Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Adult ALL (Acute Lymphoblastic Leukemia)

ABSTRACT: A set of 37 BCR-ABL positive (21 and 16 of which expressed p185 and p210, respectively) and 17 BCR-ABL negative adult ALL specimens from the ECOG/MRC intergroup study E2993. Gene expression profiling was performed using the 3DNA Array 900 Expression Array Detection Kit (Genisphere, Hatfield, PA), according to the manufacturer's instructions. Universal Human Reference RNA (Stratagene, La Jolla, CA) was used as a reference RNA. The results provide insights into molecular mechanisms and pathways associated with BCR-ABL oncogenesis. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set Computed

ORGANISM(S): Homo sapiens

SUBMITTER: Dejan Juric

PROVIDER: E-GEOD-5314 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias.

Juric Dejan D Lacayo Norman J NJ Ramsey Meghan C MC Racevskis Janis J Wiernik Peter H PH Rowe Jacob M JM Goldstone Anthony H AH O'Dwyer Peter J PJ Paietta Elisabeth E Sikic Branimir I BI

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 20070220 11

<h4>Purpose</h4>To identify gene expression patterns and interaction networks related to BCR-ABL status and clinical outcome in adults with acute lymphoblastic leukemia (ALL).<h4>Patients and methods</h4>DNA microarrays were used to profile a set of 54 adult ALL specimens from the Medical Research Council UKALL XII/Eastern Cooperative Oncology Group E2993 trial (21 p185BCR-ABL-positive, 16 p210BCR-ABL-positive and 17 BCR-ABL-negative specimens).<h4>Results</h4>Using supervised and unsupervised a ...[more]

PMID: 17312329

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Project description:Summary: Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies. Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity. In particular, microarray studies have identified molecular subtypes (luminal A, luminal B, ERBB2-associated, basal-like and normal-like) with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs). Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes. Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors. Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes. Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression. Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes. Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics. Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs. We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes. Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes. HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of 50 human breast epithelial cell lines, in comparison to a universal RNA reference. Expression data were analyzed by hierarchical clustering to identify subgroups, and gene set enrichment analysis to identify subgroup-specific gene pathways.

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Dataset Information

Adult ALL (Acute Lymphoblastic Leukemia)

Publications

Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias.

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