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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Integrative analysis to select cancer candidate biomarkers to targeted validation

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Author(s):
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Kawahara, Rebeca [1] ; Meirelles, Gabriela V. [1] ; Heberle, Henry [2] ; Domingues, Romenia R. [1] ; Granato, Daniela C. [1] ; Yokoo, Sami [1] ; Canevarolo, Rafael R. [3, 1] ; Winck, FlaviaV. [1] ; Ribeiro, Ana Carolina P. [4] ; Brandao, Thais Bianca [4] ; Filgueiras, Paulo R. [5] ; Cruz, Karen S. P. [6] ; Barbuto, Jose Alexandre [6] ; Poppi, Ronei J. [5] ; Minghim, Rosane [2] ; Telles, Guilherme P. [7] ; Fonseca, Felipe Paiva [8] ; Fox, Jay W. [9] ; Santos-Silva, Alan R. [8] ; Coletta, Ricardo D. [8] ; Sherman, Nicholas E. [9] ; Paes Leme, Adriana F. [1]
Total Authors: 22
Affiliation:
[1] CNPEM, LNBio, Lab Nacl Biociencias, Lab Espectrometria Massas, Campinas, SP - Brazil
[2] Univ Sao Paulo, Inst Ciencias Matemat & Comp, Sao Carlos, SP - Brazil
[3] Ctr Infantil Boldrini, Campinas, SP - Brazil
[4] Inst Canc Estado Sao Paulo, Sao Paulo - Brazil
[5] Univ Estadual Campinas, UNICAMP, Inst Quim, Piracicaba - Brazil
[6] Univ Sao Paulo, Inst Ciencias Biomed, Dept Imunol, BR-05508 Sao Paulo - Brazil
[7] Univ Estadual Campinas, UNICAMP, Inst Comp, Campinas, SP - Brazil
[8] Univ Estadual Campinas, UNICAMP, Fac Odontol Piracicaba, Piracicaba - Brazil
[9] Univ Virginia, WM Keck Biomed Mass Spectrometry Lab, Charlottesville, VA - USA
Total Affiliations: 9
Document type: Journal article
Source: ONCOTARGET; v. 6, n. 41, p. 43635-43652, DEC 22 2015.
Web of Science Citations: 4
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). Threeyfeature 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. (AU)

FAPESP's process: 11/22421-2 - Determination of cleavage sites of recombinant ADAM-17 in human cells
Grantee:Rebeca Kawahara Sakuma
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 09/54067-3 - Acquisition of a mass spectrometer coupled to a liquid chromatography system for increasing the capacity to meet the needs of users and for making new technologies available in the Laboratory of Mass Spectrometry
Grantee:Adriana Franco Paes Leme
Support Opportunities: Multi-user Equipment Program
FAPESP's process: 09/53839-2 - Creation of a Digital Pathology Laboratory using a histological slidescanner
Grantee:Oslei Paes de Almeida
Support Opportunities: Multi-user Equipment Program
FAPESP's process: 10/19278-0 - Study of regulation of ADAMs in oral cancer
Grantee:Adriana Franco Paes Leme
Support Opportunities: Research Grants - Young Investigators Grants