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Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110071 | GEO | 2018/12/31

REPOSITORIES: GEO

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Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [400K]

Project description:Double minutes (DMs), a major form of gene amplification, commonly carry oncogenes or chemoresistance-related genes that are associated with the occurrence, development and prognosis of tumors. Thus, probing molecular structures of DMs allows us to further understand molecular mechanisms underlying tumorigenesis. In this study, we identified four amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716. These amplification regions localized in two populations of DMs. Through a combined analysis on the results of array CGH, high throughput sequencing, multiplex-fluorescence in situ hybridization and chromosome walking results, we constructed molecular structures of the two populations of DMs at nucleotide resolution.

2018-12-31 | GSE110069 | GEO

Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [custom 180K]

2018-12-31 | GSE110070 | GEO

Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716

Project description:Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716

| PRJNA432704 | ENA

Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [400K]

Project description:Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [400K]

| PRJNA432777 | ENA

Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [custom 180K]

Project description:Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [custom 180K]

| PRJNA432774 | ENA

Whole genome amplification and its impact on CGH array profiles.

Project description:BACKGROUND: Some array comparative genomic hybridisation (array CGH) platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA) is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of starting material. A range of WGA methods are available and the multiple displacement amplification (MDA) approach has been shown to be highly accurate, although amplification bias has been reported. In the current study, WGA was used to amplify DNA extracted from whole blood. In total, six array CGH experiments were performed to investigate whether the use of whole genome amplified DNA (wgaDNA) produces reliable and reproducible results. Four experiments were conducted on amplified DNA compared to unamplified DNA and two experiments on unamplified DNA compared to unamplified DNA. FINDINGS: All the experiments involving wgaDNA resulted in a high proportion of losses and gains of genomic material. Previously, amplification bias has been overcome by using amplified DNA in both the test and reference DNA. Our data suggests that this approach may not be effective, as the gains and losses introduced by WGA appears to be random and are not reproducible between different experiments using the same DNA. CONCLUSION: In light of these findings, the use of both amplified test and reference DNA on CGH arrays may not provide an accurate representation of copy number variation in the DNA.

| S-EPMC2525645 | biostudies-literature

FGFR2 is amplified in the NCI-H716 colorectal cancer cell line and is required for growth and survival.

Project description:Aberrant kinase activation resulting from mutation, amplification, or translocation can drive growth and survival in a subset of human cancer. FGFR2 is amplified in breast and gastric cancer, and we report here the first characterization of FGFR2 gene amplification in colorectal cancer in the NCI-H716 colorectal cancer cell line. FGFR2 is highly expressed and activated in NCI-H716 cells, and FGFR selective small molecule inhibitors or FGFR2 shRNA strongly inhibited cell viability in vitro, indicating "addiction" of NCI-H716 cells to FGFR2. NCI-H716 growth in a xenograft model was also inhibited by an FGFR small molecule inhibitor. FGFR2 was required for activation of multiple downstream signaling proteins including AKT, ERK, S6RP and NFKB. Inhibition of downstream kinases such as AKT or ERK alone had modest effects on proliferation, whereas combined inhibition of AKT and ERK signaling resulted in a loss of viability similar to FGFR2 inhibition. We identified elevated FGFR2 expression in a small subset of primary colorectal cancer, however FGFR2 amplification was not observed. Although FGFR2 amplification is not common in primary colon cancer or lymph node and liver metastases, other subsets of colorectal cancer such as ascites, from which the NCI-H716 cell line was derived, have yet to be tested. These results suggest that emerging FGFR inhibitor therapeutics may have efficacy in a subset of colon cancer driven by FGFR2 amplification.

| S-EPMC4072591 | biostudies-literature

Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array-CGH.

Project description:Deletions of chromosome 6 are a common abnormality in diverse human malignancies including astrocytic tumours, suggesting the presence of tumour suppressor genes (TSG). In order to help identify candidate TSGs, we have constructed a chromosome 6 tile path microarray. The array contains 1,780 clones (778 P1-derived artificial chromosome and 1,002 bacterial artificial chromosome) that cover 98.3% of the published chromosome 6 sequences. A total of 104 adult astrocytic tumours (10 diffuse astrocytomas, 30 anaplastic astrocytomas (AA), 64 glioblastomas (GB)) were analysed using this array. Single copy number change was successfully detected and the result was in general concordant with a microsatellite analysis. The pattern of copy number change was complex with multiple interstitial deletions/gains. However, a predominance of telomeric 6q deletions was seen. Two small common and overlapping regions of deletion at 6q26 were identified. One was 1,002 kb in size and contained PACRG and QKI, while the second was 199 kb and harbours a single gene, ARID1B. The data show that the chromosome 6 tile path array is useful in mapping copy number changes with high resolution and accuracy. We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs.

| S-EPMC2760128 | biostudies-literature

Over-expression of YAP1 in NCI-H716 colorectal cancer cells

Project description:YAP1 plays importance roles in development of colorectal cancer as evidenced by their overexpression in colorectal cancer and their expression promoted cell proliferation and survival of colorectal cancer cells. In order to understand potential roles of YAP1 in colorectal cancer, we over-expressed constitutively active YAP1 mutant in NCI-H716 colorectal cancer cells and identified and analyzed genes whose expression is activated by YAP1 activation in colorectal cancer. Pre-clinical study

2015-02-04 | E-GEOD-50490 | biostudies-arrayexpress

Over-expression of YAP1 in NCI-H716 colorectal cancer cells

2015-02-04 | GSE50490 | GEO