E-GEOD-57000 - Microarray analysis of H460 parental and H460 holoclone (stem-like cell)-derived tumors

Status
Released on 23 April 2014, last updated on 3 June 2014
Organism
Homo sapiens
Samples (8)
Array (1)
Protocols (8)
Description
BACKGROUND: Cancer stem-like cells were isolated from human H460 non-small cell lung cancer cells by limiting dilution assays and by their holoclone morphology, followed by assessment of their self-renewal capacity, tumor growth, vascularity, and tumor blood perfusion. H460 holoclones were used to implant H460 holoclone-derived tumors, which grew slower than parental H460 tumors, but displayed significant increases in microvessel density and tumor blood perfusion. Microarray analysis identified differentially regulated genes in the holoclone-derived tumors, of which many were associated with angiogenesis. The differentially regulated genes include several small leucine-rich proteoglycans that may modulate angiogenesis and serve as novel therapeutic targets for inhibiting cancer stem cell-driven angiogenesis.(Cancer Letters Vol 346, Issue 1, 28 April 2014, Pages 63–73; PMID: 24334139; PMCID: PMC3947657). Implanted tumors derived from H460 parental cells, or from each of four independent H460 holoclones, were implanted subcutaneously in scid immunodeficient mice. Tumors derived from the 4 holoclones (designated H460/2E1, H460/2H3, H460/3F1, and H460/2E7) were used for global transcriptome/microarray analysis in direct comparison to H460 tumors grown from parental H460 cells. For each H460 holoclone-derived tumor line or H460 parental cell-derived tumor, total RNA was prepared from n=7 to n=10 individual tumors and used to prepare two independent pools of tumor RNA (each pool comprised of RNA isolated n=3-5 tumors) for use in a two color microarray analysis. Tumor RNA pools were prepared by combining equal amounts of RNA from each individual tumor to minimize the impasct of inter-tumoral variation on gene expression profiles. All RNAs had an RNA integrity number >8.0, determined using an Agilent Bioanalyzer 2100 instrument. cDNAs transcribed from pools of RNA for each holoclone-derived tumor line and for each parental H460 cell-derived tumor pool, were labeled with Alexa 647 or Alexa 555 dyes in a fluorescent reverse pair (dye swap) design for competitive hybridization to Agilent Whole Human Genome Microarrays.
Experiment type
transcription profiling by array 
Contacts
David J. Waxman <djw@bu.edu>, David J Waxman, Eugene Manley Jr
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-57000.idf.txt
Sample and data relationshipE-GEOD-57000.sdrf.txt
Raw data (1)E-GEOD-57000.raw.1.zip
Processed data (1)E-GEOD-57000.processed.1.zip
Array designA-GEOD-13497.adf.txt
Links