Unknown,Transcriptomics,Genomics,Proteomics

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Methylation analysis of 12 corresponding pairs of TECs and NECs isolated from human CRC patients with different prognostic TMEs

ABSTRACT: Methylation analysis of 12 corresponding pairs of tumor endothelial cells (TECs) and normal endothelial cells (NECs) isolated from human colorectal carcinoma (CRC) patients with different prognostic tumor microenvironments (TMEs: Th1-TME vs Control-TME): High and low GBP-1 expression in the tumors detected by IHC was used to categorize the patient-derived cells into Th1-TME and Control-TME (compare Naschberger et al, J Clin Invest 2016 and Naschberger et al, Int J Cancer 2008). Isolation of the samples was done according to Naschberger et al, JoVE 2018. The analysis is paralleled by omics-analysis of the same cell cultures at the transcriptome (E-MTAB-10465) and genome level (E-MEXP-3993).

ORGANISM(S): Homo sapiens

SUBMITTER: Elisabeth Naschberger

PROVIDER: E-MTAB-10467 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In patients with severe kidney disease AVF are surgically placed in order to create good access for hemodialysis. In these dialysis patients the failure rates of AVF can be as high as 24% within 6 months after surgery, causing ineffective dialysis and necessitating additional clinical interventions. The pathological processes known to lead to AVF failure are beginning to be unravelled include the formation of venous neointimal hyperplasia (VNIH), thrombosis (Chang et al. PMID 16105066), and venous stenosis (Kanterman et al. PMID7892454, Tang et al. 1998), resulting in a reduced blood flow through the fistula. We established a rat model for AVF failure in human kidney dialysis patients. The characterization of this model has been previously described (Globerman et al. 2011, PubmedID:22002501). In this model the AVFs are surgically constructed in the right leg by connecting the superficial epigastric vein SEV to the common femoral artery (CFA), resulting in exposure of the SEV to arterial pressure with pulsatile and low resistant flow patterns (Globerman et al. 2011, PMID22002501). In the present study we utilized this AVF model in order to assess the effects of arterialized flow, with consequent pathological changes of the vessel wall due to surgical AVF instalment, on the transcriptome of endothelium from the SEV. Within the SEV these pathologies of the vessel wall include the formation of NIH in the main branch, and stenosis in the side branches. By employing this rat model we assessed the changes of the endothelial transcriptome in relation to these pathologies in order to gain mechanistic understanding of the potential roles of venous endothelium in AVF failure, as well as to identify potential biomarkers preceding AVF failure. AVF surgery was performed on N=6 rats, and 13-14 days after surgery the rats were sacrificed. AVFs were extracted from the rats, and microarray transcriptome analyses were performed on luminal endothelial cells that isolated from four different sites of the AVF by employing Laser Capture Microdissection (LCM). These sites included (i) N=5 AVF sections of the superficial epigastric vein (SEV) with neointimal hyperplasia (NIH), (ii) N=3 AVF sections of SEV side branches with luminal stenosis, (iii), N=6 sections of the SEV located distally from a ligation thereby omitting exposure to arterialized flow and consequently preventing the development of NIH or stenosis, and (iv) N=3 sections of the AVF common femoral artery without signs of NIH or stenosis.

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Methylation analysis of 12 corresponding pairs of TECs and NECs isolated from human CRC patients with different prognostic TMEs

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