Project description:We investigate the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation using paired tumour and normal samples from colorectal cancer patients undergoing colonic resection.
| E-MEXP-3715 | biostudies-arrayexpress
Project description:16 paired samples of colorectal cancer patients
Project description:Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases per year. Overall, prognosis of CRC largely depends on the disease stage and metastatic status. As precision oncology for patients with CRC continues to improve, this study aimed to integrate genomic, transcriptomic, and proteomic analyses to identify significant differences in expression during CRC progression using a unique set of paired patient samples while considering tumour heterogeneity.We analysed fresh-frozen tissue samples prepared under strict cryogenic conditions of matched healthy colon mucosa, colorectal carcinoma, and liver metastasis from the same patients. Somatic mutations of known cancer-related genes were analysed using Illumina's TruSeq Amplicon Cancer Panel; the transcriptome was assessed comprehensively using Clariom D microarrays. The global proteome was evaluated by liquid chromatography-coupled mass spectrometry (LC‒MS/MS) and validated by two-dimensional difference in-gel electrophoresis. Subsequent unsupervised principal component clustering, statistical comparisons, and gene set enrichment analyses were calculated based on differential expression results.Although panomics revealed low RNA and protein expression of CA1, CLCA1, MATN2, AHCYL2, and FCGBP in malignant tissues compared to healthy colon mucosa, no differentially expressed RNA or protein targets were detected between tumour and metastatic tissues. Subsequent intra-patient comparisons revealed highly specific expression differences (e.g., SRSF3, OLFM4, and CEACAM5) associated with patient-specific transcriptomes and proteomes.Our research results highlight the importance of inter- and intra-tumour heterogeneity as well as individual, patient-paired evaluations for clinical studies. In addition to changes among groups reflecting CRC progression, we identified significant expression differences between normal colon mucosa, primary tumour, and liver metastasis samples from individuals, which might accelerate implementation of precision oncology in the future.
Project description:Genome-wide DNA methylation of colorectal cancer patients with lymph node metastases showed global loss of DNA methylation in CG-poor, non-CpG island (CGI) regions. Overall CGI methylation was increased in tumour samples. Differential methylation analysis of CGIs identified 60 putative biomarkers, with >20% increase in DNA methylation in both primary tumour and metastasis samples compared to normal adjacent tissue.
Project description:Genomic DNA samples were extracted from microdissected colorectal tumour tissue and then compared against normal DNA extracted from the peripheral blood from the same patients.
Project description:DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.
Project description:The main objective of the study was to identify potential diagnostic and follow up markers along with therapeutic targets for breast cancer. We performed gene expression studies using the microarray technology on 65 samples including 41 breast tumours [24 early stage, 17 locally advanced, 18 adjacent normal tissue [paired normal] and 6 apparently normal from breasts which had been operated for non-malignant conditions. All the samples had frozen section done – tumours needed to have 70% or more tumour cells; paired normal and apparently normal had to be morphologically normal with no tumour cells.
Project description:Gene expression profiles of various isolated normal and tumour cell types The goal was to identify genes differentially expressed in different cell types between normal and tumour tissues. To this end, different cell types (endothelial cells, macrophages and epithelial cells) were isolated from non-paired primary normal colon tissues and colorectal carcinomas and subsequently RNA was isolated. Endothelial cells and epithelial cells were isolated using facs-sorting, whereas macrophages were isolated by means of plastic adherence. For comparison RNA was also isolated from non-paired whole normal colon tissue and whole tumour colorectal carcinomas (so called “bulk”). RNA was processed and hybridized onto Agilent microarrays. Primary goal was to establish an endothelial cell genetic profile. For this we compared the gene expression of tumour endothelial cells (TECs) with normal endothelial cells (NECs).