title: Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer.
abstract: A large fraction of transcripts are expressed antisense to introns of known genes in the human genome. Here we show the construction and use of a cDNA microarray platform enriched in intronic transcripts to assess their biological relevance in pathological conditions. To validate the approach, prostate cancer was used as a model, and 27 patient tumor samples with Gleason scores ranging from 5 to 10 were analyzed. We find that a considerably higher fraction (6.6%, [23/346]) of intronic transcripts are significantly correlated (P< or =0.001) to the degree of prostate tumor differentiation (Gleason score) when compared to transcripts from unannotated genomic regions (1%, [6/539]) or from exons of known genes (2%, [27/1369]). Among the top twelve transcripts most correlated to tumor differentiation, six are antisense intronic messages as shown by orientation-specific RT-PCR or Northern blot analysis with strand-specific riboprobe. Orientation-specific real-time RT-PCR with six tumor samples, confirmed the correlation (P=0.024) between the low/high degrees of tumor differentiation and antisense intronic RASSF1 transcript levels. The need to use intron arrays to reveal the transcriptome profile of antisense intronic RNA in cancer has clearly emerged.
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brasil.
authors.forename: Eduardo M
authors.initials: EM
authors.lastname: Reis
authors.forename: Helder I
authors.initials: HI
authors.lastname: Nakaya
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Louro
authors.forename: Flavio C
authors.initials: FC
authors.lastname: Canavez
authors.forename: Aurea V F
authors.initials: AV
authors.lastname: Flatschart
authors.forename: Giulliana T
authors.initials: GT
authors.lastname: Almeida
authors.forename: Camila M
authors.initials: CM
authors.lastname: Egidio
authors.forename: Apuã C
authors.initials: AC
authors.lastname: Paquola
authors.forename: Abimael A
authors.initials: AA
authors.lastname: Machado
authors.forename: Fernanda
authors.initials: F
authors.lastname: Festa
authors.forename: Denise
authors.initials: D
authors.lastname: Yamamoto
authors.forename: Renato
authors.initials: R
authors.lastname: Alvarenga
authors.forename: Camille C
authors.initials: CC
authors.lastname: da Silva
authors.forename: Glauber C
authors.initials: GC
authors.lastname: Brito
authors.forename: Sérgio D
authors.initials: SD
authors.lastname: Simon
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Moreira-Filho
authors.forename: Katia R
authors.initials: KR
authors.lastname: Leite
authors.forename: Luiz H
authors.initials: LH
authors.lastname: Camara-Lopes
authors.forename: Franz S
authors.initials: FS
authors.lastname: Campos
authors.forename: Etel
authors.initials: E
authors.lastname: Gimba
authors.forename: Giselle M
authors.initials: GM
authors.lastname: Vignal
authors.forename: Hamza
authors.initials: H
authors.lastname: El-Dorry
authors.forename: Mari C
authors.initials: MC
authors.lastname: Sogayar
authors.forename: Marcello A
authors.initials: MA
authors.lastname: Barcinski
authors.forename: Aline M
authors.initials: AM
authors.lastname: da Silva
authors.forename: Sergio
authors.initials: S
authors.lastname: Verjovski-Almeida
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D006801:Humans; D007438:Introns; D008297:Male; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011471:Prostatic Neoplasms / Q000235:genetics / Q000473:pathology*; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism*
chemical_list: D016372:RNA, Antisense