High-Throughput Acoustic FFPE Proteomics Reveals ATP5IF1-Associated Mitochondrial Remodeling in Acral Melanoma

ABSTRACT: Formalin-fixed, paraffin-embedded (FFPE) archives underpin dermatopathology and translational oncology, enabling clinically annotated melanoma cohorts, but cohort-scale proteomics remains limited by labor and variability in upstream processing. We established a plate-scale, acoustic FFPE proteomics workflow and integrated it with AI-assisted digital pathology to support composition-aware molecular profiling from routine sections. The optimized pipeline reduces handling steps, improves reproducibility, and supports rapid parallel processing in a 96-well format. Deep data-independent acquisition mass spectrometry of 40 primary melanomas spanning acral lentiginous, lentigo maligna, superficial spreading, and nodular subtypes quantified more than 8,200 protein groups and a mean of 5,200 proteins per tumor. Proteome profiles resolved melanoma subtypes and defined an acral lentiginous melanoma program enriched for translation/biogenesis and extracellular matrix/adhesion processes with relative depletion of lipid and fatty-acid metabolism and peroxisomal pathways. Supervised feature selection highlighted TNC, POSTN, EIF4A1, and ARF4 and uncovered selective depletion of ATP5IF1, a regulator of mitochondrial ATP synthase, in acral lentiginous melanoma. ATP5IF1 depletion persisted after adjustment for mitochondrial proxies and coincided with higher glycolysis relative to Complex V. This pathology-integrated, high-throughput FFPE proteomics framework enables scalable retrospective discovery and reveals subtype-specific mitochondrial remodeling in an underrepresented melanoma subtype.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Skin

DISEASE(S): Skin Melanoma

SUBMITTER: Jeovanis Gil  

LAB HEAD: Jeovanis Gil

PROVIDER: PXD074156 | Pride | 2026-09-09

REPOSITORIES: Pride