PXD015981

PXD015981 is an original dataset announced via ProteomeXchange.

Title	Proteomics analysis of Formalin Fixed Paraffin Embedded tissues in the investigation of prostate cancer
Description	As proteins represent cell function, proteomic analysis of prostate tissues may elucidate the mechanisms of prostate cancer (PCa) progression. To that end, formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources, but associated with large analytical difficulties due to protein cross-linking. Our aim is to characterize tissue protein changes associated with castration resistant PCa. This study focused at the development of a reliable protocol for the proteomic analysis of FFPE tissues which was followed by a pilot study using FFPE PCa clinical samples to investigate whether the optimized protocol can provide biologically relevant data in the context of PCa. Archival FFPE mouse tissues were processed using seven protein extraction protocols including combinations of homogenization means (beads, sonication, boiling) and buffers (Tris-HCl and Urea-Thiourea). The proteomics output was evaluated by SDS electrophoresis and high resolution LC-MS/MS analysis. FFPE tissues (3 sections, 15������������������m each per sample) from 10 patients with PCa corresponding to tumor (GS=6 or GS���������������������������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 using Cytsoscape and Open Targets tool. A combination of cell lysis by Tris-HCl, SDS and DTE with bead homogenization, sonication and boiling provided most efficient protein extraction from FFPE tissues based on protein identifications and reproducibility. Comparison between the FFPE and matched FF tissues showed a substantial overlap in protein identifications (502 common out of 1,216 IDs commonly identified in all FF samples and 530 IDs commonly identified in all FFPE samples) with a strong correlation in relative abundances (rs=0.846, p<.001). Proteins significantly deregulated between PCa GS���������������������������8 and PCa GS=6 represented extracellular matrix organisation, phosphorylation and gluconeogenesis pathways, while proteins deregulated between cancerous tissues and benign counterparts, reflected increased translation, peptide synthesis and protein metabolism in the former, as expected. Further disease association analysis using the Open Targets platform showed that 60% of the differentially expressed proteins in cancer versus normal adjacent were significantly associated with PCa. These 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. A large scale study including 160 clinical FFPE prostate cancer and benign tissues to define protein changes associated with aggressive PCa, is planned.
HostingRepository	PRIDE
AnnounceDate	2019-11-15
AnnouncementXML	Submission_2020-01-29_07:02:37.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015981
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Vasiliki Lygirou
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Acetyl; Carbamidomethyl
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-23 01:32:58	ID requested
1	2019-11-15 00:48:38	announced
2	2019-12-11 00:50:56	announced	2019-12-11: Updated publication reference for PubMed record(s): 31682457.
⏵ 3	2020-01-29 07:02:39	announced	2019-12-11: Updated publication reference for PubMed record(s): 31682457. 2020-01-29: Updated publication reference for PubMed record(s): 31682457.

Mantsiou A, Makridakis M, Fasoulakis K, Katafigiotis I, Constantinides CA, Zoidakis J, Roubelakis MG, Vlahou A, Lygirou V, Proteomics Analysis of Formalin Fixed Paraffin Embedded Tissues in the Investigation of Prostate Cancer. J Proteome Res, 19(7):2631-2642(2020) [pubmed]

submitter keyword: FFPE tissue, FF tissue, Prostate cancer, mouse, human, Thermo Q Exactive, Orbitrap Elite

Antonia Vlahou
contact affiliation	Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, 11527, Athens, Greece
contact email	vlahoua@bioacadmemy.gr
lab head
Vasiliki Lygirou
contact affiliation	Biomedical Research Foundation, Academy of Athens
contact email	vlygirou@bioacademy.gr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD015981

PRIDE project URI

• PRIDE
  1. PXD015981
     1. Label: PRIDE project
     2. Name: Proteomics analysis of Formalin Fixed Paraffin Embedded tissues in the investigation of prostate cancer