Determination of the protein expression profiles of breast cancer cell lines by quantitative proteomics using iTRAQ labelling and tandem mass spectrometry.
Breast cancer is the principal cancer in women worldwide. Although there are serum tumor markers such as CEA and HER2, they are detected in advanced stages of the disease and used as progression and recurrence markers. Therefore, there is a necessity for the identification of new markers that might lead to an early detection and also provide evidence of an effective treatment. The aim of this work was to determine the differential protein expression profiles of four breast cancer cell lines in comparison to a normal control cell line by iTRAQ labelling and tandem mass spectrometry, in order to identify putative biomarkers of the disease. We identified 1,020 iTRAQ-labelled polypeptides with at least one peptide identified with more than 95% in confidence. Overexpressed polypeptides in all cancer cell lines were 78, whilst the subexpressed were 128. We categorised them with PANTHER program into biological processes, being the metabolic pathways the most affected. We detected six groups of proteins with the STRING program involved in DNA topology, glycolysis, translation initiation, splicing, pentose pathway, and proteasome degradation. The main subexpressed protein network included mitochondrial proteins involved in oxidative phosphorylation. We propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer.


CONCLUSIONS
We report a set of differentially expressed proteins in the MCF7 and T47D (Luminal A), MDA-MB-231 (Claudin low) and SK-BR-3 (HER2(+)) breast cancer cell lines that have not been previously reported in breast cancer disease. From these proteins, we propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. On the other hand, we propose sets of unique polypeptides in each breast cancer cell line that can be useful in the classification of different subtypes of breast cancer.
Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México. Electronic address: karla_grises@hotmail.com.
Karla Grisel
KG
Calderón-González
Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España. Electronic address: mluz.valero@uv.es.
Ma Luz
ML
Valero Rustarazo
Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México. Electronic address: azu_car2000@yahoo.com.mx.
Maria Luisa
ML
Labra-Barrios
Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México. Electronic address: cesar_bazan@hotmail.com.
César Isaac
CI
Bazán-Méndez
Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México. Electronic address: taveratapia@hotmail.com.
Alejandra
A
Tavera-Tapia
Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México. Electronic address: maestherha2@yahoo.com.mx.
Maria Esther
ME
Herrera-Aguirre
Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España. Electronic address: sandelpi@uv.es.
Manuel M
MM
Sánchez del Pino
AB SCIEX, 500 Old Connecticut Path, Framingham, MA 01701, USA. Electronic address: gallego7@gmail.com.
José Luis
JL
Gallegos-Pérez
Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México. Electronic address: hgm@xanum.uam.mx.
Humberto
H
González-Márquez
Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México. Electronic address: manolo@cell.cinvestav.mx.
Jose Manuel
JM
Hernández-Hernández
Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Miguel Hidalgo, C.P. 11340, México, D. F., México. Electronic address: leonavila60@yahoo.com.mx.
Gloria
G
León-Ávila
Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México. Electronic address: sergiorocue@gmail.com.
Sergio
S
Rodríguez-Cuevas
Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México. Electronic address: fguisa@fucam.org.mx.
Fernando
F
Guisa-Hohenstein
Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México. Electronic address: jpluna@cell.cinvestav.mx.
Juan Pedro
JP
Luna-Arias
D014408:Biomarkers, Tumor / Q000737:chemistry / Q000378:metabolism*; D001943:Breast Neoplasms / Q000737:chemistry / Q000378:metabolism*; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D009363:Neoplasm Proteins / Q000737:chemistry / Q000378:metabolism*; D010449:Peptide Mapping / Q000379:methods*; D013194:Staining and Labeling / Q000379:methods
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
Breast cancer; Cell lines; Putative biomarkers; Quantitative proteomics; Tandem mass spectrometry; iTRAQ labelling