Transcriptomics

Dataset Information

3

Affymetrix SNP6 copy number data on ovarian cancer cell lines


ABSTRACT: Background: Ovarian carcinomas consist of at least five distinct diseases: high-grade serous, low-grade serous, clear cell, endometrioid, and mucinous. Biomarker and molecular characterization may represent a more biologically relevant basis for grouping and treating this family of tumors, rather than site of origin. Molecular characteristics have become the new standard for clinical pathology, however development of tailored type-specific therapies is hampered by a failure of basic research to recognize that model systems used to study these diseases must also be stratified. Unrelated model systems do offer value for study of biochemical processes but specific cellular context needs to be applied to assess relevant therapeutic strategies. Methods: We have focused on the identification of clear cell carcinoma cell line models. A panel of 32 “ovarian cancer” cell lines has been classified into histological types using a combination of mutation profiles, IHC mutation-surrogates, and a validated immunohistochemical model. All cell lines were identity verified using STR analysis. Results: Many described ovarian clear cell lines have characteristic mutations (including ARID1A and PIK3CA) and an overall molecular/immuno-profile typical of primary tumors. Mutations in TP53 were present in the majority of high-grade serous cell lines. Advanced genomic analysis of bona-fide clear cell carcinoma cell lines also support copy number changes in typical biomarkers such at MET and HNF1B and a lack of any recurrent expressed re-arrangements. Conclusions: As with primary ovarian tumors, mutation status of cancer genes like ARID1A and TP53 and a general immuno-profile serve well for establishing histological type of ovarian cancer cell We describe specific biomarkers and molecular features to re-classify generic “ovarian carcinoma” cell lines into type specific categories. Our data supports the use of prototype clear cell lines, such as TOV21G and JHOC-5, and questions the use of SKOV3 and A2780 as models of high-grade serous carcinoma. The DNA copy number of 10 ovarian cancer cell lines was examined and changes in copy number of genes whose expression is assumed to be critical to the phenotype of ovarian clear cell carcinoma was evaluated. Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values were generated in Partek Genomics Suite (v 6.6) using a Partek corporation distributed baseline file of normal (2N) genomic DNA and default parameters. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19). The characteristic "literature reported histotype" is the reported histological subtype for each cell line from the originating laboratory or cell bank (repository). The characteristic "Predicted histology" is based on parameters described in Anglesio et al. (PLOS ONE 2013. in press), including immunohistochemical phenotype, presence of typical mutations, consistency in growth characteristics, and DNA copy number. All cell lines were grown under recomended conditions, collected near confluence (80%) and not subjected to any experimental treatments or modifications.

ORGANISM(S): Homo sapiens  

SUBMITTER: D G Huntsman   Michael S Anglesio  M A Spillman  W Yang  D R Cochrane  S E Kalloger  K Shumansky  S P Shah 

PROVIDER: E-GEOD-48351 | ArrayExpress | 2013-08-01

SECONDARY ACCESSION(S): GSE48351PRJNA209802

REPOSITORIES: GEO, ArrayExpress

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