Genome-wide maps of SOX9 binding sites in human colorectal cancer cells
ABSTRACT: Aberrant expression of SOX9 in human colorectal cancer cells suggests its roles in the development of colorectal cancer. To gain insight into SOX9-mediated transcriptional regulation in colorectal cancer cells, we attempted to identify its physiological targets on a genome-scale using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) in HT-29, human colorectal cancer cells. SOX9 CHIP-seq was carried out using HT-29 cells.
Project description:To elucidate whether F. nucleatum plays a role in colorectal cancer tumorigenesis, RNA-seq analysis was performed to compare the gene expression profiles of F. nucleatum treated HT-29 cell line or not. Overall design: RNA-seq was performed in HT-29 colorectal cancer cells after F. nucleatum treatment
Project description:The aim of this study is to characterize generated stable spheroid cultures (SC) directly derived from fresh surgical specimens of three patients and compare them to their differentiated counterpart as well as to SC derived from established colorectal cancer cell lines HT-29 and HCT-116.
Project description:Colorectal cancer HT-29 cell line is a comonly-used human cancer cell line. We have used this cell line for examining the effect of various anticancer compounds on gene expression and we obtained gene expression data of untreated HT-29 cells as a control data for the analysis. Overall design: We extracted RNA from HT-29 cells and obtained gene expression data.
Project description:Interferon-induced transmembrane protein 1 (IFITM1) is one of the three members of the interferon-induced transmembrane family and has recently been identified as a new molecular marker in human colorectal cancer. However, its functional roles in colorectal cancer are still elusive. In this study, we investigate the gene expression profiling of HT-29 cells with IFITM1 knockdown. We revealed that several invasive- and carcinogenesis-related genes were differentially expressed. We transfected siRNAs targeting firefly luciferase and human IFITM1 mRNAs into HT-29 colorectal adenocarcinoma cells. At 72 h post-transfection, total RNA was harvested for microarray hybridization. A siLuc-transfected sample was used as the baseline control.
Project description:Interferon-induced transmembrane protein 1 (IFITM1) is one of the three members of the interferon-induced transmembrane family and has recently been identified as a new molecular marker in human colorectal cancer. However, its functional roles in colorectal cancer are still elusive. In this study, we investigate the gene expression profiling of HT-29 cells with IFITM1 knockdown. We revealed that several invasive- and carcinogenesis-related genes were differentially expressed. Overall design: We transfected siRNAs targeting firefly luciferase and human IFITM1 mRNAs into HT-29 colorectal adenocarcinoma cells. At 72 h post-transfection, total RNA was harvested for microarray hybridization. A siLuc-transfected sample was used as the baseline control.
Project description:Analysis of colorectal cancer (CRC) cell line HT-29 treated with Sodium Butyrate. Sodium Butyrate, a HDAC inhibitor present in gut, can differentiate the undifferentiated HT-29 to enterocytes by the induction of brush border enzyme alkaline phosphatase. Results provide the transcriptional profiling underlying the butyrate-induced differentiation of CRC. Overall design: Two-condition experiment, Butyrate treated vs. untreated HT-29 cells. Two Time points: 24 hours and 48 hours. Biological replicates: 2 control replicates, two 24 hours butyrate treated replicates and two 48 hours butyrate treated replicates.
Project description:Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer. We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated. HT-29 monolayer cells were grown in DMEM/F12 media supplemented with 10% FBS, and 1X Antibiotic-Antimycotic liquid (AA); and spheroids were grown in stem cell media [DMEM:F12, 1X AA, 1X B27, epidermal growth factors, and fibroblast growth factor for five days. Total RNA was isolated using the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol. RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The arrays were scanned with the Affymetrix 3000 7G plus scanner.
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. Overall design: Single cell clones were generated from SW480 and HT-29 cells to compare their clonal evolution and heterogeneity
Project description:Active immunotherapy is a promising strategy for anti-angiogenic cancer therapy. Recently, we have reported that a vaccine using human umbilical vein endothelial cells (HUVECs) induced specific anti-endothelial immune responses in the most of immunized patients, and resulted in tumor regression in some patients with recurrent malignant brain tumors, whereas not in colorectal cancer patients. In this study, we hypothesized that non-hypoxic perivascular tumor associated macrophages (TAMs) in colorectal cancer, but not in glioblastoma, might negatively alter the therapeutic efficacy of anti-angiogenic active immunotherapy. To test this hypothesis, we examined global gene expression profiles of non-hypoxic macrophages stimulated in vitro by soluble factors released from tumor cells of human glioblastoma U-87MG (‘brain TAMs’) or colorectal adenocarcinoma HT-29 (‘colon TAMs’). Overall design: Murine non-hypoxic TAMs were induced in vitro by incubation with soluble factors released from human cancer cell lines U-87MG ('brain TAMs') or HT-29 ('colon TAMs'), for RNA extraction and subsequent hybridization on Affymetrix microarrays. To evaluate homogeneous macrophage populations at different tumour developmental stages, RNA aliquots of control macrophages and TAMs obtained at five different time-points, i.e. 8h, 16h, 24h, 32h and 40h, were pooled and used for screening of differentially expressed genes. The experiments for TAMs as well as for control unstimulated macrophages were performed in triplicates.