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Series GSE50451 Query DataSets for GSE50451
Status Public on Dec 23, 2014
Title Microarray analysis of Merkel cell carcinoma (MCC) tumors, small cell lung cancer (SCLC) tumors, and MCC cell lines
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
Overall design RNA was extracted from MCC cell lines and MCC and SCLC tumor samples and hybridized to Affymetrix microarrays for transcriptome profiling.
Contributor(s) Brownell I, Daily K
Citation(s) 25521454, 38398178
Submission date Aug 29, 2013
Last update date Mar 07, 2024
Contact name Isaac Brownell
Organization name National Cancer Institute
Department Dermatology Branch
Street address 10 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (77)
GSM1219436 MT01
GSM1219437 MT02
GSM1219438 MT03
BioProject PRJNA217507

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50451_ComBat_GSE36133samples.txt.gz 740 b (ftp)(http) TXT
GSE50451_RAW.tar 191.4 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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