title: Integrative analysis to select cancer candidate biomarkers to targeted validation.
abstract: Targeted 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.
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Rebeca
authors.initials: R
authors.lastname: Kawahara
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Gabriela V
authors.initials: GV
authors.lastname: Meirelles
authors.affiliation: Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil.
authors.forename: Henry
authors.initials: H
authors.lastname: Heberle
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Romênia R
authors.initials: RR
authors.lastname: Domingues
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Daniela C
authors.initials: DC
authors.lastname: Granato
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Sami
authors.initials: S
authors.lastname: Yokoo
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.|Centro Infantil Boldrini, Campinas, Brazil.
authors.forename: Rafael R
authors.initials: RR
authors.lastname: Canevarolo
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Flavia V
authors.initials: FV
authors.lastname: Winck
authors.affiliation: Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil.
authors.forename: Ana Carolina P
authors.initials: AC
authors.lastname: Ribeiro
authors.affiliation: Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil.
authors.forename: Thaís Bianca
authors.initials: TB
authors.lastname: Brandão
authors.affiliation: Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.
authors.forename: Paulo R
authors.initials: PR
authors.lastname: Filgueiras
authors.affiliation: Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil.
authors.forename: Karen S P
authors.initials: KS
authors.lastname: Cruz
authors.affiliation: Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil.
authors.forename: José Alexandre
authors.initials: JA
authors.lastname: Barbuto
authors.affiliation: Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.
authors.forename: Ronei J
authors.initials: RJ
authors.lastname: Poppi
authors.affiliation: Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil.
authors.forename: Rosane
authors.initials: R
authors.lastname: Minghim
authors.affiliation: Instituto de Computação, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil.
authors.forename: Guilherme P
authors.initials: GP
authors.lastname: Telles
authors.affiliation: Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.
authors.forename: Felipe Paiva
authors.initials: FP
authors.lastname: Fonseca
authors.affiliation: W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA.
authors.forename: Jay W
authors.initials: JW
authors.lastname: Fox
authors.affiliation: Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Santos-Silva
authors.affiliation: Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil.
authors.forename: Ricardo D
authors.initials: RD
authors.lastname: Coletta
authors.affiliation: W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA.
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Sherman
authors.affiliation: Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.
authors.forename: Adriana F
authors.initials: AF
authors.lastname: Paes Leme
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis*; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D015151:Immunoblotting; D013058:Mass Spectrometry; D009369:Neoplasms / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction; D046888:Tissue Array Analysis
chemical_list: D014408:Biomarkers, Tumor
keywords: candidate biomarker; discovery; integrative analysis; proteomics; targeted