Project description:In total, 89 samples were collected from 89 patients with colorectal cancer (CRC), of which 66 patients had stage IV CRC. We sequenced the mRNAs purified from the formalin-fixed paraffin embedded (FFPE) blocks.
Project description:Here, we report the genomic-scale characterization of locally advanced colon cancer transcriptome. Paraffin embedded samples was used to asses differences between normal colon, primary colon tumor an lymph node metastasis.
Project description:Recent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex -omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed an innovative multi-objective optimisation method which effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. We have found 9 signatures of colorectal cancer prognosis comprising a total of 19 circulating microRNAs. The identified signatures predict the patients’ survival outcome and target pathways underlying colorectal cancer progression. The altered expression of the microRNAs within these signatures was confirmed in two independent public datasets of plasma and tumour samples of patients in early stage versus advanced colorectal cancer.
Project description:We thought the immediate effects of APC inactivation may represent unexplored therapeutic vulnerabilities in later stages of advanced colorectal adenocarcinoma. We performed transcriptome profiling of epithelial colon organoids immediately after APC inactivation and cross-referenced gene expression changes to the transcriptomes of several mouse models of colon cancer, including colon tumors in an inflammation-induced CRC model (AOM-DSS), a model of familial adenomatous polyposis (FAP, the Apcmin mouse), and an implantation-based model of metastatic adenocarcinoma using Apc/Trp53/KrasG12D/Smad4 quadruple-mutant tumor organoids15 (APKS tumoroids). Of the roughly 150 genes whose expression is acutely induced upon APC loss and remains elevated in these colon cancer models.
Project description:MicroRNAs (miRNAs) are small non-coding RNA molecules which function as negative gene regulators. The tissue expression profile of miRNAs shows great promise as a novel biomarker for diagnosis of cancer and other diseases. In addition, some recent reports have demonstrated that are present in human serum and plasma which could make them an ideal non-invasive biomarker for diagnosis of cancer. The aim of this study is to analyze the value/efficacy of the expression profile of plasma miRNAs in differentiating between patients with advanced adenomas and CRC and healthy individuals. The microRNA profiling study comprises serum plasmas from 20 Control, 21 colorectal cancer,20 advanced adenomas.The study also include some samples from patients after treatment.