Dataset Information

Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by DIA proteomics

ABSTRACT: Triple negative breast cancer (TNBC) accounts for 15-20% of all breast carcinomas and it is clinically characterized by an aggressive phenotype and bad prognosis. TNBC does not benefit from any targeted therapy, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of one hundred twenty-five formalin-fixed paraffin-embedded samples from patients diagnosed with triple negative breast cancer were analyzed by mass spectrometry using data-independent acquisition. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were used to characterize molecular groups. Additionally, a predictive signature related with relapse was defined. Two molecular groups with differences in several biological processes as glycolysis, translation and immune response, were defined in this cohort, and a prognostic signature based on the abundance of proteins RBM3 and NIPSNAP1 was defined. This predictor split the population into low-risk and high-risk groups. The differential processes identified between the two molecular groups may serve to design new therapeutic strategies in the future and the prognostic signature could be useful to identify a population at high-risk of relapse that could be directed to clinical trials.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast

DISEASE(S): Breast Cancer

SUBMITTER: Cristina Chiva

LAB HEAD: Juan Ángel Fresno Vara

PROVIDER: PXD021491 | Pride | 2022-02-14

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	160706_S_CCES_01_02_DIA.raw	Raw
	160706_S_CCES_02_03_DIA.raw	Raw
	160706_S_CCES_03_02_DIA.raw	Raw
	160706_S_CCES_04_02_DIA.raw	Raw
	160706_S_CCES_05_02_DIA.raw	Raw

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Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data-independent acquisition proteomics.

García-Adrián Silvia S Trilla-Fuertes Lucía L Gámez-Pozo Angelo A Chiva Cristina C López-Vacas Rocío R López-Camacho Elena E Zapater-Moros Andrea A Lumbreras-Herrera María I MI Hardisson David D Yébenes Laura L Zamora Pilar P Sabidó Eduard E Fresno Vara Juan Ángel JÁ Espinosa Enrique E

Proteomics 20211027 3

Triple negative breast cancer accounts for 15%-20% of all breast carcinomas and is clinically characterized by an aggressive phenotype and poor prognosis. Triple negative tumors do not benefit from targeted therapies, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of 125 formalin-fixed paraffin-embedded samples from patients diagnosed with non-metastatic triple negative breast cancer were analyzed using data-independent acq ...[more]

PMID: 34624180

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