{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T01:56:34Z","timestamp":1790733394819,"version":"4.1.0"},"posted":{"date-parts":[[2026,8,13]]},"group-title":"Molecular Biology","reference-count":19,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Berta Kamprad Foundation, Lund, Sweden","award":["FBKS-2025-18 - (671)"],"award-info":[{"award-number":["FBKS-2025-18 - (671)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,8,13]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>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\u00ae 780 liquid handling workstation (Tecan \u00a9) 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\u2013II. The automated workflow achieved superior protein identification (6,146 \u00b1 860 vs. 4,941 \u00b1 1,091 proteins; p &lt; 0.0001) with lower technical variability, while maintaining highly comparable global proteomic profiles as confirmed by principal component analysis and hierarchical clustering. A total of 8,305 proteins (96.1%) were identified by both methods, supporting the reproducibility and equivalence of the automated approach. Patients were stratified by the presence (N=21) or absence (N=33) of histological regression in the primary tumor. Proteomic comparison revealed 97 upregulated and 226 downregulated proteins in regressing melanomas, with pathway enrichment analysis demonstrating elevated mitochondrial and translational activity alongside reduced innate immune and complement pathway activation in the regression group. No statistically significant differences in overall, disease-free, or progression-free survival were observed between groups, consistent with the early-stage composition of the cohort. Digital pathology validated tissue morphology preservation across processing conditions. These findings support the integration of automated FFPE processing with proteomic and digital pathology workflows as a scalable platform for precision melanoma research.<\/jats:p>\n                <jats:sec>\n                  <jats:title>TOC Figure<\/jats:title>\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"744404v1_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>","DOI":"10.64898\/2026.08.12.744404","type":"posted-content","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T22:50:15Z","timestamp":1786661415000},"source":"Crossref","is-referenced-by-count":1,"title":["From Routine Pathology to Precision Oncology: Automated FFPE Tissue Processing for Large-Scale Molecular Studies"],"prefix":"10.64898","author":[{"given":"J\u00e9ssica","family":"Guedes","sequence":"first","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrzej","family":"Sliwa-Gonzalez","sequence":"additional","affiliation":[{"name":"Tecan, Seestrasse 103, 8708 M\u00e4nnedorf, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3605-839X","authenticated-orcid":false,"given":"Leticia","family":"Szadai","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"},{"name":"Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Geiger","sequence":"additional","affiliation":[{"name":"Tecan, Seestrasse 103, 8708 M\u00e4nnedorf, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5387-1059","authenticated-orcid":false,"given":"Nicole","family":"Woldmar","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marisol Ayala","family":"Reyes","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1449-1145","authenticated-orcid":false,"given":"Ramiro Alonso","family":"Bastida","sequence":"additional","affiliation":[{"name":"Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana Lashidua Fern\u00e1ndez","family":"Coto","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"},{"name":"Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7217-6433","authenticated-orcid":false,"given":"Henriett","family":"Oskol\u00e1s","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matilda","family":"Marko-Varga","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lesley","family":"Schultz","sequence":"additional","affiliation":[{"name":"Tecan, Seestrasse 103, 8708 M\u00e4nnedorf, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7450-7216","authenticated-orcid":false,"given":"Roger","family":"Appelqvist","sequence":"additional","affiliation":[{"name":"Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabet","family":"Wieslander","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Malm","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7140-8925","authenticated-orcid":false,"given":"Gy\u00f6rgy","family":"Marko-Varga","sequence":"additional","affiliation":[{"name":"Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary"},{"name":"Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea"},{"name":"1st Department of Surgery, Tokyo Medical University, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3601-3893","authenticated-orcid":false,"given":"Jeovanis","family":"Gil","sequence":"additional","affiliation":[{"name":"Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026081705301949000_2026.08.12.744404v1.1","doi-asserted-by":"publisher","DOI":"10.3390\/medsci9040063"},{"key":"2026081705301949000_2026.08.12.744404v1.2","doi-asserted-by":"publisher","DOI":"10.1002\/jso.26329"},{"key":"2026081705301949000_2026.08.12.744404v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.critrevonc.2020.103208"},{"key":"2026081705301949000_2026.08.12.744404v1.4","doi-asserted-by":"publisher","DOI":"10.1001\/jamadermatol.2015.2938"},{"key":"2026081705301949000_2026.08.12.744404v1.5","unstructured":"Cost, Insurance and Financial Help for Keytruda."},{"key":"2026081705301949000_2026.08.12.744404v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41698-022-00321-4"},{"key":"2026081705301949000_2026.08.12.744404v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.jprot.2025.105482"},{"key":"2026081705301949000_2026.08.12.744404v1.8","doi-asserted-by":"crossref","unstructured":"Vallius, T. ; Shi, Y. ; Novikov, E. ; Pant, S.M. ; Pelletier, R. ; Chen, Y.-A. ; Tefft, J.B. ; Johnson, A.N. ; Maliga, Z. ; Wan, G .; et al. Spatial Determinants of Tumor Cell Dedifferentiation and Plasticity in Primary Cutaneous Melanoma 2025.","DOI":"10.1101\/2025.06.21.660851"},{"key":"2026081705301949000_2026.08.12.744404v1.9","doi-asserted-by":"publisher","DOI":"10.3109\/10520290903039078"},{"key":"2026081705301949000_2026.08.12.744404v1.10","doi-asserted-by":"publisher","DOI":"10.1369\/0022155411400866"},{"key":"2026081705301949000_2026.08.12.744404v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16935-w"},{"key":"2026081705301949000_2026.08.12.744404v1.12","doi-asserted-by":"publisher","DOI":"10.1080\/14737140.2018.1489246"},{"key":"2026081705301949000_2026.08.12.744404v1.13","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.0c00850"},{"key":"2026081705301949000_2026.08.12.744404v1.14","doi-asserted-by":"publisher","DOI":"10.1002\/cncr.35897"},{"key":"2026081705301949000_2026.08.12.744404v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.canlet.2023.216223"},{"key":"2026081705301949000_2026.08.12.744404v1.16","doi-asserted-by":"publisher","DOI":"10.1001\/jamadermatol.2020.5032"},{"key":"2026081705301949000_2026.08.12.744404v1.17","doi-asserted-by":"publisher","DOI":"10.3390\/cancers13236066"},{"key":"2026081705301949000_2026.08.12.744404v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-17204-5"},{"key":"2026081705301949000_2026.08.12.744404v1.19","unstructured":"OpenAI. ChatGPT (GPT-5.1) [Large Language Model]."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.08.12.744404","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T12:30:29Z","timestamp":1786969829000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.08.12.744404"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":19,"URL":"https:\/\/doi.org\/10.64898\/2026.08.12.744404","relation":{},"subject":[],"published":{"date-parts":[[2026,8,13]]},"subtype":"preprint"}}