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Series GSE22301 Query DataSets for GSE22301
Status Public on Dec 01, 2010
Title Gene expression data from melanoma cell lines and melanocyte controls
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The two most common melanoma histopathologic subtypes, superficial spreading (SSM) and nodular melanoma (NM), are believed to represent sequential phases of linear progression from radial to vertical growth. Studies suggest, however, that SSM and NM are biologically distinct. We utilized an integrative genomic approach to examine the possibility that SSM and NM are the result of independent pathways characterized by unique molecular alterations. Cell lines including SSM, NM, metastatic melanoma, and melanocyte controls were evaluated for copy number changes and differential mRNA expression using single nucleotide polymorphism array (SNP 6.0, Affymetrix) and gene array (U133A 2.0, Affymetrix). Data sets were integrated to identify copy number alterations that correlated with gene expression, and array results were validated using immunohistochemistry on human tissue microarrays (TMAs) and an external data set. The functional effect of genomic deletion was assessed by lentiviral overexpression. Integrative genomics revealed 8 genes in which NM/SSM-specific copy number alterations were correlated with NM/SSM differential gene expression (P<0.05, Spearman’s rank). Pathways analysis of differentially expressed genes (N=114) showed enrichment for metabolic-related processes. SSM-specific genomic deletions (DIS3, MTAP, G3BP2, SEC23IP, USO1) were verified in an expanded panel of cell lines, and forced overexpression of MTAP in SSM resulted in reduced cell growth. Metabolism-related gene ALDH7A1 was verified as overexpressed in NM using human TMAs.The identification of recurrent genomic deletions in SSM not present in NM challenges the linear model of melanoma progression and supports the unique molecular classification of SSM and NM.
Overall design Gene expression profiling using Affymetrix U133A 2.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP).
Contributor(s) Osman I
Citation(s) 21343389
Submission date Jun 11, 2010
Last update date Dec 06, 2018
Contact name Iman Osman
Phone 212-263-9089
Fax 212-263-9090
Organization name New York University School of Medicine
Department Urology
Street address 522 First Avenue, SML405
City New York
State/province NY
ZIP/Postal code 10016
Country USA
Platforms (1)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (22)
GSM555116 Normal human melanocyte_HEM-N
GSM555117 Immortalized melanocyte_Hermes1
GSM555118 Immortalized melanocyte_Hermes2B
This SubSeries is part of SuperSeries:
GSE22306 Integrative genomics identifies molecular alterations that differentiate superficial spreading and nodular melanoma
BioProject PRJNA129249

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
GSE22301_RAW.tar 43.5 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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