Project description:Targeted proteomics data was acquired from plasma extracellular vesicles; two pooled colorectal cancer group and two pooled healthy volunteers group. Non-targeted protemics data (selected reaction monitoring: SRM) was acquired from plasma extracellular vesicles; 209 colorectal cancer patients and 109 healthy volunteers.
Project description:Despite relevant clinical and/or familial presentations suggesting a hereditary predisposition (early-onset, multiple primary tumors, familial aggregation), targeted genomic analysis based on the phenotype are often non contributive. As somatic cancer genes are limited, the hypothesis is that the targeted next-generation sequencing of 200 genes, selected for their implications in cancers may contribute to the understanding of many selected patients’ presentation by the identification of germline deleterious mutations, and may identified phenotype overlapping and/or mosaicisms. The focus will be put on early-onset breast, ovarian, colorectal cancer or pediatric cancers and multiple primary tumors.
Project description:LncRNA plays an important role in gene regulation, but its impact on the pathogenesis of colorectal cancer and the biological function of cancer cells is unclear. In this study, we will use the next generation sequencing technique to study the differences of the expression profiles of lncRNA and mRNA in colorectal cancer tissues, analyzing the differentially expressed genes by GO/KEGG enrichment, and predicting the new lncRNAs’ function. Our results revealed that Comparing with the nontumor colorectal tissues, 1019 lncRNAs (512 upregulated, 507 downregulated) and 3221 mRNAs (1606 upregulated, 1615 downregulated) were differentially expressed in tumor colorectal tissues (fold change>2 and P<0.05).
Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study is to compare gene expressions in colorectal tumor versus adjacent normal colorectal tissue.
Project description:Background: The Ras pathway genes KRAS, BRAF or ERBBs have somatic mutations in ~60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway, or whether they have acquired mutations in genes hitherto not known to belong to the pathway. Methods: To address the second possibility, and extend the compendium of Ras pathway genes, we used genome-wide transposon mutagenesis of two human colorectal cancer cell systems deprived of their activating KRAS or BRAF allele to identify genes enabling growth in low glucose, a Ras pathway phenotype, when targeted. Results: Of the 163 recurrently targeted genes in the two different genetic backgrounds, one third were known cancer genes and one-fifth had links to the EGFR/Ras/MAPK pathway. When compared to cancer genome sequencing datasets, 9 genes also mutated in human colorectal cancers were identified. Among these, stable knock-down of FOXO3, NCOA3, and TCF7L2 restored growth in low glucose but reduced MEK/MAPK phosphorylation, reduced anchorage-independent growth, and modulated expressions of GLUT1 and Ras pathway related proteins. Knock-down of NCOA3 and FOXO3 significantly decreased the sensitivity to cetuximab of KRAS mutant but not wild-type cells. Conclusions: This work establishes a proof-of-concept that human cell based genome-wide forward genetic screens can assign genes to pathways with clinical importance in human colorectal cancer.
Project description:We present TORNADO-seq —a high-throughput, a high-content drug discovery platform that for the first time uses next-generation sequencing (NGS) based, targeted RNA-seq in organoids monitoring the expression of 206 genes for the evaluation of complex mixtures of cellular phenotypes. TORNADO-seq is a fast, highly-reproducible, time- and cost-effective (5$ per sample including sequencing cost) method that we used to find drugs that enrich for differentiated cell phenotypes in intestinal organoids. These drugs are highly efficacious against cancer compared to wild type organoids and may therefore become promising candidates in CRC treatment. Further, TORNADO-seq facilitated in-depth insight on the mode of action of these drugs.
Project description:Purpose: To identify the contribution of PRDM2 c.4459delA mutation to colorectal tumorigenesis Methods: We employed rAAV-mediated genome editing to correct somatic PRDM2 c.4459delA mutation in homozygously mutated cell line. Using next-generation sequencing we have compared transcriptional profile of parental and PRDM2-corrected cells. Results: RNA-seq profiling revealed that several hallmark cancer gene sets are affected by PRDM2 c.4459delA
