Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.

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 t...

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Autores principales:	Dirce Maria Carraro, Elisa Napolitano Ferreira, Gustavo de Campos Molina, Renato David Puga, Eduardo Fernandes Abrantes, Adriana Priscila Trapé, Bedrich L Eckhardt, Diana Noronha Nunes, Maria Mitzi Brentani, Wadih Arap, Renata Pasqualini, Helena Brentani, Emmanuel Dias-Neto, Ricardo Renzo Brentani
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/11de31141a2749b8b8c448d12b996b31
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spelling	oai:doaj.org-article:11de31141a2749b8b8c448d12b996b312021-11-18T06:51:35ZPoly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.1932-620310.1371/journal.pone.0021022https://doaj.org/article/11de31141a2749b8b8c448d12b996b312011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21731642/?tool=EBIhttps://doaj.org/toc/1932-6203We 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.Dirce Maria CarraroElisa Napolitano FerreiraGustavo de Campos MolinaRenato David PugaEduardo Fernandes AbrantesAdriana Priscila TrapéBedrich L EckhardtDiana Noronha NunesMaria Mitzi BrentaniWadih ArapRenata PasqualiniHelena BrentaniEmmanuel Dias-NetoRicardo Renzo BrentaniPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 6, p e21022 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dirce Maria Carraro Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Renata Pasqualini Helena Brentani Emmanuel Dias-Neto Ricardo Renzo Brentani Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
description	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.
format	article
author	Dirce Maria Carraro Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Renata Pasqualini Helena Brentani Emmanuel Dias-Neto Ricardo Renzo Brentani
author_facet	Dirce Maria Carraro Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Renata Pasqualini Helena Brentani Emmanuel Dias-Neto Ricardo Renzo Brentani
author_sort	Dirce Maria Carraro
title	Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
title_short	Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
title_full	Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
title_fullStr	Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
title_full_unstemmed	Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
title_sort	poly (a)+ transcriptome assessment of erbb2-induced alterations in breast cell lines.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/11de31141a2749b8b8c448d12b996b31
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Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.

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