Please use this identifier to cite or link to this item: http://repositorio.unicamp.br/jspui/handle/REPOSIP/235277
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dc.contributor.CRUESPUNIVERSIDADE ESTADUAL DE CAMPINASpt_BR
dc.contributor.authorunicampFilgueiras, Paulo Robertopt_BR
dc.contributor.authorunicampPoppi, Ronei Jesuspt_BR
dc.contributor.authorunicampTelles, Guilherme Pimentelpt_BR
dc.contributor.authorunicampFonseca, Felipe Paivapt_BR
dc.contributor.authorunicampSantos-Silva, Alan Rogerpt_BR
dc.contributor.authorunicampDella Coletta, Ricardopt_BR
dc.typeArtigopt_BR
dc.titleIntegrative analysis to select cancer candidate biomarkers to targeted validationpt_BR
dc.contributor.authorKawahara, Rebecapt_BR
dc.contributor.authorMeirelles, Gabriela V.pt_BR
dc.contributor.authorHeberle, Henrypt_BR
dc.contributor.authorDomingues, Romênia R.pt_BR
dc.contributor.authorGranato, Daniela C.pt_BR
dc.contributor.authorYokoo, Samipt_BR
dc.contributor.authorCanevarolo, Rafael R.pt_BR
dc.contributor.authorWinck, Flavia V.pt_BR
dc.contributor.authorRibeiro, Ana Carolina P.pt_BR
dc.contributor.authorBrandão, Thaís Biancapt_BR
dc.contributor.authorFilgueiras, Paulo R.pt_BR
dc.contributor.authorCruz, Karen S. P.pt_BR
dc.contributor.authorBarbuto, José Alexandrept_BR
dc.contributor.authorPoppi, Ronei J.pt_BR
dc.contributor.authorMinghim, Rosanept_BR
dc.contributor.authorTelles, Guilherme P.pt_BR
dc.contributor.authorFonseca, Felipe Paivapt_BR
dc.contributor.authorFox, Jay W.pt_BR
dc.contributor.authorSantos-Silva, Alan R.pt_BR
dc.contributor.authorColetta, Ricardo D.pt_BR
dc.contributor.authorSherman, Nicholas E.pt_BR
dc.contributor.authorPaes Leme, Adriana F.pt_BR
unicamp.authorPaulo R Filgueiras, Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.pt_BR
unicamp.authorRonei J Poppi, Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.pt_BR
unicamp.authorGuilherme P Telles, Instituto de Computação, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil.pt_BR
unicamp.authorFelipe Paiva Fonseca, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.pt_BR
unicamp.authorAlan R Santos-Silva, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.pt_BR
unicamp.authorRicardo D Coletta, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.pt_BR
unicamp.author.externalRebeca Kawahara, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
unicamp.author.externalGabriela V Meirelles, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
unicamp.author.externalHenry Heberle, Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil.pt
unicamp.author.externalRomênia R Domingues, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
unicamp.author.externalDaniela C Granato, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
unicamp.author.externalSami Yokoo, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
unicamp.author.externalRafael R Canevarolo, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil. Centro Infantil Boldrini, Campinas, Brazil.pt
unicamp.author.externalFlavia V Winck, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
unicamp.author.externalAna Carolina P Ribeiro, Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil.pt
unicamp.author.externalThaís Bianca Brandão, Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil.pt
unicamp.author.externalKaren S P Cruz, Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil.pt
unicamp.author.externalJosé Alexandre Barbuto, Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil.pt
unicamp.author.externalRosane Minghim, Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil.pt
unicamp.author.externalJay W Fox, W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA.pt
unicamp.author.externalNicholas E Sherman, W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA.pt
unicamp.author.externalAdriana F Paes Leme, Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.pt
dc.subjectProteômicapt_BR
dc.subject.otherlanguageProteomicspt_BR
dc.description.abstractTargeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS.en
dc.description.abstractTargeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MSpt
dc.relation.ispartofOncotargetpt_BR
dc.relation.ispartofabbreviationOncotargetpt_BR
dc.publisher.cityOrchard Park, NYpt_BR
dc.publisher.countryEstados Unidospt_BR
dc.publisherImpact Journalspt_BR
dc.date.issued2015pt_BR
dc.date.monthofcirculationDec.pt_BR
dc.identifier.citationOncotarget. v. 6, n. 41, p. 43635-43652, 2015-Dec.pt_BR
dc.language.isoengpt_BR
dc.description.volume6pt_BR
dc.description.issuenumber41pt_BR
dc.description.firstpage43635pt_BR
dc.description.lastpage43652pt_BR
dc.rightsabertopt_BR
dc.sourcePubMedpt_BR
dc.sourcePUBMEDpt_br
dc.identifier.eissn1949-2553pt_BR
dc.identifier.doi10.18632/oncotarget.6018pt_BR
dc.identifier.urlhttp://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=6018pt_BR
dc.description.sponsorshipFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOpt_BR
dc.description.sponsorshipCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOpt_BR
dc.description.sponsorship1FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOpt_BR
dc.description.sponsorship1CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOpt_BR
dc.description.sponsordocumentnumber2009/54067-3; 2010/19278-0; 2011/22421-2; 2009/53839-2pt_BR
dc.description.sponsordocumentnumber470567/2009-0; 470549/2011-4; 301702/2011-0; 470268/2013-1pt_BR
dc.date.available2016-05-23T19:40:22Z-
dc.date.accessioned2016-05-23T19:40:22Z-
dc.description.provenanceMade available in DSpace on 2016-05-23T19:40:22Z (GMT). No. of bitstreams: 1 pmed_26540631.pdf: 5511548 bytes, checksum: d73eb58783809d6c3d7d3c9f4aede557 (MD5) Previous issue date: 2015 Bitstreams deleted on 2020-05-14T20:38:54Z: pmed_26540631.pdf,. Added 1 bitstream(s) on 2020-05-14T20:43:14Z : No. of bitstreams: 1 26540631.pdf: 478343 bytes, checksum: 8196be6590a879ede8688f2c3e5e2457 (MD5) Bitstreams deleted on 2020-06-04T12:48:09Z: 26540631.pdf,. Added 1 bitstream(s) on 2020-06-04T12:53:20Z : No. of bitstreams: 1 26540631.pdf: 5965445 bytes, checksum: 20ea1b4fad198cf4c278e861859a0134 (MD5)en
dc.identifier.urihttp://repositorio.unicamp.br/jspui/handle/REPOSIP/235277-
dc.identifier.idPubmed26540631pt_BR
dc.contributor.departmentsem informaçãopt_BR
dc.contributor.departmentDepartamento de Química Analíticapt_BR
dc.contributor.departmentDepartamento de Teoria da Computaçãopt_BR
dc.contributor.departmentsem informaçãopt_BR
dc.contributor.departmentDepartamento de Diagnóstico Oralpt_BR
dc.contributor.departmentDepartamento de Diagnóstico Oralpt_BR
dc.contributor.unidadeInstituto de Químicapt_BR
dc.contributor.unidadeInstituto de Químicapt_BR
dc.contributor.unidadeInstituto de Computaçãopt_BR
dc.contributor.unidadeFaculdade de Odontologia de Piracicabapt_BR
dc.contributor.unidadeFaculdade de Odontologia de Piracicabapt_BR
dc.contributor.unidadeFaculdade de Odontologia de Piracicabapt_BR
dc.subject.keywordCandidate biomarkerpt_BR
dc.subject.keywordIntegrative analysispt_BR
dc.subject.keywordDiscoverypt_BR
dc.subject.keywordTargetedpt_BR
dc.identifier.source26540631-
dc.creator.orcidsem informaçãopt_BR
dc.creator.orcidsem informaçãopt_BR
dc.creator.orcid0000-0003-2608-4807pt_BR
dc.creator.orcidsem informaçãopt_BR
dc.creator.orcid0000-0003-2040-6617pt_BR
dc.creator.orcid0000-0001-5285-3046pt_BR
dc.type.formArtigo-
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