Molecular markers associated with nonepithelial ovarian cancer in formalin-fixed, paraffin-embedded specimens by genome wide expression profiling

Koon Vui-Kee, Ahmad Zailani Hatta Mohd Dali, Isa Mohamed Rose, Razmin Ghazali, A. Rahman A. Jamal, Norfilza Mohd Mokhtar

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Nonepithelial ovarian cancer (NEOC) is a rare cancer that is often misdiagnosed as other malignant tumors. Research on this cancer using fresh tissues is nearly impossible because of its limited number of samples within a limited time provided. The study is to identify potential genes and their molecular pathways related to NEOC using formalin-fixed paraffin embedded samples. Total RNA was extracted from eight archived NEOCs and seven normal ovaries. The RNA samples with RNA integrity number >2.0, purity >1.7 and cycle count value <28 cycles were hybridized to the Illumina Whole-Genome DASL assay (cDNA-mediated annealing, selection, extension, and ligation). We analyzed the results using the GeneSpring GX11.0 and FlexArray software to determine the differentially expressed genes. Microarray results were validated using an immunohistochemistry method. Statistical analysis identified 804 differentially expressed genes with 443 and 361 genes as overexpressed and underexpressed in cancer, respectively. Consistent findings were documented for the overexpression of eukaryotic translation elongation factor 1 alpha 1, E2F transcription factor 2, and fibroblast growth factor receptor 3, except for the down-regulated gene, early growth response 1 (EGR1). The immunopositivity staining for EGR1 was found in the majority of cancer tissues. This finding suggested that the mRNA level of a transcript did not always match with the protein expression in tissues. The current gene profile can be the platform for further exploration of the molecular mechanism of NEOC.

Original languageEnglish
Pages (from-to)243-250
Number of pages8
JournalKaohsiung Journal of Medical Sciences
Volume28
Issue number5
DOIs
Publication statusPublished - May 2012

Fingerprint

Paraffin
Ovarian Neoplasms
Formaldehyde
Genome
Genes
RNA
Neoplasms
E2F1 Transcription Factor
Receptor, Fibroblast Growth Factor, Type 3
Peptide Elongation Factor 1
Growth
Diagnostic Errors
Ligation
Ovary
Software
Complementary DNA
Immunohistochemistry
Staining and Labeling
Messenger RNA
Research

Keywords

  • Gene expression
  • Microarray analysis
  • Ovarian cancer

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Molecular markers associated with nonepithelial ovarian cancer in formalin-fixed, paraffin-embedded specimens by genome wide expression profiling. / Vui-Kee, Koon; Mohd Dali, Ahmad Zailani Hatta; Mohamed Rose, Isa; Ghazali, Razmin; A. Jamal, A. Rahman; Mohd Mokhtar, Norfilza.

In: Kaohsiung Journal of Medical Sciences, Vol. 28, No. 5, 05.2012, p. 243-250.

Research output: Contribution to journalArticle

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