title: Multiple gene expression analyses in paraffin-embedded tissues by TaqMan low-density array: Application to hedgehog and Wnt pathway analysis in ovarian endometrioid adenocarcinoma.
abstract: Recent studies have shown the hedgehog and Wnt families of signaling proteins to be associated with tumor initiation, growth, and survival. However, these pathways remain unexplored in ovarian endometrioid adenocarcinoma (OEA). Here, we describe a novel TaqMan low-density array to examine the expression of 26 and 20 genes in the hedgehog and Wnt pathways, respectively, in six matched snap-frozen and formalin-fixed, paraffin-embedded (FPE) OEA specimens. Expression values were normalized to uninvolved ovarian epithelium. Gene expression in matched frozen and FPE tissues demonstrated significant concordance (r = 0.92, P < 0.0001). However, comparison of amplified and unamplified RNA from frozen OEA tissues revealed an altered molecular profile in amplified RNA. Amplification of RNA from FPE tissues was not successful. The expression of Desert hedgehog (DHH), Indian hedgehog (IHH), Hedge-hog interacting protein (HHIP), Wnt10B, Wnt9B, and Wnt inhibitory factor (WIF1) were tumor-specific with no detectable expression in normal ovarian epithelium. In addition, several genes were significantly (P < 0.025) down-regulated in OEA, including cyclin E2, Porcupine, c-Myc, and Axin 2 (4.8-, 3.6-, 2.9-, and 1.9-fold, respectively). TaqMan low-density array provides an effective multivariate technique for examining gene expression in RNA isolated from either snap-frozen or archival FPE tissues and can identify tumor-specific genes, possibly leading to novel treatments.
authors.affiliation: Department of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL 34294-3300, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Steg
authors.forename: Wenquan
authors.initials: W
authors.lastname: Wang
authors.forename: Carmelo
authors.initials: C
authors.lastname: Blanquicett
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Grunda
authors.forename: Isam A
authors.initials: IA
authors.lastname: Eltoum
authors.forename: Kangsheng
authors.initials: K
authors.lastname: Wang
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Buchsbaum
authors.forename: Selwyn M
authors.initials: SM
authors.lastname: Vickers
authors.forename: Suzanne
authors.initials: S
authors.lastname: Russo
authors.forename: Robert B
authors.initials: RB
authors.lastname: Diasio
authors.forename: Andra R
authors.initials: AR
authors.lastname: Frost
authors.forename: Al F
authors.initials: AF
authors.lastname: LoBuglio
authors.forename: William E
authors.initials: WE
authors.lastname: Grizzle
authors.forename: Martin R
authors.initials: MR
authors.lastname: Johnson
mesh_terms: D000818:Animals; D018269:Carcinoma, Endometrioid / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D005629:Frozen Sections; D020869:Gene Expression Profiling; D053823:Hedgehog Proteins; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D016612:Paraffin Embedding / Q000379:methods; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction; D015534:Trans-Activators / Q000032:analysis*; D051153:Wnt Proteins / Q000032:analysis*
chemical_list: D005404:Fixatives; D053823:Hedgehog Proteins; D015534:Trans-Activators; D051153:Wnt Proteins; D005557:Formaldehyde