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Updated: May 13, 2026
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Shotgun proteomics of archival triple-negative breast cancer samples
Angelo Gámez-Pozo1, Nuria Ibarz Ferrer, Eva Ciruelos
1Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.
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.
Insights
Proteomics analysis of triple-negative breast cancer (TNBC) identified over 1000 proteins, including CD44 and PARP1. These findings offer new therapeutic targets and biomarkers for TNBC, improving understanding of its molecular alterations.
Area of Science:
- Oncology
- Proteomics
- Molecular Biology
Background:
- Triple-negative breast cancer (TNBC) represents 15-20% of breast cancers with a poorer prognosis.
- Current adjuvant chemotherapy for TNBC is often suboptimal, necessitating novel therapeutic targets.
- There is an urgent need for a new functional taxonomy and therapeutic targets for TNBC.
Purpose of the Study:
- To analyze the proteome of triple-negative breast cancer (TNBC) using a high-throughput proteomics approach.
- To identify potential new therapeutic targets and biomarkers for TNBC.
- To characterize signaling pathways involved in TNBC development.
Main Methods:
- High-throughput proteomics analysis.
- Utilized routinely archived formalin-fixed, paraffin-embedded tumor tissues.
- Employed shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS).
Main Results:
- Identified and quantified over 1000 protein groups in TNBC.
- Highlighted proteins of significant interest, such as CD44 and PARP1.
- Characterized signaling pathways potentially linked to TNBC genesis and progression.
Conclusions:
- Proteomics offers a powerful tool for clinically relevant studies using archival samples.
- Shotgun LC-MS/MS can discover novel biomarkers for TNBC.
- The study provides insights into the molecular alterations underlying TNBC.
