E-GEOD-31013 - Transcription profiling by array of spontaneous lung tumors in mice to compare to human non-small cell lung cancer

Status
Released on 21 June 2012, last updated on 1 May 2015
Organism
Mus musculus
Samples (12)
Array (1)
Protocols (8)
Description
Introduction: Lung cancer is the leading cause of cancer-related death in people. There are several chemically induced and genetically modified mouse models used to study lung cancer. We hypothesized that spontaneous murine (B6C3F1) lung tumors can serve as a model to study human non-small cell lung cancer (NSCLC). Methods: RNA was extracted from untreated 2-year-old B6C3F1 mouse spontaneous lung (SL) tumors and age-matched normal lung tissue from a chronic inhalation NTP study. Global gene expression analysis was performed using Affymetrix Mouse Genome 430 2.0 GeneChip® arrays. After data normalization, for each probe set, pairwise comparisons between groups were made using a bootstrap t-test while controlling the mixed directional false discovery rate (mdFDR) to generate a differential gene expression list. IPA, KEGG, and EASE software tools were used to evaluate the overrepresented cancer genes and pathways. Results: MAPK and TGF-beta pathways were overrepresented within the dataset. Almost all of the validated genes by quantitative real time RT-PCR had comparable directional fold changes with the microarray data. The candidate oncogenes included Kras, Braf, Raf1, Id2, Hmga1, Cks1b, and Foxf1. The candidate tumor suppressor genes included Rb1, Cdkn2a, Hnf4a, Tcf21, Ptprd, Hpgd, Hopx, Ogn, Id4, Hoxa5, Smad6, Smad7, Zbtb16, Cyr61, Dusp4, and Ifi16. In addition, several genes important in lung development were also differentially expressed, such as Smad6, Hopx, Sox4, Sox9 and Mycn. Conclusion: In this study, we have demonstrated that several cancer genes and signaling pathways relevant for human NSCLC were similarly altered in spontaneous murine lung tumors. Six spontaneous lung tumors and six normal lungs (as controls) from 2-year-old B6C3F1 mice.
Experiment types
transcription profiling by array, disease state design
Contacts
NIEHS Microarray Core <microarray@niehs.nih.gov>, Arun R Pandiri, Hue-Hae L Hong, Keith R Shockley, Kevin E Gerrish, Mark J Hoenerhoff, Pierre R Bushel, Robert C Sills, Scott S Auerbach, Shyamal D Peddada, Stephanie A Lahousse, Thai-Vu Ton, Vincent Ziglioli
Citation
Differential Transcriptomic Analysis of Spontaneous Lung Tumors in B6C3F1 Mice: Comparison to Human Non-Small Cell Lung Cancer. Pandiri AR, Sills RC, Ziglioli V, Ton TV, Hong HH, Lahousse SA, Gerrish KE, Auerbach SS, Shockley KR, Bushel PR, Peddada SD, Hoenerhoff MJ.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-31013.idf.txt
Sample and data relationshipE-GEOD-31013.sdrf.txt
Raw data (1)E-GEOD-31013.raw.1.zip
Processed data (1)E-GEOD-31013.processed.1.zip
Array designA-AFFY-45.adf.txt
Links