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E-GEOD-50451 - Microarray analysis of Merkel cell carcinoma (MCC) tumors, small cell lung cancer (SCLC) tumors, and MCC cell lines

Status
Released on 23 December 2014, last updated on 2 January 2015
Organism
Homo sapiens
Samples (77)
Arrays (2)
Protocols (11)
Description
When using cell lines to study cancer, phenotypic similarity to the original tumor is paramount. Yet, little has been done to characterize how closely Merkel cell carcinoma (MCC) cell lines model native tumors. To determine their similarity to MCC tumor samples, we characterized MCC cell lines via gene expression microarrays. Using whole transcriptome gene expression signatures and a computational bioinformatic approach, we identified significant differences between variant cell lines (UISO, MCC13, and MCC26) and fresh frozen MCC tumors. Conversely, the classic WaGa and Mkl-1 cell lines more closely represented the global transcriptome of MCC tumors. When compared to publicly available cancer lines, WaGa and Mkl-1 cells were similar to other neuroendocrine tumors, but the variant cell lines were not. WaGa and Mkl-1 cells grown as xenografts in mice had histological and immunophenotypical features consistent with MCC, while UISO xenograft tumors were atypical for MCC. Spectral karyotyping and short tandem repeat analysis of the UISO cells matched the original cell line's description, ruling out contamination. Our results validate the use of transcriptome analysis to assess the cancer cell line representativeness and indicate that UISO, MCC13, and MCC26 cell lines are not representative of MCC tumors, whereas WaGa and Mkl-1 more closely model MCC. RNA was extracted from MCC cell lines and MCC and SCLC tumor samples and hybridized to Affymetrix microarrays for transcriptome profiling.
Experiment type
transcription profiling by array 
Contacts
Citation
Assessment of Cancer Cell Line Representativeness using Microarrays for Merkel Cell Carcinoma. Daily K, Coxon A, Williams JS, Lee C, Coit DG, Busam KJ, Brownell I. , PMID:25521454
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-50451.idf.txt
Sample and data relationshipE-GEOD-50451.sdrf.txt
Raw data (2)E-GEOD-50451.raw.1.zip, E-GEOD-50451.raw.2.zip
Processed data (1)E-GEOD-50451.processed.1.zip
Additional data (1)E-GEOD-50451.additional.1.zip
Array designsA-AFFY-37.adf.txt, A-AFFY-44.adf.txt
Links