High-throughput acoustic FFPE proteomics reveals ATP5IF1-associated mitochondrial alterations in acral melanoma
High-throughput acoustic FFPE proteomics reveals ATP5IF1-associated mitochondrial alterations in acral melanoma
Cohort-scale proteomics from archived FFPE tissue has long been bottlenecked not by mass spectrometry performance, but by inconsistent upstream sample processing. This study tackles that bottleneck directly, applying Adaptive Focused Acoustics® (AFA®) on the Covaris R230 in a 96-well plate format to standardize tissue homogenization across dozens of archival melanoma specimens at once.
AFA’s role was central to the outcome: consistent, reproducible tissue disruption is what made it possible to recover more than 8,200 protein groups across the cohort and resolve a distinct, previously unreported metabolic signature in acral lentiginous melanoma, an underrepresented and often overlooked melanoma subtype. It’s a clear example of AFA-enabled sample prep delivering discovery-grade data from material that would otherwise sit underused in pathology archives.
György Marko-Varga previewed this research at EACR 2026, as part of a broader melanoma proteogenomics program. Watch the Presentation →
For labs looking for an AFA-based path to FFPE protein extraction at lower throughput, Covaris’s truPREP® Protein FFPE Kit offers a validated, tube-based option (processing individual FFPE scrolls on the R230).
Fernández-Coto D.L., Ayala M., Alonso R., Palmqvist A., García M.F., Balderas-López S.F., Oskolas H., Christersson L., Fulöp L., Szigeti B., Olivera-Rodríguez V.H., Marko-Varga M., Horvatovich P., Malm J., Szadai L., Herrera-Goepfert R., Szasz A.M., Encarnación-Guevara S., Marko-Varga G., et al.
Molecular & Cellular Proteomics. 2026;101620.
doi: 10.1016/j.mcpro.2026.101620
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, is designed to improve 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 QuPath-derived tumor content, and coincided with higher glycolysis relative to Complex V. This pathology-integrated, high-throughput FFPE proteomics framework enables scalable retrospective discovery and suggests subtype-specific metabolic alterations consistent with mitochondrial remodeling in an underrepresented melanoma subtype.
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