Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differences in RNA expression between primary and metastatic colon tumor

ABSTRACT: Here, we report the genomic-scale characterization of metastatic colon cancer transcriptome. Fresh-frozen samples was used to asses differences between normal colon, primary colon tumor an liver metastasis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE89393 | GEO | 2018/09/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteomic analysis of protein ubiquitination events in human primary and metastatic colon adenocarcinoma tissues

Project description:Protein ubiquitination is essential for multiple physiological processes through regulating the stability or function of target proteins and has been found to play critical roles in human cancers. However, the protein ubiquitination profile of human metastatic colon adenocarcinoma tissue has not been elucidated yet. In this study, a proprietary ubiquitin branch (K-ε-GG) antibody-based label-free quantitative proteomics and bioinformatics were performed to identify the global protein ubiquitination profile between human primary (Colon) and metastatic colon adenocarcinoma (Meta) tissues.

2020-07-27 | PXD020597 |

Poorly metastatic HCT116 vs metastatic E1 colon cancer cell lines

Project description:Comparison of gene expression between poorly metastatic HCT116 colon cancer cell line and the in-vivo derived metastatic E1 cell line, which has EMT (epithelial to mesenchymal transition) features.

2011-03-01 | GSE13759 | GEO

Poorly metastatic HCT116 vs metastatic E1 colon cancer cell lines

2011-03-01 | E-GEOD-13759 | biostudies-arrayexpress

TMED9-gated CNIH4 and TGFa signaling promotes pro-metastatic states in human primary colon cancer cells

Project description:How cells in primary tumors initially become pro-metastatic is not understood. A previous genome-wide RNAi screen uncovered colon cancer metastatic suppressor and WNT promoting functions of TMED3, a member of the p24 ER-to-Golgi protein secretion family. Repression of WNT signaling upon knock-down (kd) of TMED3 might thus be sufficient to drive metastases. However, searching for transcriptional influences on other family members here we find that TMED3 kd leads to enhanced TMED9, that TMED9 acts downstream of TMED3 and that TMED9 kd compromises metastasis. Importantly, TMED9 pro-metastatic function is linked to but distinct from the repression of TMED3-WNT-TCF signaling. Functional rescue of the migratory deficiency of TMED9 kd cells identifies TGFa as a mediator of TMED9 pro-metastatic activity. Moreover, TMED9 kd compromises the membrane localization, and thus function, of TGFa. Analyses in three colon cancer cell types highlight a TMED9-dependent gene set that includes CNIH4, a member of the CORNICHON family of TGFa exporters. Our data indicate that TGFA and CNIH4, which display predictive value for disease-free survival, promote colon cancer cell metastatic behavior and suggest that TMED9 pro-metastatic function involves the modulation of the secretion of TGFa ligand. Finally, TMED9/TMED3 antagonism impacts WNT-TCF and GLI signaling, where TMED9 primacy over TMED3 leads to the establishment of a positive feedback loop together with CNIH4, TGFa and GLI1 that enhances metastases. We suggest that primary colon cancer cells can transition between two states characterized by secretion-transcription regulatory loops gated by TMED3 and TMED9 that modulate their metastatic proclivities.

2019-07-01 | GSE125282 | GEO

Transcriptome of locally advanced colorectal tumours

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.

2019-05-02 | GSE100243 | GEO

Oncogenic gene fusions in primary colon cancers

Project description:This study represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. The project goal was to identify novel oncogenic gene fusions in these data. In addition, we studied the detected gene fusions at the molecular level and defined their effects on downstream pathways.

| EGAS00001002197 | EGA

Comparison of Nanostring nCounter data on FFPE colon cancer samples and Affymetrix microarray data on matched frozen tissues

Project description:The prognosis of colorectal cancer (CRC) stage II and III patients is still a challenge due to the difficulties of finding robust biomarkers and assays. The majority of published gene signatures of CRC have been generated on frozen colorectal tissues. Because collection of fresh frozen tissues is not routine and the quantity and quality of RNA derived from formalin-fixed paraffin-embedded (FFPE) tissues is vastly inferior to that derived from fresh frozen tissue, a clinical test for improving staging of colon cancer will need to be designed for FFPE tissues in order to be widely applicable. We have designed a custom Nanostring nCounter assay for quantitative assessment of expression of 414 gene elements consisting of multiple published gene signatures for colon cancer prognosis, and systematically compared the gene expression quantification between nCounter data from FFPE and Affymetrix microarray array data from matched frozen tissues using 414 genes.

2015-10-27 | GSE62932 | GEO

Expression data from different samples of a single ccRCC patient: 8 primary intra-tumor samples and 2 metastatic tumor samples

Project description:We have sampled several tumour regions from a single ccRCC patient after 6 weeks everolimus treatment, including both primary and metastatic site samples to investigate intra-tumour heterogeneity. We selected 8 samples from the primary tumour, and 2 samples from a chestwall metastatic site for expression analysis using microarray data. All samples were fresh frozen upon extraction.

2011-08-24 | E-GEOD-31610 | biostudies-arrayexpress

Single cell transcriptome landscape of primary and metastatic tumor in colon cancer

Project description:Colorectal Cancer ranks as the second-leading cause of cancer-related death worldwide. Recent progress in colon cancer research has vastly expanded our understanding of colon cancer on the cellular and molecular levels and have improved the survival of CRC patients considerably. However, most of these genomic and gene expression profiling were usually characterized by bulk tumor tissue. In order to further understanding colon cancer, knowledge at the single cell level is urgently needed and expected to have clinical utility in cancer treatment. Single-cell transcriptome profiling of tumor tissues allows the characterization of heterogeneous tumor cells with neighbor microenvironment cell components and investigation of underlying mechanism of tumorigenesis and metastasis. Here, we adopt single cell RNA-Seq to colon cancer and analyze 3,585 cells from 6 patients with matching adjacent normal tissues, primary tumors and metastatic tumors. Most of tumor cells exhibit copy number variations and diverse CNV patterns existed. Novel markers have been identified to distinguish tumour from normal cells and even work for cancer cells that did not have CNVs. Compared with adjacent normal tissue, the number of stem cell and Paneth cell increased and the surrounding cancer-association cells like immune cells in microenvironment increased in tumour region. Moreover, the interaction of tumour cell and microenvironment cells have been elaborated. Our results demonstrate that colon cancer transcriptome has a wide range of intratumoral heterogeneity, which is shaped by tumor cells and cancer associated cells in the surrounding microenvironment.

2022-07-30 | GSE110009 | GEO

Single cell transcriptome landscape of primary and metastatic tumor in colon cancer

Project description:Single cell transcriptome landscape of primary and metastatic tumor in colon cancer

| PRJNA432551 | ENA