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A degradomic landscape of proteolytic remodeling in melanoma lung metastasis

ABSTRACT: Melanoma metastasis involves extensive remodeling of the tumor microenvironment, yet the proteolytic processes underlying pulmonary colonization remain poorly defined. Using the B16F10 intravenous melanoma model in C57BL/6J mice, we performed an integrative degradomic analysis of metastatic lung tissue, plasma, and the secretome of early-passaged primary cultures derived from metastatic foci. Semi-specific database searches identified nearly 8,000 semi-tryptic peptides across compartments, with the secretome exhibiting the highest burden of cleavage events, indicative of an intensely proteolytic microenvironment. Cleavage profiles were compartment-specific, dominated by actin in metastatic lung tissue, a2-macroglobulin in plasma, and SPARC in the secretome. Cleavage-site motif analysis revealed conserved His/Ser (P1/P1 prime) preferences in tissue and plasma, whereas the secretome showed a distinct Leu/Ser pattern. Discriminant-feature analysis uncovered unique proteolytic signatures for each compartment, and peptide-level mapping implicated at least 12 proteases (including MMP2, cathepsin D, and cathepsin E) as major contributors to metastatic niche remodeling. Functional enrichment demonstrated coordinated impacts on extracellular matrix organization, inflammation, and metabolic adaptation. These results define a compartment-resolved degradomic landscape of melanoma lung metastasis, highlight proteases driving metastatic remodeling, and provide cleavage signatures with potential value for biomarker discovery.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Andre Zelanis

PROVIDER: MSV000100089 | MassIVE | Wed Dec 03 11:04:00 GMT 2025

REPOSITORIES: MassIVE

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