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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide copy number analysis of patient-derived gliobastoma cell cultures

ABSTRACT: Genome-wide copy number variation profiles were analyzed in the patient-derived gliobastoma cell culture samples. For this purpose, gDNA was analyzed using the CytoScan® assay in combination with a one-color based labeling and hybridization protocol. Signals on the CytoScan® HD microarrays were detected using the Affymetrix GeneChip® 3000 Scanner.

ORGANISM(S): Homo sapiens

SUBMITTER: Roland Kälin

PROVIDER: E-MTAB-7649 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Targeting APLN/APLNR Improves Antiangiogenic Efficiency and Blunts Proinvasive Side Effects of VEGFA/VEGFR2 Blockade in Glioblastoma.

Mastrella Giorgia G Hou Mengzhuo M Li Min M Stoecklein Veit M VM Zdouc Nina N Volmar Marie N M MNM Miletic Hrvoje H Reinhard Sören S Herold-Mende Christel C CC Kleber Susanne S Eisenhut Katharina K Gargiulo Gaetano G Synowitz Michael M Vescovi Angelo L AL Harter Patrick N PN Penninger Josef M JM Wagner Ernst E Mittelbronn Michel M Bjerkvig Rolf R Hambardzumyan Dolores D Schüller Ulrich U Tonn Jörg-Christian JC Radke Josefine J Glass Rainer R Kälin Roland E RE

Cancer research 20190204 9

Antiangiogenic therapy of glioblastoma (GBM) with bevacizumab, a VEGFA-blocking antibody, may accelerate tumor cell invasion and induce alternative angiogenic pathways. Here we investigate the roles of the proangiogenic apelin receptor APLNR and its cognate ligand apelin in VEGFA/VEGFR2 antiangiogenic therapy against distinct subtypes of GBM. In proneural GBM, apelin levels were downregulated by VEGFA or VEGFR2 blockade. A central role for apelin/APLNR in controlling GBM vascularization was corr ...[more]

PMID: 30718358

Similar Datasets

Genome-wide copy number analysis of patient-derived gliobastoma cell cultures

Project description:Genome-wide copy number variation profiles were analyzed in the patient-derived gliobastoma cell culture samples. For this purpose, gDNA was analyzed using the CytoScan® assay in combination with a one-color based labeling and hybridization protocol. Signals on the CytoScan® HD microarrays were detected using the Affymetrix GeneChip® 3000 Scanner.

2021-07-07 | E-MTAB-9341 | biostudies-arrayexpress

Amplicon-based targeted re-sequencing analysis of target genes in human DNA samples using the Illumina TruSeq Custom Amplicon technology

Project description:Amplicon-based targeted re-sequencing analysis was performed in the patient-derived gliobastoma cell culture samples. For this purpose, genomic DNA (gDNA) was isolated and DNA libraries were prepared using the TruSeq Custom Amplicon Low Input (Illumina, Inc.) technology. By this, a pool of 375 amplicons was generated for each single sample in order to enrich for the target genes ATRX1, EGFR, IDH1, NF1, PDGFRA, PIK3CG, PIK3R1, PTEN, RB1 and TP53. Sequencing was performed on the Illumina MiSeq® next generation sequencing system (Illumina Inc.) and its 2 x 250 bp paired-end v2 read chemistry. The resulting reads were quality controlled and mapped against the human reference genome (hg19). For all samples, sequence variations of the amplified regions of interest in comparison to the human reference sequence were identified and filtered based on reliability.

2021-07-07 | E-MTAB-9343 | biostudies-arrayexpress

Genomic profiling of immature hematopoietic cells to obtain insights into imatinib resistance

Project description:Chronic myeloid leukemia (CML) epitomizes successful targeted therapy, with 86% of patients in the chronic phase treated with tyrosine kinase inhibitors (TKIs) attaining remission. However, resistance to TKIs occurs during treatment, and patients with resistance to TKIs progress to the acute phase called Blast Crisis (BC), wherein the survival is restricted to 7-11 months. About 80 % of patients in BC are unresponsive to TKIs. This issue can be addressed by identifying a molecular signature which can predict resistance in CML-CP prior to treatment as well as by delineating the molecular mechanism underlying resistance. Herein, we report genomic analysis of CML patients and imatinib-resistant K562 cell line to achieve the same. Thirteen CML patients (sensitive and resistant to TKIs) and 2 BMT donors (as control) were recruited for the study. DNA was isolated from an enriched CD34+ fraction for each sample as well as from K562 cells made resistant to imatinib which provided a model system for further molecular investigations. DNA was subjected to Cytoscan HD array (Affymatrix) analysis from patient samples and cell lines. Affymetrix CytoScan™ HD array (Applied Biosystems™, Cat# 901835) chip consists of 2.6 M oligonucleotide probes across the genome, including 1953K unique non-polymorphic probes and 750K bi-allelic SNP (single nucleotide polymorphism) probes. Our study identified accumulation of aberrations on chromosomes 1, 3, 7, 16 and 22 as predictive of occurrence of resistance. Further, recurrent amplification in chromosomal region 8q11.2-12.1 was detected in highly resistant K562 cells as well as CML patients. The genes present in this region were analyzed to understand molecular mechanism of imatinib resistance.

2024-01-01 | E-MTAB-11899 | biostudies-arrayexpress

Karyotype analysis of human naive embryonic stem cells

Project description:Human pluripotent cell lines were derived from blastocyst-stage embryos and propagated in self-renewal conditions that maintain features of naive pluripotency characteristic of mouse embryonic stem cells. Genomic integrity of the HNES1 cell line was assessed with the Affymetrix CytoScan 750K array.

2016-03-01 | E-MTAB-4463 | biostudies-arrayexpress

Large genomic alteration of 7q in two patients with multiple primary cancers, including triple negative breast cancer, and family history of malignant neoplasms

Project description:A great percentage of patients with multiple primary cancers (MPCs) and family history of cancer are suspected to have a hereditary cancer predisposition syndrome. However, only a small proportion of these cases are explained by mutations in high-penetrance genes, suggesting the involvement of undiscovered genes in cancer predisposition. In this study, we report the molecular and clinical characterization of two unrelated patients with MPCs, a positive family history of cancer, no germline pathogenic mutations in BRCA1, BRCA2 and TP53 genes and large genomic rearrangements mapped on chromosome 7q. Genomic rearrangements were assessed with Affymetrix CytoScan HD Array platform in two unrelated patients (Patient 1 and Patient 2) with multiple primary cancers. Additionally, the mother of Patient 2 and four children (the son of Patient 1 and three children of Patient 2) were also evaluated.

2016-02-15 | E-GEOD-77138 | biostudies-arrayexpress

two amniotic fluid sample performed by affymetrix cytoscan HD

Project description:The uploaded results of two samples were SNParray results in our research of which fetal CNVs were detected by noninvasive prenatal test (NIPT) and confirmed by microarray results. Sample ZNY162 received prenatal diagnosis because at 17 gestational week the pregnant woman received NIPT showing 23Mb microdeletion in Chr18. Later ultrasound examination showed developmental anomalies of feet and the 13th ribs. The pregnant woman received amniocentesis and SNParray at the 21st gestational week, which confirmed the existence of the microdeletion in Chr18. DNA was extracted from 10ml amniotic fluid and tested by Affymetrix CytoScan HD array to detect CNVs in whole genome, showing arr 18q22.3q23(69,461,933-78,014,123) Ã1. Sample LMQ155 received prenatal diagnosis because of advanced maternal age and NIPT result of a 2.29Mb microduplication in Chr13 at 15 gestational week. Amniocentesis was performed at the 17th gestational week. Affymetrix CytoScan HD array were used to detect fetal CNVs in whole genome, which showed arr 13q21.2(60,399,612-61,730,194) Ã3 that was consistent with NIPT result.

2016-11-16 | E-MTAB-4738 | biostudies-arrayexpress

Copy number variants analysis of heterotaxy syndrome patients with congenital heart defects

Project description:To identify the molecular causes of heterotaxy syndrome patients with congenital heart defects, an Affymetrix CytoScan HD array was used to identify possible pathogenic CNVs in 63 patients. A total of 59 samples passed initial quality control.

2018-05-24 | E-MTAB-6820 | biostudies-arrayexpress

CGH analysis of an extramedullary muletiple myeloma PDX

Project description:A patient derived orthotopic xenograft (PDOX) was generated from a patient with an aggressive EMM to study in-depth genetic and epigenetic events and drug responses related to extramedullary disease. One of these studies was the evaluation of genetic imbalances by Affymetrix Cytoscan 750K array. The PDOX was derived from a fresh punch of an extramedullary cutaneous lesion that was orthotopically implanted in a NSG mouse. The PDOX mimicked histologic and phenotypic features of patient’s tumor. Cytogenetic studies revealed a hyperploid genome with multiple genetic poor-prognosis alterations. Copy number alterations were detected in all chromosomes.

2021-06-18 | E-MTAB-10630 | biostudies-arrayexpress

Affymetrix CytoscanHD data for genomic plasticity of osteosarcoma cell lines

Project description:To identify chromosomal aberrations during passaging of parental SAOS-2 osteosarcoma cells with low metastatic potential and of SAOS-2-derived LM5 cells with increased metastatic potential DNA of early and late passage SAOS-2 and LM5 cells was analyzed by Affymetrix Cytoscan HD genotyping arrays

2015-05-01 | E-GEOD-67125 | biostudies-arrayexpress

Tracing the development of acute myeloid leukemia in CBL-syndrome

Project description:Comparison of copy number variations of acute myeloid leukemia mononuclear cells and the given cell types collected during complete remission of the acute myeloid leukemia

2014-02-12 | E-MEXP-3997 | biostudies-arrayexpress

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