowel disease. Fistulae are extensions of the intestinal tract that may form connections with other organs. These are a common complication of CrohnM-bM-^@M-^Ys disease affecting up to 50% of patients with the most common including perianal and rectovaginal fistulae. The dysregulated growth observed in fistulae shares several major characteristics seen in the development of tumours. These similarities include epithelial-to-mesenchymal transition (EMT), invasive cell growth, increased extracellular matrix production and remodelling, up-regulated local expression of growth factors such as IGF-1 and the down-regulation of apoptosis pathways. Although several susceptibility loci have been described within CrohnM-bM-^@M-^Ys disease there is no individual gene or mutation that identifies susceptibility or the subsequent formation of fistulae within all people. Copy-number variation (CNV) is one mechanism that may explain much of this genetic complexity. CNV may be caused by a variety of mechanisms such as cycles of chromosomal breakage/fusion/bridging that are typical within chronically inflamed tissue. Interestingly CNV shows locus-specific mutation rates between individuals higher than that of SNPs and has been associated with complex Mendelian traits including disease susceptibility. In this current study we performed array comparative genomic hybridisation (aCGH) analysis of active fistulae resected from patients as part of a previous surgical intervention. As the control for comparison we employed tissue taken from the same patient within the same surgery at an uninvolved site of the gastrointestinal tract. This matched control was employed to better investigate CNV specific to the fistula tissue of each individual avoiding complications associated with the large number of CNV present within the healthy population. Major question addressed by the work: What are the differences in genetic copy-number within localised intestinal fistula tissue of individuals with CrohnM-bM-^@M-^Ys disease compared to healthy intestinal tissue from the same individual? Samples were selected from patients presenting with CrohnM-bM-^@M-^Ys Disease fistulae at Eastern Health Department of Gastroenterology and Hepatology (Arnold Street, Box Hill, Victoria, Australia). The 8 samples used in this study were formalin-fixed paraffin-embedded (FFPE) specimens following a surgical intervention to remove fistula tissue. To focus on changes within the individual patient we used tissue taken from the same surgery at an uninvolved region of the intestine as the matched control for CNV analysis.

Dataset Information

Array-based comparative genomic hybridization (aCGH) analysis of human hepatocarcinomas of different histological grades and tumor-adjacent non-tumorous liver tissues

Publications

Gene networks and transcriptional regulators associated with liver cancer development and progression.

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