Identification of Prostate-Enriched Proteins by In-depth Proteomic Analyses of Expressed Prostatic Secretions in Urine

Urinary expressed prostatic secretion or “EPS-urine”
is proximal tissue fluid that is collected after a digital rectal
exam (DRE). EPS-urine is a rich source of prostate-derived proteins
that can be used for biomarker discovery for prostate cancer (PCa)
and other prostatic diseases. We previously conducted a comprehensive
proteome analysis of direct expressed prostatic secretions (EPS). In the current study,
we defined the proteome of EPS-urine employing Multidimensional Protein
Identification Technology (MudPIT) and providing a comprehensive catalogue
of this body fluid for future biomarker studies. We identified 1022
unique proteins in a heterogeneous cohort of 11 EPS-urines derived
from biopsy negative noncancer diagnoses with some benign prostatic
diseases (BPH) and low-grade PCa, representative of secreted prostate
and immune system-derived proteins in a urine background. We further
applied MudPIT-based proteomics to generate and compare the differential
proteome from a subset of pooled urines (pre-DRE) and EPS-urines (post-DRE)
from noncancer and PCa patients. The direct proteomic comparison of
these highly controlled patient sample pools enabled us to define
a list of prostate-enriched proteins detectable in EPS-urine and distinguishable
from a complex urine protein background. A combinatorial analysis
of both proteomics data sets and systematic integration with publicly
available proteomics data of related body fluids, human tissue transcriptomic
data, and immunohistochemistry images from the Human Protein Atlas
database allowed us to demarcate a robust panel of 49 prostate-derived
proteins in EPS-urine. Finally, we validated the expression of seven
of these proteins using Western blotting, supporting the likelihood
that they originate from the prostate. The definition of these prostatic
proteins in EPS-urine samples provides a reference for future investigations
for prostatic-disease biomarker studies.