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bioRxivMolecular BiologyPreprint

From Routine Pathology to Precision Oncology: Automated FFPE Tissue Processing for Large-Scale Molecular Studies

Jéssica Guedes, Andrzej Sliwa-GonzaleziD, Letícia SzadaiiD, Philipp Geiger, Nicole WoldmariD, Marisol Ayala ReyesiD, Ramiro Alonso-BastidaiD, Diana Lashidua Fernández Coto, Henriett OskolásiD, Matilda Marko-Varga, Lesley Schultz, Roger AppelqvistiD, Elisabet Wieslander, Johan MalmiD, György Marko‐VargaiD, Jeovanis GiliD

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Abstract

Melanoma incidence continues to rise globally, with formalin-fixed paraffin-embedded (FFPE) tissue archives representing an invaluable resource for large-scale retrospective proteomic studies. However, inconsistent deparaffinization remains a critical pre-analytical bottleneck limiting protein yield, reproducibility, and downstream data quality. In this study, we developed and validated a fully automated FFPE deparaffinization workflow using the Fluent(R) 780 liquid handling workstation (Tecan (C)) and evaluated its performance against a conventional manual protocol in a cohort of 54 patients with primary cutaneous melanoma, predominantly at early AJCC 8th edition stage I-II. The automated workflow achieved superior protein identification (6,146 {+/-} 860 vs. 4,941 {+/-} 1,091 proteins; p View larger version (49K): org.highwire.dtl.DTLVardef@1a3ea5dorg.highwire.dtl.DTLVardef@6fb8edorg.highwire.dtl.DTLVardef@d60a4dorg.highwire.dtl.DTLVardef@3e47b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

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