Transcriptomic profilings of CT45A1-expressing colorectal cacner cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE193554 | GEO | 2025/01/11
REPOSITORIES: GEO
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Project description:Transcriptomic profilings of CT45A1-expressing colorectal cacner cells.
| PRJNA796592 | ENA
Project description:MicroRNAs regulate the biological aggressiveness of colorectal cancer (CRC) cells and might serve as potential prognostic factors and therapeutic targets. In this study, we therefore globally profiled microRNAs associated with aggressive growth in CRC cells, in an attempt to identify novel prognostic biomarkers in CRC patients. In detail, two different CRC cell lines (Caco-2 and HRT-18) with completely different growth rates and different E-cadherin expression were profiled for differences in more than 1000 human microRNAs by using microarray technology.
2014-01-13 | GSE53095 | GEO
Project description:MicroRNAs regulate the biological aggressiveness of colorectal cancer (CRC) cells and might serve as potential prognostic factors and therapeutic targets. In this study, we therefore globally profiled microRNAs associated with aggressive growth in CRC cells, in an attempt to identify novel prognostic biomarkers in CRC patients. In detail, two different CRC cell lines (Caco-2 and HRT-18) with completely different growth rates and different E-cadherin expression were profiled for differences in more than 1000 human microRNAs by using microarray technology. Two-condition experiment, HRT-18 vs. Caco-2. Biological replicates: 3, independently grown and harvested. On each array, one BR of HRT-18 cells was directly compared to one BR of Caco-2 cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.
2014-01-13 | E-GEOD-53095 | biostudies-arrayexpress
Project description:We established combined 2D/3D, in vitro/in vivo model systems representing the heterogeneity of colorectal cancer (CRC) with regards to different molecular subtypes. Comparative characterization of stable luciferase expressing derivatives of well-established CRC cell lines, derived spheroids and subcutaneous xenograft tumors showed that the 3D-spheroid cultures resembled xenografts more closely than 2D-cultured cells do. The model systems can be used in preclinical research applications to study new therapy approaches and represents the biological heterogeneity of CRC.
2023-10-10 | GSE241569 | GEO
Project description:The N-Myc Downstream-Regulated Gene 4 (NDRG4), a prominent biomarker for colorectal cancer (CRC), is specifically expressed by enteric neurons. Considering that nerves are important members of the tumor microenvironment, we here establish different Ndrg4 knockout (Ndrg4-/-) CRC models and an in-direct co-culture of primary enteric nervous system (ENS) cells and intestinal organoids to identify whether the ENS, via NDRG4, affects intestinal tumorigenesis. Linking immunostainings and gastrointestinal motility (GI) assays, we show that absence of Ndrg4 does not trigger any functional or morphological GI-abnormalities. However, combining in vivo, in vitro and quantitative proteomics data, we uncover that Ndrg4 knockdown is associated with enlarged intestinal adenoma development and that organoid growth is boosted by the Ndrg4-/- ENS cell secretome, which is enriched for Nidogen-1 (Nid1) and Fibulin-2 (Fbln2). Moreover, NID1 and FBLN2 are expressed in enteric neurons, enhance tumorigenic capacities of CRC cells and are enriched in human CRC secretomes. Hence, we provide evidence that the ENS, via loss of Ndrg4, is involved in colorectal pathogenesis and that ENS-derived Nidogen-1 and Fibulin-2 enhance colorectal carcinogenesis.
2021-04-23 | PXD024502 | Pride
Project description:Claret2009 - Predicting phase III overall survival in colorectal cancer
This model is described in the article:
Model-based prediction of
phase III overall survival in colorectal cancer on the basis of
phase II tumor dynamics.
Claret L, Girard P, Hoff PM, Van
Cutsem E, Zuideveld KP, Jorga K, Fagerberg J, Bruno R.
J. Clin. Oncol. 2009 Sep; 27(25):
4103-4108
Abstract:
PURPOSE: We developed a drug-disease simulation model to
predict antitumor response and overall survival in phase III
studies from longitudinal tumor size data in phase II trials.
METHODS: We developed a longitudinal exposure-response
tumor-growth inhibition (TGI) model of drug effect (and
resistance) using phase II data of capecitabine (n = 34) and
historical phase III data of fluorouracil (FU; n = 252) in
colorectal cancer (CRC); and we developed a parametric survival
model that related change in tumor size and patient
characteristics to survival time using historical phase III
data (n = 245). The models were validated in simulation of
antitumor response and survival in an independent phase III
study (n = 1,000 replicates) of capecitabine versus FU in CRC.
RESULTS: The TGI model provided a good fit of longitudinal
tumor size data. A lognormal distribution best described the
survival time, and baseline tumor size and change in tumor size
from baseline at week 7 were predictors (P < .00001).
Predicted change of tumor size and survival time distributions
in the phase III study for both capecitabine and FU were
consistent with observed values, for example, 431 days (90%
prediction interval, 362 to 514 days) versus 401 days observed
for survival in the capecitabine arm. A modest survival
improvement of 39 days (90% prediction interval, -21 to 110
days) versus 35 days observed was predicted for capecitabine.
CONCLUSION: The modeling framework successfully predicted
survival in a phase III trial on the basis of capecitabine
phase II data in CRC. It is a useful tool to support
end-of-phase II decisions and design of phase III studies.
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2017-08-31 | MODEL1708310001 | BioModels
Project description:Microarray-based comparative genomic hybridization of CRC DNA samples from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma. Microarray-based comparative genomic hybridization of CRC DNA samples against a common reference.
2012-11-01 | E-GEOD-25228 | biostudies-arrayexpress
Project description:To identify novel hypermethylated genes in colorectal cancer (CRC) and to test their potential application in CRC early diagnosis, we performed a genome-wide screening of 57,723 CpG dinucleotides covering 4,010 genes in paired DNA samples extracted from 3 fresh frozen CRC tissues and their matching non-tumor adjacent tissues from a cohort of 3 CRC patients undergoing curative surgery using MIRA-based microarray. We also validated candidate hypermethylated genes screened by MIRA-based microarray in independent CRC samples using combined bisulfite restriction analysis. A total of 297 CpG dinucleotides in CRC covering 211 genes were found to be hypermethylated in CRC tissues. From these 211 candidate methylated genes, seven novel methylated genes were picked up for validation and three genes were confirmed to be methylated in cancer samples but not in non-cancer samples.We also compared the methylation levels of these three novel hypermethylated genes with those of Vimentin and SEPT9, well-known hypermethylated genes in CRC, and found that methylated PHOX2B, FGF12 and GAD2 were better than methylated Vimentin and SEPT9 in differentiating CRC cancer tissue from normal tissue. Significant enrichment analysis of GO terms of the hypermethylated genes showed that a high proportion of hypermethylated genes in tumor tissues are involved in regulation of transcription. Paired experiments, colorectal cancer tissue vs. adjacent non-cancer tissue. Biological replicates: 3 cancer replicates, 3 paired non-cancer replicates.
2011-11-14 | E-GEOD-33545 | biostudies-arrayexpress
Project description:We ortho-topically implanted 16 human colorectal cancer (CRC) cell lines onto the cecal walls of nude mice . To identify the genes possibly involved in EMT of CRC, we analyze the EMT related changes with the orthotopic implantation method in vivo in combination with that of gene expression profiles using a cDNA microarray in vitro. We analyzed 16 human colorectal cancer cell lines. For each cell line, the experiments were carried out twice.
2013-09-01 | E-GEOD-49811 | biostudies-arrayexpress
Project description:lncRNAs contributes to the development of colorectal cancer (CRC). Analysis of tumor tissues and adjacent non-tumor tissues from 6 colorectal cancer patients was conducted. Results indicate insight into molecular signature of the tumorigenesis of CRC.
2018-02-17 | GSE110715 | GEO