{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T08:03:17Z","timestamp":1792569797195,"version":"4.5.0"},"reference-count":86,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T00:00:00Z","timestamp":1572825600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T00:00:00Z","timestamp":1572825600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T00:00:00Z","timestamp":1572825600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100010665","name":"H2020 Marie Sklodowska-Curie Actions","doi-asserted-by":"publisher","award":["721746"],"award-info":[{"award-number":["721746"]}],"id":[{"id":"10.13039\/100010665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Prostate cancer (PCa) is one of the leading causes of death in men worldwide. The molecular features, associated with the onset and progression of the disease, are under vigorous investigation. Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources for large-scale studies; however, their application in proteomics is limited due to protein cross-linking. In this study, the adjustment of a protocol for the proteomic analysis of FFPE tissues was performed which was followed by a pilot application on FFPE PCa clinical samples to investigate whether the optimized protocol can provide biologically relevant data for the investigation of PCa. For the optimization, FFPE mouse tissues were processed using seven protein extraction protocols including combinations of homogenization methods (beads, sonication, boiling) and buffers (SDS based and urea\u2013thiourea based). The proteome extraction efficacy was then evaluated based on protein identifications and reproducibility using SDS electrophoresis and high resolution LC-MS\/MS analysis. Comparison between the FFPE and matched fresh frozen (FF) tissues, using an optimized protocol involving protein extraction with an SDS-based buffer following beads homogenization and boiling, showed a substantial overlap in protein identifications with a strong correlation in relative abundances (rs = 0.819, p &amp;lt; 0.001). Next, FFPE tissues (3 sections, 15 \u03bcm each per sample) from 10 patients with PCa corresponding to tumor (GS = 6 or GS \u2265 8) and adjacent benign regions were processed with the optimized protocol. Extracted proteins were analyzed by GeLC-MS\/MS followed by statistical and bioinformatics analysis. Proteins significantly deregulated between PCa GS \u2265 8 and PCa GS = 6 represented extracellular matrix organization, gluconeogenesis, and phosphorylation pathways. Proteins deregulated between cancerous and adjacent benign tissues, reflected increased translation, peptide synthesis, and protein metabolism in the former, which is consistent with the literature. In conclusion, the results support the relevance of the proteomic findings in the context of PCa and the reliability of the optimized protocol for proteomics analysis of FFPE material.<\/jats:p>","DOI":"10.1021\/acs.jproteome.9b00587","type":"journal-article","created":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T12:37:14Z","timestamp":1572871034000},"page":"2631-2642","source":"Crossref","is-referenced-by-count":28,"title":["Proteomics\nAnalysis of Formalin Fixed Paraffin Embedded\nTissues in the Investigation of Prostate Cancer"],"prefix":"10.1021","volume":"19","author":[{"given":"Anna","family":"Mantsiou","sequence":"first","affiliation":[{"name":"Biomedical Research Foundation of the Academy of Athens , , 4 Soranou Ephessiou Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manousos","family":"Makridakis","sequence":"additional","affiliation":[{"name":"Biomedical Research Foundation of the Academy of Athens , , 4 Soranou Ephessiou Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantinos","family":"Fasoulakis","sequence":"additional","affiliation":[{"name":"Ippokrateio General Hospital of Athens , , 114 Vasilissis Sofias Avenue , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ioannis","family":"Katafigiotis","sequence":"additional","affiliation":[{"name":"National and Kapodistrian University of Athens, Medical School , , 17 Agiou Thoma Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Constantinos A.","family":"Constantinides","sequence":"additional","affiliation":[{"name":"National and Kapodistrian University of Athens, Medical School , , 17 Agiou Thoma Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4557-3430","authenticated-orcid":true,"given":"Jerome","family":"Zoidakis","sequence":"additional","affiliation":[{"name":"Biomedical Research Foundation of the Academy of Athens , , 4 Soranou Ephessiou Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria G.","family":"Roubelakis","sequence":"additional","affiliation":[{"name":"National and Kapodistrian University of Athens, Medical School , , 75 Mikras Assias Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonia","family":"Vlahou","sequence":"additional","affiliation":[{"name":"Biomedical Research Foundation of the Academy of Athens , , 4 Soranou Ephessiou Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1555-1326","authenticated-orcid":true,"given":"Vasiliki","family":"Lygirou","sequence":"additional","affiliation":[{"name":"Biomedical Research Foundation of the Academy of Athens , , 4 Soranou Ephessiou Street , ,","place":["Athens, Greece, 11527"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2019,11,4]]},"reference":[{"key":"2026081714244883100_cit1","doi-asserted-by":"publisher","first-page":"394","DOI":"10.3322\/caac.21492","article-title":"Global cancer statistics 2018: GLOBOCAN estimates of incidence and\nmortality worldwide for 36 cancers in 185 countries","volume":"68","author":"Bray","year":"2018","journal-title":"Ca-Cancer J. Clin."},{"key":"2026081714244883100_cit2","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1016\/j.urolonc.2013.09.017","article-title":"Prostate cancer biomarkers: an update","volume":"32","author":"Romero\nOtero","year":"2014","journal-title":"Urol Oncol"},{"key":"2026081714244883100_cit3","doi-asserted-by":"publisher","first-page":"127rv3","DOI":"10.1126\/scitranslmed.3003180","article-title":"Beyond\nPSA: the next generation of prostate cancer biomarkers","volume":"4","author":"Prensner","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"2026081714244883100_cit4","first-page":"221","article-title":"The use of biomarkers in prostate cancer screening\nand treatment","volume":"19","author":"Alford","year":"2017","journal-title":"Rev. Urol"},{"key":"2026081714244883100_cit5","doi-asserted-by":"publisher","first-page":"7","DOI":"10.12688\/f1000research.14499.1","article-title":"Recent advances\nin prostate cancer\nresearch: large-scale genomic analyses reveal novel driver mutations\nand DNA repair defects","volume":"7","author":"Frank","year":"2018","journal-title":"F1000Res"},{"key":"2026081714244883100_cit6","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1080\/14789450.2018.1491796","article-title":"Tissue proteomics\nstudies in the\ninvestigation of prostate cancer","volume":"15","author":"Mantsiou","year":"2018","journal-title":"Expert Rev.\nProteomics"},{"key":"2026081714244883100_cit7","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.neo.2017.10.009","article-title":"Proteomic characterization of prostate cancer\nto distinguish nonmetastasizing and metastasizing primary tumors and\nlymph node metastases","volume":"20","author":"Mu\u0308ller","year":"2018","journal-title":"Neoplasia"},{"key":"2026081714244883100_cit8","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1016\/j.jprot.2018.11.009","article-title":"High sensitivity proteomics of prostate\ncancer tissue microarrays\nto discriminate between healthy and cancerous tissue","volume":"197","author":"Turia\u0301k","year":"2019","journal-title":"J. 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Biol."},{"key":"2026081714244883100_cit100","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools\nand resources in 2019: improving support for quantification data","volume":"47","author":"Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026081714244883100_cit25","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.ebiom.2019.02.040","article-title":"Proteomics based identification of KDM5\nhistone demethylases associated with cardiovascular disease","volume":"41","author":"Mokou","year":"2019","journal-title":"EBioMedicine"},{"key":"2026081714244883100_cit26","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.125638","article-title":"Systems biology identifies cytosolic PLA2 as a target in vascular\ncalcification treatment","author":"Schanstra","year":"2019","journal-title":"JCI Insight"},{"key":"2026081714244883100_cit27","first-page":"85","article-title":"[Basal-luminal epithelial cell differentiation\nin prostate cancer is associated with epithelial-mesenchymal transition\nand epithelium migration in the mesenchyme]","author":"Korshak","year":"2016","journal-title":"Urologiia"},{"key":"2026081714244883100_cit28","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1007\/s10555-013-9470-4","article-title":"Validation\nof proposed prostate cancer biomarkers with\ngene expression data: a long road to travel","volume":"33","author":"Amaro","year":"2014","journal-title":"Cancer Metastasis Rev."},{"key":"2026081714244883100_cit29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0066278","article-title":"Differentially\nexpressed\nandrogen-regulated genes in androgen-sensitive tissues reveal potential\nbiomarkers of early prostate cancer","volume":"8","author":"Altintas","year":"2013","journal-title":"PLoS One"},{"key":"2026081714244883100_cit30","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1038\/s41419-018-1096-6","article-title":"Integrative analysis of transcriptomics and clinical data uncovers\nthe tumor-suppressive activity of MITF in prostate cancer","volume":"9","author":"Valcarcel-Jimenez","year":"2018","journal-title":"Cell Death Dis."},{"key":"2026081714244883100_cit31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0065005","article-title":"Variable metastatic potentials correlate\nwith differential plectin and vimentin expression in syngeneic androgen\nindependent prostate cancer cells","volume":"8","author":"Burch","year":"2013","journal-title":"PLoS One"},{"key":"2026081714244883100_cit32","doi-asserted-by":"publisher","first-page":"25","DOI":"10.4111\/kju.2010.51.1.25","article-title":"Alteration\nof Antithrombin III and D-dimer Levels in\nClinically Localized Prostate Cancer","volume":"51","author":"Hong","year":"2010","journal-title":"Korean\nJ. Urol"},{"key":"2026081714244883100_cit33","doi-asserted-by":"publisher","first-page":"253","DOI":"10.4149\/neo_2018_161217N648","article-title":"An extensive study of the mechanism of prostate cancer metastasis","volume":"65","author":"Wang","year":"2018","journal-title":"Neoplasma"},{"key":"2026081714244883100_cit34","doi-asserted-by":"publisher","first-page":"238","DOI":"10.4103\/aja.aja_15_17","article-title":"The role of peroxisome\nproliferator-activated\nreceptor gamma in prostate cancer","volume":"20","author":"Elix","year":"2018","journal-title":"Asian J.\nAndrol."},{"key":"2026081714244883100_cit35","doi-asserted-by":"publisher","first-page":"2810","DOI":"10.1038\/emboj.2012.112","article-title":"A transcriptional repressor co-regulatory network\ngoverning androgen response in prostate cancers","volume":"31","author":"Chng","year":"2012","journal-title":"EMBO J."},{"key":"2026081714244883100_cit36","doi-asserted-by":"publisher","first-page":"454256","DOI":"10.1155\/2015\/454256","article-title":"Identification and validation of potential\nnew biomarkers for prostate cancer diagnosis and prognosis using 2D-DIGE\nand MS","volume":"2015","author":"Geisler","year":"2015","journal-title":"Biomed Res. Int."},{"key":"2026081714244883100_cit37","doi-asserted-by":"publisher","first-page":"680136","DOI":"10.1155\/2013\/680136","article-title":"Proteoglycan expression in normal human prostate\ntissue and prostate cancer","volume":"2013","author":"Suhovskih","year":"2013","journal-title":"ISRN Oncol"},{"key":"2026081714244883100_cit38","doi-asserted-by":"publisher","first-page":"716","DOI":"10.7150\/jca.17779","article-title":"The controversial\nrole of phospholipase\nC epsilon (PLC\u03b5) in cancer development and progression","volume":"8","author":"Tyutyunnykova","year":"2017","journal-title":"J. Cancer"},{"key":"2026081714244883100_cit39","doi-asserted-by":"publisher","first-page":"2435","DOI":"10.1016\/j.juro.2008.01.091","article-title":"The heterochromatin protein 1 family is regulated in\nprostate development and cancer","volume":"179","author":"Shapiro","year":"2008","journal-title":"J. Urol."},{"key":"2026081714244883100_cit40","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1002\/pros.21292","article-title":"Differential\nexpression of peroxiredoxins in prostate\ncancer: consistent upregulation of PRDX3 and PRDX4","volume":"71","author":"Basu","year":"2011","journal-title":"Prostate"},{"key":"2026081714244883100_cit41","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1016\/j.tranon.2018.11.014","article-title":"Exosomal Release of L-Plastin by Breast\nCancer Cells Facilitates Metastatic Bone Osteolysis","volume":"12","author":"Tiedemann","year":"2019","journal-title":"Transl Oncol"},{"key":"2026081714244883100_cit42","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.canlet.2005.01.037","article-title":"Comparative gene and\nprotein expression in primary cultures of epithelial\ncells from benign prostatic hyperplasia and prostate cancer","volume":"227","author":"Rose","year":"2005","journal-title":"Cancer Lett."},{"key":"2026081714244883100_cit43","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1002\/path.993","article-title":"Expression of basal cell keratins\nin human prostate cancer metastases and cell lines","volume":"195","author":"van\nLeenders","year":"2001","journal-title":"J. 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Neural Transm"},{"key":"2026081714244883100_cit45","doi-asserted-by":"publisher","first-page":"1347174","DOI":"10.1155\/2018\/1347174","article-title":"Reduced Levels\nof ATP Synthase Subunit ATP5F1A Correlate\nwith Earlier-Onset Prostate Cancer","volume":"2018","author":"Feichtinger","year":"2018","journal-title":"Oxid Med.\nCell Longev"},{"key":"2026081714244883100_cit46","doi-asserted-by":"publisher","first-page":"1130","DOI":"10.1038\/onc.2011.312","article-title":"Identification\nof stromally expressed molecules\nin the prostate by tag-profiling of cancer-associated fibroblasts,\nnormal fibroblasts and fetal prostate","volume":"31","author":"Orr","year":"2012","journal-title":"Oncogene"},{"key":"2026081714244883100_cit47","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1007\/s12253-017-0302-7","article-title":"Eukaryotic elongation\nfactor 2 (eef2) is a potential biomarker of\nprostate cancer","volume":"24","author":"Zhang","year":"2018","journal-title":"Pathol. Oncol. Res."},{"key":"2026081714244883100_cit48","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1006\/excr.2001.5234","article-title":"beta-Lapachone-induced\napoptosis in human prostate\ncancer cells: involvement of NQO1\/xip3","volume":"267","author":"Planchon","year":"2001","journal-title":"Exp.\nCell Res."},{"key":"2026081714244883100_cit49","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1475-2867-4-5","article-title":"Potential mechanism\nof phytochemical-induced apoptosis in human prostate adenocarcinoma\ncells: Therapeutic synergy in genistein and beta-lapachone combination\ntreatment","volume":"4","author":"Kumi-Diaka","year":"2004","journal-title":"Cancer Cell Int."},{"key":"2026081714244883100_cit50","doi-asserted-by":"publisher","first-page":"3247","DOI":"10.3892\/or.2015.4322","article-title":"Differences in urinary proteins related to surgical\u2019\n\u2018 margin status after radical prostatectomy","volume":"34","author":"Heger","year":"2015","journal-title":"Oncol. Rep."},{"key":"2026081714244883100_cit51","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1089\/gtmb.2013.0226","article-title":"Screening biomarkers of prostate cancer by integrating\nmicroRNA and mRNA microarrays","volume":"17","author":"Feng","year":"2013","journal-title":"Genet. Test.\nMol. Biomarkers"},{"key":"2026081714244883100_cit52","doi-asserted-by":"publisher","first-page":"R195","DOI":"10.1530\/ERC-19-0009","article-title":"ErbB-2 signaling in advanced prostate\ncancer progression and potential therapy","volume":"26","author":"Miller","year":"2019","journal-title":"Endocr.-Relat.\nCancer"},{"key":"2026081714244883100_cit53","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1039\/C8MO00170G","article-title":"Metabolic deregulation in prostate cancer","volume":"14","author":"Srihari","year":"2018","journal-title":"Mol. Omics"},{"key":"2026081714244883100_cit54","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s40170-016-0161-9","article-title":"The role\nof tumor metabolism as a driver of prostate\ncancer progression and lethal disease: results from a nested case-control\nstudy","volume":"4","author":"Kelly","year":"2016","journal-title":"Cancer Metab"},{"key":"2026081714244883100_cit55","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1097\/CCO.0000000000000367","article-title":"Targeting\nof protein translation as a new treatment paradigm for prostate cancer","volume":"29","author":"Ramamurthy","year":"2017","journal-title":"Curr. Opin. Oncol."},{"key":"2026081714244883100_cit56","doi-asserted-by":"publisher","first-page":"D1056","DOI":"10.1093\/nar\/gky1133","article-title":"Open Targets Platform:\nnew developments and\nupdates two years on","volume":"47","author":"Carvalho-Silva","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2026081714244883100_cit57","doi-asserted-by":"publisher","first-page":"1416","DOI":"10.1038\/labinvest.3700337","article-title":"A nondestructive\nmolecule extraction method allowing\nmorphological and molecular analyses using a single tissue section","volume":"85","author":"Chu","year":"2005","journal-title":"Lab. 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Appl."},{"key":"2026081714244883100_cit60","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1369\/jhc.5B6851.2006","article-title":"Protein extraction\nfrom formalin-fixed, paraffin-embedded tissue sections: quality evaluation\nby mass spectrometry","volume":"54","author":"Shi","year":"2006","journal-title":"J. Histochem. 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