Label-free proteomics analysis of mixed membrane fractions isolated from triple negative breast cancer cell lines with different TNM stages compared to a healthy breast cell line revealed profound metabolic reprogramming and coordinated upregulation of Warburg effect machinery and suppression of OXPHOS components

ABSTRACT: Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype with limited therapeutic options and the poorest clinical outcomes. Using high-resolution nUPLC-QTOF-MS/MS, we performed comprehensive proteomics profiling of TNBC cell lines representing disease progression stages: HCC-1937 (stage IIB), HCC-1599 (stage IIIA), and MDA-MB-231 (stage IV), benchmarked against non-tumorigenic healthy MCF-12F cells. From 11,864 initially detected proteins, stringent quality filtering yielded 5,623 high-confidence proteins spanning a dynamic range of six orders of magnitude. Differential protein abundance analysis revealed striking stage-specific proteomic signatures, with 381, 490, and 550 DAPs identified in HCC-1937, HCC-1599, and MDA-MB-231, respectively, with no overlap among the three TNBC cell lines. Sparse PLS-DA and k-means clustering demonstrated clear proteomics stratification correlating with clinical staging. STRING network topology analysis uncovered dysregulated hubs in oxidative phosphorylation, mitochondrial electron transport chain complexes (Complex I, III, IV), glycolytic enzymes, and cytoskeletal remodeling proteins. Functional enrichment revealed profound metabolic reprogramming with coordinated upregulation of Warburg effect machinery and suppression of OXPHOS components. Cancer hallmark analysis identified enrichment in tissue invasion/metastasis (FDR < 0.001), immune evasion, genomic instability, and inflammatory signaling across all TNBC stages. These stage-resolved proteomics landscapes provide mechanistic insights into TNBC progression and identify potential therapeutic vulnerabilities and prognostic biomarker candidates for precision oncology approaches.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Rodolfo Moreno Castillo  

LAB HEAD: Juan Pedro Luna Arias

PROVIDER: PXD071351 | Pride | 2026-10-19

REPOSITORIES: Pride