Nuria Ibarz Ferrer

Centro Nacional de Epidemiología

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Fernando Garcı́a

Spanish National Cancer Research Centre

Angelo Gámez‐Pozo

Hospital Universitario Puerta del Mar

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Juan Ángel Fresno Vara

Instituto de Salud Carlos III

Kurt R. Brunden

University of Pennsylvania

Virginia M.‐Y. Lee

University of Pennsylvania

Michael J. James

Synlogic (United States)

Keith Ashman

TissuPath

Justin S. Potuzak

McLean Hospital

Amos B. Smith

University of Pennsylvania

Carlo Ballatore

University of California, San Diego

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University of Pennsylvania

Hospital Universitario La Paz

Institute on Aging

Institute for Neurodegenerative Disorders

Philadelphia University

Hospital La Paz Institute for Health Research

Instituto de Salud Carlos III

Universidad Autónoma de Madrid

Centro de Investigación Biomédica en Red de Cáncer

California University of Pennsylvania

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Shotgun proteomics of archival triple‐negative breast cancer samples

PROTEOMICS - CLINICAL APPLICATIONS (2013)

Angelo Gámez‐Pozo Nuria Ibarz Ferrer Eva Ciruelos Rocío López‐Vacas Fernando Garcı́a

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 CD 44 and PARP 1. 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.

Triple-negative breast cancer

Proteome

10.1002/prca.201200048

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High‐Throughput Phosphoproteomics from Formalin‐Fixed, Paraffin‐Embedded Tissues

Current Protocols in Chemical Biology (2012)

Angelo Gámez‐Pozo Iker Sánchez‐Navarro Nuria Ibarz Ferrer Fernando Garcı́a Keith Ashman

Abstract Liquid chromatography coupled with tandem mass spectrometry–based high‐throughput proteomics allows detection and characterization of thousands of peptides and their post‐translational modifications in a single sample. Protein phosphorylation affects most eukaryotic cellular processes, and its deregulation is considered a hallmark of cancer and other diseases. High‐throughput phosphoproteomics may enable monitoring of altered signaling pathways as a means of stratifying tumors and facilitating the discovery of new drugs. Unfortunately, the development of molecular tests for clinical use is constrained by the limited availability of fresh frozen, clinically annotated samples, and protocols that allow the use of human archival formalin‐fixed, paraffin‐embedded samples are required. The protocols in this article describe a global procedure for evaluating hundreds of protein phosphorylation sites in protein extracts obtained from formalin‐fixed, paraffin‐embedded tissues. Curr. Protoc. Chem. Biol . 4:161‐175 © 2012 by John Wiley & Sons, Inc.

Phosphoproteomics

10.1002/9780470559277.ch110242

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The characterization of microtubule-stabilizing drugs as possible therapeutic agents for Alzheimer's disease and related tauopathies

Pharmacological Research (2010)

Kurt R. Brunden Yuemang Yao Justin S. Potuzak Nuria Ibarz Ferrer Carlo Ballatore

Tauopathy

Epothilones

Tau protein

Frontotemporal lobar degeneration

Radioligand

Membrane permeability

10.1016/j.phrs.2010.12.002

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Citations (148)