title: Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma.
abstract: Breast cancer is a heterogeneous disease whose molecular diversity is not well reflected in clinical and pathological markers used for prognosis and treatment selection. As tumor cells secrete proteins into the extracellular environment, some of these proteins reach circulation and could become suitable biomarkers for improving diagnosis or monitoring response to treatment. As many signaling pathways and interaction networks are altered in cancerous tissues by protein phosphorylation, changes in the secretory phosphoproteome of cancer tissues could reflect both disease progression and subtype. To test this hypothesis, we compared the phosphopeptide-enriched fractions obtained from proteins secreted into conditioned media (CM) derived from five luminal and five basal type breast cancer cell lines using label-free quantitative mass spectrometry. Altogether over 5000 phosphosites derived from 1756 phosphoproteins were identified, several of which have the potential to qualify as phosphopeptide plasma biomarker candidates for the more aggressive basal and also the luminal-type breast cancers. The analysis of phosphopeptides from breast cancer patient plasma and controls allowed us to construct a discovery list of phosphosites under rigorous collection conditions, and second to qualify discovery candidates generated from the CM studies. Indeed, a set of basal-specific phosphorylation CM site candidates derived from IBP3, CD44, OPN, FSTL3, LAMB1, and STC2, and luminal-specific candidates derived from CYTC and IBP5 were selected and, based on their presence in plasma, quantified across all cell line CM samples using Skyline MS1 intensity data. Together, this approach allowed us to assemble a set of novel cancer subtype specific phosphopeptide candidates for subsequent biomarker verification and clinical validation.
authors: Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, California 94945;
authors: Anna M
authors: AM
authors: Zawadzka
authors: Birgit
authors: B
authors: Schilling
authors: Michael P
authors: MP
authors: Cusack
authors: Alexandria K
authors: AK
authors: Sahu
authors: Penelope
authors: P
authors: Drake
authors: Susan J
authors: SJ
authors: Fisher
authors: Christopher C
authors: CC
authors: Benz
authors: Bradford W
authors: BW
authors: Gibson
mesh_terms: D000230:Adenocarcinoma / Q000378:metabolism*; D014408:Biomarkers, Tumor / Q000378:metabolism*; D001943:Breast Neoplasms / Q000097:blood / Q000378:metabolism*; D018270:Carcinoma, Ductal, Breast / Q000378:metabolism*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D061986:MCF-7 Cells; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods*; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor; D010750:Phosphoproteins