Dataset Information

Characterization of the human urine proteome in Prostate Cancer

ABSTRACT: Prostate cancer (PCa) is one of the most prevalent cancers among men and the fifth leading cause of cancer-related death in men. Currently, PCa suspicion is based on abnormal digital rectal examination and/or raised PSA serum levels, with prostate needle biopsy being required for a definitive diagnosis. Histopathological classification of tumours based on GS grading, cancer staging and PSA levels are used to predict the indolent or aggressive progression of the tumour as well as the likelihood of disease recurrence. These diagnosis and prognosis tools for PCa have revealed limited usefulness, especially PSA testing, which despite organ-specificity is not cancer-specific, being associated with low specificity. In this vein, new markers have been proposed in order to increase the accuracy of PCa detection, most of them proteins. Despite the significant efforts that have been undertaken for discovering other biomarkers for PCa management, few were translated into clinical practice. The simple and non-invasive nature of urine collection along with its proteome stability and storing many secreted proteins of prostate origin, makes the identification of PCa urinary biomarkers an attractive approach. With this in mind, we aimed to compare the urinary proteome profile of PCa patients with non-cancer patients in order to identify non-invasive candidate biomarkers for PCa prediction. To fulfil this task, we followed a shotgun LC-MS/MS approach using an Orbitrap instrument. A combination of two different software packages, MaxQuant and Proteome Discover was used to increase the robustness of analysis and enhance the search for new biomarkers. Proteins quantification was based on a label-free quantification approach (false discovery rate (FDR) 1%). The present dataset was used to disclosure potential markers in PCa management.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

DISEASE(S): Prostate Adenocarcinoma

SUBMITTER: Tânia Lima

LAB HEAD: Rui Vitorino

PROVIDER: PXD017902 | Pride | 2022-05-19

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	RAW.zip	Other
	SEARCH_MaxQuant.zip	Other
	SEARCH_ProteomeDiscoverer.zip	Other
	uniprot-humanproteome_UP000005640.fasta	Fasta

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Publications

Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study.

Lima Tânia T Barros António S AS Trindade Fábio F Ferreira Rita R Leite-Moreira Adelino A Barros-Silva Daniela D Jerónimo Carmen C Araújo Luís L Henrique Rui R Vitorino Rui R Fardilha Margarida M

Cancers 20220415 8

To identify new protein targets for PCa detection, first, a shotgun discovery experiment was performed to characterize the urinary proteome of PCa patients. This revealed 18 differentially abundant urinary proteins in PCa patients. Second, selected targets were clinically tested by immunoblot, and the soluble E-cadherin fragment was detected for the first time in the urine of PCa patients. Third, the proteogenome landscape of these PCa patients was characterized, revealing 1665 mutant protein is ...[more]

PMID: 35454907

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