Shotgun proteomics of archival triple-negative breast cancer samples

Authors

  • Angelo Gámez-Pozo,

    1. Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
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  • Nuria Ibarz Ferrer,

    1. Unidad de Proteómica, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
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  • Eva Ciruelos,

    1. Servicio de Oncología, Instituto de Investigación Hospital Universitario Doce de Octubre-i+12, Madrid, Spain
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  • Rocío López-Vacas,

    1. Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
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  • Fernando García Martínez,

    1. Unidad de Proteómica, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
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  • Enrique Espinosa,

    1. Servicio de Oncología Médica, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
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  • Juan Ángel Fresno Vara

    Corresponding author
    • Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
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Correspondence: Dr. Juan Ángel Fresno Vara, Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular (INGEMM), Instituto de Investigación Hospital Universitario La Paz-Idi PAZ, Paseo de la Castellana, 261-28046 Madrid, Spain

E-mail: juanangel.fresno@idipaz.es

Fax: +34-91-2071040

Abstract

Purpose

Triple-negative breast cancer (TNBC) accounts for 15–20% of all breast cancers, and has a worse prognosis compared with hormone receptor-positive disease. Its unfavorable outcome and the lack of hormonal receptors determine the use of adjuvant chemotherapy as part of the standard treatment for these tumors, although several studies have documented that the current standard combination chemotherapy is suboptimal. Therefore, a new functional taxonomy of breast cancer and new targets for therapeutic development are urgently needed.

Experimental design

In this study, we have analyzed the proteome of TNBC applying a high-throughput proteomics approach to routinely archived formalin-fixed, paraffin-embedded tumor tissues.

Results

We have been able to identify and quantify more than 1000 protein groups. Some of these proteins are of outstanding interest in the biology and clinical management of this disease, such as CD44 and PARP1. Moreover, we have characterized some signaling pathways that could be related to TNBC genesis and development.

Conclusion and clinical relevance

Our results open up new avenues for the use of proteomics technologies in clinically relevant studies using archival samples. Shotgun LC-MS/MS studies could serve to discover new biomarkers and may provide clues to the genesis of TNBC and underlying molecular alterations.

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