Project description:We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines (Caco-2, HT-29,HCT-116), one human breast adenocarcinoma cell line (MCF-7) and one human prostate adenocarcinoma cell line (PC3) were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.
Project description:RNAseq is performed (50bp single end reads) on SW480, HT-29, HCT-15, HCT-116, COLO 205, and COLO 320 cell lines after DMSO or JQ1 treatment
Project description:Whole transcriptome expression levels of SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs or Stealth Negative Control Medium GC siRNAs, analyzed by HTA 2.0 microarrays
Project description:Intratumor heterogeneity is a major challenge in cancer treatment. To decipher patterns of chromosomal heterogeneity, we analyzed six colorectal cancer cell lines by multiplex interphase FISH. The mismatch repair deficient cell lines DLD-1 and HCT116 had the most stable copy numbers, whereas aneuploid cell lines displayed a higher degree of instability. We subsequently assessed the clonal evolution of a single cell in two aneuploid cell lines, SW480 and HT-29, which both have near-triploid karyotypes but different degrees of chromosomal instability. The clonal compositions of the single cell-derived daughter cell lines, as assessed by multiplex FISH, differed for HT-29 and SW480. Daughters of HT-29 were stable, clonal, and had little heterogeneity. Daughters of SW480 were more heterogeneous, with the single cell-derived daughter cell lines separating into two distinct populations with different ploidy (hyper-diploid and near-triploid), morphology, gene expression and tumorigenicity. To better understand the evolutionary trajectory for the two SW480 populations, we constructed phylogenetic trees which showed ongoing instability in the daughter cell lines.. When analyzing the evolutionary development over time, most single cell-derived daughter cell lines maintained their major clonal pattern, with the exception of one daughter of SW480 that showed a switch involving a loss of APC. Our meticulous analysis of the clonal evolution and composition of these colorectal cancer models shows that all chromosomes are subject to segregation errors, however, specific net genomic imbalances are maintained. Karyotype evolution is driven by the necessity to arrive at and maintain a specific plateau of chromosomal copy numbers as the drivers of carcinogenesis.
Project description:To investigate the presence and abundance of piRNAs in Colorectal Cancer (CRC), we performed deep-sequencing of the small RNA transcriptome of eight human CRC cell lines (HT-115, Caco-2, SW-1417, SW 403, COLO 205, HT-29, HCT 116 and RKO).
Project description:To establish the role of Slug in CRC, we created a genetic CRC model for Slug expression. As parental cells, we selected HT-29 cells that display a pronounced epithelial phe-notype. HT-29 cells were transfected with Slug, and two stable Slug-expressing clones. (Slug1, Slug2) were isolated. As transfection control, we used HT-29 cells transfected with empty vector (control). To characterize the influence of Slug on gene ex-pression, transcriptome analysis was performed for the four HT-29 cell lines as well as for the corresponding tumor xenografts. Global expression profiling showed that Slug-overexpressing cells and tumors were clustered together while the parental and control cells and tumors formed a separate cluster. Next, a two-step analysis was carried out. First, a subtractive analysis was carried out comparing the gene profiles of Slug-expressing cells and tumors with the corresponding parental/control samples. Genes were considered to be significantly upregulated by Slug if the fold change (FC) was greater than +2 and downregulated if the fold change was less than −2 with p-values (false dis-covery rates) less than 0.01
Project description:To investigate potential differences between strong and weak oscillators at the gene expression level we carried out a transcriptome analysis for each cell line. Our results indicate that phenotypic circadian clock differences are reflected by gene expression differences both in genes of the core network, but also in additional genes not directly associated with circadian clock functions. We carried out a gene expression analysis of 6 colon cancer cell lines (HCT116, HT-29, RKO, SW480, LIM1512 and CaCo2) for each the RNA was collected at two time points (0hr and 48 hr after syncronization). As a reference the osteosarcoma U2OS cell line was used. No treatment was applied.
Project description:Defining molecular features that can predict the response to chemotherapy for stage II-III colorectal cancer (CRC) patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed and Paraffin-Embedded (FFPE). Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) is one platform marketed for high-throughput gene expression profiling for FFPE tissue samples. In this study, we analyzed the whole transcriptom gene expression of 156 CRC patient samples measured by this platform to identify biomarkers predicting the response to chemotherapy for stage II-III CRC patients.
