Poly (A)(+) Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines

Author(s):Show less -

Carraro, Dirce Maria ^[1] ; Ferreira, Elisa Napolitano ^{[2, 1]} ; Molina, Gustavo de Campos ^[1] ; Puga, Renato David ^[1] ; Abrantes, Eduardo Fernandes ^[1] ; Trape, Adriana Priscila ^[3] ; Ekhardt, Bedrich L. ^[4] ; Nunes, Diana Noronha ^{[4, 1]} ; Brentani, Maria Mitzi ^[3] ; Arap, Wadih ^[4] ; Pasqualini, Renata ^[4] ; Brentani, Helena ^{[3, 1]} ; Dias-Neto, Emmanuel ^{[3, 4, 1]} ; Brentani, Ricardo Renzo ^[1]

Affiliation

^[1] Hosp AC Camargo Fund Antonio Prudente, Ctr Int Ensino & Pesquisa, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Inst Biociencias, Sao Paulo - Brazil

^[3] Univ Sao Paulo, Fac Med, Sao Paulo - Brazil

^[4] Univ Texas MD Anderson Canc Ctr, David H Koch Ctr, Houston, TX 77030 - USA

• Document type: Journal article
• Source: PLoS One; v. 6, n. 6 JUN 22 2011.
• Web of Science Citations: 12

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. (AU)

• FAPESP's process: 98/14335-2 - Antonio Prudente Cancer Research Center
• Grantee: Fernando Augusto Soares
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC