MRNA sequencing of highly and lowly metastatic human colorectal cancer PDXs
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA575218 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed in-vivo selection of human patient derived colorectal cancer xenografts. 4 independent highly-liver metastatic sub-lines (lvm PDXs) were generated. Those lvm PDXs were harvested with the corresponding parental PDX tumors from mice and then we performed MACS mice cell depletion followed by FACS sorting to obtain human EpCAM positive and mice MHC negatitve populations. total RNA was extracted from those ex-vivo tumors and high-throuput sequencing was performed
2019-10-02 | GSE138248 | GEO
Project description:In this study we want present a bank of metastatic colorectal cancer (mCRC) Patient Derived Organoids (PDOs) obtained from Patient Derived Xenografts (PDXs). These models are annotated with different omics to advance our understanding of CRC. We wanted to create a resource for the scientific community to assess the predictive reliability of these preclinical models. We performed comparative analyses between PDOs and matched PDXs to assess the similarities of these two platforms regarding molecular profiles and transcriptional classification. Moreover, we analyzed how these models respond to Cetuximab, a chimeric monoclonal antibody, normally given to patients after chemotherapy, that inhibits EGFR. After having assessed models’ reliability with Cetuximab, we aimed at identifying potential synergistic drugs to individuate new possible therapeutic prospects.
2023-03-01 | GSE204805 | GEO
Project description:The goal was to identify genes that promote liver metastasis of colorectal cancer. Microarray analysis was performed to compare gene expression and altered biological pathways between a poorly metastatic CT26 cell line as compared to an isogenic highly metastatic CT26 FL3 cell line that was isolated by in vivo selection in an orthotopic mouse model of colon cancer metastasis to the liver. Gene expression in CT26-FL3 and parental CT26 cells were determined using the Agilent platform. Four independent samples each were analyzed.
2016-03-30 | E-GEOD-67675 | biostudies-arrayexpress
Project description:A prediction of peritoneal recurrence is of significance using metastasis-related biomarker. This work describes a combined analysis of proteome and transcriptome data for biomarker discovery in highly metastatic cell line. We used nano-flow liquid chromatography (LC) linear ion trap time-of-flight mass spectrometry (LIT-TOF MS) and cDNA microarray to identify specific protein differentially expressed between a highly metastatic stomach cancer cell line MKN-45-P and its parental cell line MKN-45. In total, 240 proteins were found to be expressed between the two cell lines. Of these, 75 proteins (31%) and 49 proteins (20%) were only identified from MKN-45-P and MKN-45 respectively. An mRNA expression of 1533 genes was up-regulated in MKN-45-P compared with MKN-45. No close correlation was found between proteomic and transcriptomic analysis. Interestingly, 4 of 240 proteins (1.6%) were involved in the up-regulated mRNA expression. Comparison analysis of gene expression between highly metastatic gastric cancer cell line MKN-45-P and its parental cell line MKN-45.
2010-06-08 | E-GEOD-21328 | biostudies-arrayexpress
Project description:The goal was to identify genes that promote liver metastasis of colorectal cancer. Microarray analysis was performed to compare gene expression and altered biological pathways between a poorly metastatic CT26 cell line as compared to an isogenic highly metastatic CT26 FL3 cell line that was isolated by in vivo selection in an orthotopic mouse model of colon cancer metastasis to the liver.
2016-03-30 | GSE67675 | GEO
Project description:Bank of metastatic colorectal cancer (mCRC) of Patient Derived Xenografts (PDXs)
| EGAS00001006492 | EGA
Project description:MicroRNAs are noncoding, endogenous small RNAs that regulate target genes by cleavage of the targeted mRNA or translational repression. We investigated the microRNAome using 2-color microarrays in a highly invasive human breast cancer cell line, MDA-MB-231 (sub line 4175) and a non-invasive breast epithelial cell line, MCF10A. We found 13 miRNAs that were up-regulated and 9 were down-regulated significantly in 4175 cells (p <0.05, fold change >2) compared with MCF10A cells. We compared the highly metastatic human breast cell lines MDA-MB-231 (4175 subline) with non-metastatic MCF10A cell lines. Two 4175 sublines and two MCF10A cell lines, independently grown and harvested. Dye swap was performed.
2010-05-15 | E-GEOD-17350 | biostudies-arrayexpress
Project description:To characterize metastatic progression of colorectal cancer, we performed mass spectrometry-based proteome analysis using large clinical cohort samples.
2024-01-16 | PXD031705 | Pride
Project description:Response to drug therapy in individual colorectal cancer (CRC) patients is associated with tumor biology. Here we describe the genomic landscape of tumor samples of a homogeneous well-annotated series of patients with metastatic CRC of two phase III clinical trials, CAIRO and CAIRO2. DNA copy number aberrations of 349 patients are determined. Within three treatment arms, 194 chromosomal sub-regions are associated with progression free survival PFS (uncorrected single-test p-values < 0.005). These sub-regions are filtered for effect on mRNA expression, using an independent data set from The Cancer Genome Atlas (TCGA) which returned 171 genes. Three chromosomal regions are associated with a significant difference in PFS between treatment arms with or without irinotecan. One of these regions, 6q16.1-q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of metastatic CRC reveals a number of DNA copy number aberrations associated with response to drug therapy. aCGH data of colorectal cancers of patients from 2 clinical trials (CAIRO, CAIRO2). 105 patients were treated with capecitabine first line (CAIRO arm A), 111 patients were treated with capecitabine and irinotecan first line (CAIRO arm B), and 133 patients were treated with capecitabine, oxaliplatin and bevacizumab (CAIRO2 arm A).
2014-11-14 | E-GEOD-36864 | biostudies-arrayexpress
Project description:Three separate experiments were carried out using MeDIP-seq and cfMeDIP-seq for methylome analysis. For the first experiment, different starting amounts of HCT116 cell line DNA, sheared to mimic cell-free DNA, were analyzed using MeDIP-seq and cfMeDIP-seq. In the second experiment the limit of detection of cfMeDIP-seq was tested using varying dilutions of colorectal cancer cell line DNA (HCT116) with multiple myeloma cell line DNA (MM1.S). For both cell line DNA samples, the DNA was sheared to mimic cell-free DNA. In the final experiment, we tested the enrichment of human ctDNA using cfMeDIP-seq performed on plasma collected from patient-derived xenografts (PDXs) generated in mice from two colorectal cancer patients.
2018-04-01 | GSE79838 | GEO