title: Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
abstract: We report the first quantitative and qualitative analysis of the poly (A)⁺ transcriptome of two human mammary cell lines, differentially expressing (human epidermal growth factor receptor) an oncogene over-expressed in approximately 25% of human breast tumors. Full-length cDNA populations from the two cell lines were digested enzymatically, individually tagged according to a customized method for library construction, and simultaneously sequenced by the use of the Titanium 454-Roche-platform. Comprehensive bioinformatics analysis followed by experimental validation confirmed novel genes, splicing variants, single nucleotide polymorphisms, and gene fusions indicated by RNA-seq data from both samples. Moreover, comparative analysis showed enrichment in alternative events, especially in the exon usage category, in ERBB2 over-expressing cells, data indicating regulation of alternative splicing mediated by the oncogene. Alterations in expression levels of genes, such as LOX, ATP5L, GALNT3, and MME revealed by large-scale sequencing were confirmed between cell lines as well as in tumor specimens with different ERBB2 backgrounds. This approach was shown to be suitable for structural, quantitative, and qualitative assessment of complex transcriptomes and revealed new events mediated by ERBB2 overexpression, in addition to potential molecular targets for breast cancer that are driven by this oncogene.
authors: Centro Internacional de Ensino e Pesquisa, Hospital AC Camargo, São Paulo, São Paulo, Brazil. dirce.carraro@accamargo.org.br
authors: Dirce Maria
authors: DM
authors: Carraro
authors: Elisa Napolitano
authors: EN
authors: Ferreira
authors: Gustavo
authors: G
authors: de Campos Molina
authors: Renato David
authors: RD
authors: Puga
authors: Eduardo Fernandes
authors: EF
authors: Abrantes
authors: Adriana Priscila
authors: AP
authors: Trapé
authors: Bedrich L
authors: BL
authors: Eckhardt
authors: Bedrich L
authors: BL
authors: Ekhardt
authors: Diana Noronha
authors: DN
authors: Nunes
authors: Maria Mitzi
authors: MM
authors: Brentani
authors: Wadih
authors: W
authors: Arap
authors: Renata
authors: R
authors: Pasqualini
authors: Helena
authors: H
authors: Brentani
authors: Emmanuel
authors: E
authors: Dias-Neto
authors: Ricardo Renzo
authors: RR
authors: Brentani
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D001483:Base Sequence; D001940:Breast / Q000166:cytology* / Q000378:metabolism*; D002460:Cell Line; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling; D050939:Gene Fusion / Q000235:genetics; D015723:Gene Library; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D011061:Poly A / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics / Q000378:metabolism*; D015203:Reproducibility of Results
chemical_list: D011061:Poly A; D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human