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proteomes Article Comparative Proteomics Analysis of Urine Reveals Down-Regulation of Acute Phase Response Signaling and LXR/RXR Activation Pathways in Prostate Cancer Katarina Davalieva 1,*, Sanja Kiprijanovska 1, Ivana Maleva Kostovska 1, Sotir Stavridis 2, Oliver Stankov 2, Selim Komina 3, Gordana Petrusevska 3 and Momir Polenakovic 1 1 Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Krste Misirkov 2, 1000 Skopje, Macedonia; [email protected] (S.K.); [email protected] (I.M.K.); [email protected] (M.P.) 2 University Clinic for Urology, University Clinical Centre “Mother Theresa”, 1000 Skopje, Macedonia; [email protected] (S.S.); [email protected] (O.S.) 3 Institute of Pathology, Medical Faculty, University “St. Cyril and Methodius”, 1000 Skopje, Macedonia; [email protected] (S.K.); [email protected] (G.P.) * Correspondence: [email protected]; Tel.: +389-2-3235-410; Fax: +389-2-3115-434 Received: 15 November 2017; Accepted: 25 December 2017; Published: 29 December 2017 Abstract: Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, benign prostate hyperplasia, bladder cancer, and renal cancer, coupled with bioinformatics analysis, were performed. Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively. In silico analysis indicated activation, binding, and cell movement of subset of immune cells as the top affected cellular functions in PCa, together with the down-regulation of Acute Phase Response Signaling and Liver X Receptor/ Retinoid X Receptor (LXR/RXR) activation pathways. The most promising biomarkers were 35, altered in PCa when compared to more than one group. Half of these have confirmed localization in normal or PCa tissues. Twenty proteins (CD14, AHSG, ENO1, ANXA1, CLU, COL6A1, C3, FGA, FGG, HPX, PTGDS, S100A9, LMAN2, ITIH4, ACTA2, GRN, HBB, PEBP1, CTSB, SPP1) are oncogenes, tumor suppressors, and multifunctional proteins with highly confirmed involvement in PCa, while 9 (AZU1, IGHG1, RNASE2, PZP, REG1A, AMY1A, AMY2A, ACTG2, COL18A1) have been associated with different cancers, but not with PCa so far, and may represent novel findings. LC-MS/MS data are available via ProteomeXchange with identifier PXD008407. Keywords: proteomics; non-invasive biomarker; prostate cancer; urine; LC-MS/MS; 2-D DIGE/MS 1. Introduction Despite the intense research of prostate cancer (PCa) in the last years, it still remains the second most common cause of malignancy death in men of all ages [1]. Screening and detection of PCa are still mainly based on serum prostate specific antigen (PSA), which is more sensitive than specific for PCa [2] and produces a significant portion of false negative [3] and false positive [4] results. The high necessity for the more reliable screening tool has driven an extensive research which delivered a number of new potential biomarkers for screening and/or diagnosis of PCa [5–8]. These biomarkers are peptides, proteins, RNA transcripts, DNA methylations, and large-scale mitochondrial DNA deletions [8]. Some of these have already entered into clinical practice, but mainly as a supplement to PSA testing or as an additional supplement to biopsy-based diagnosis and prognosis of PCa. Proteomes 2018, 6, 1; doi:10.3390/proteomes6010001 www.mdpi.com/journal/proteomes Proteomes 2018, 6, 1 2 of 25 It has been widely accepted now that understanding the pathophysiology of PCa as complex, heterogenic disease and the discovery of more sensitive/specific tools for disease detection requires a systems approach. Comparative proteomics studies have a significant and important role in this by aiming to detect and quantify proteins with altered abundance without prior biological knowledge, which subsequently may reveal candidate biomarkers. Proteomics studies have identified a large number of putative biomarkers for screening, differentiation between disease stages, and prognosis [9–11], and many are tested for their clinical utility. Several possible non-invasive or minimally invasive biomarkers sources, each with advantages and limitations, are under current investigation, including urine, serum, plasma, and prostatic fluids. The goal of the PCa biomarker field, as well as the cancer biomarker field in general, is to develop simple, non-invasive tests that can allow for early cancer detection, classify the tumor so the patient can receive the most appropriate therapy, and monitor disease progression, regression, and recurrence [12]. The ideal PCa screening biomarker in addition to the high sensitivity and specificity for PCa should be non-invasive, easy accessible, and present at concentrations that are detectable by current technologies. The research so far has proven that one molecular marker based tests does not possess enough power for clinical use and this concept is replaced by the global assessment strategy and the development of multiplex biomarker assays. This makes sense when one considers the heterogeneity of prostate tumors, complex interactions between various molecules within a single pathway and the cross-talk between molecular pathways. Although detecting PCa using diagnostic markers still remains a challenge, the advent of new high-throughput proteomics techniques and systematic searches through rigorous experimental design and in-depth quantitative studies is driving biomarker discovery forward [13]. In order to detect proteins that are sensitive and specific enough to detect early stages of PCa, we performed a complex comparative proteomic study analyzing urine as a source for non-invasive biomarkers. In clinical proteomics, urine has become a preferred choice for biomarker discovery, especially for the detection and diagnosis of urological conditions because it can be sampled non-invasively in large quantities [14], contains soluble and stable proteins/peptides from plasma or urogenital tract, and it has a lower dynamics range of protein concentrations compared with other biofluids [15]. To date, several urinary biomarkers have been identified and considered for use in PCa screening, each with varying levels of evidence [16]. Our preliminary comparative study of urine from PCa and benign prostate hyperplasia (BPH) patients using two-dimensional Difference Gel Electrophoresis coupled with Mass Spectrometry (2-D DIGE/MS) , revealed a panel of acute phase response proteins as a non-invasive biomarkers for PCa [17]. Although the observed accuracy of the individual proteins was similar to the PSA, their combination yielded a greater accuracy when compared to individual tests. In the current study, using both 2-D DIGE/MS and label-free Liquid Chromatography—tandem Mass Spectrometry (LC-MS/MS), we compared urine samples from patients with early PCa stages and Gleason score between 6 and 7 with samples from patients with BPH and other urological cancers, namely bladder and renal. The main goal of this study was to discover a diagnostic biomarker or a set of biomarkers in urine, which were sufficiently sensitive to detect PCa in its early stages and specific enough to separate the disease from BPH or other urological cancers. 2. Materials and Methods 2.1. Samples The urine samples were collected from men attending the University Clinic for Urology, University Clinical Centre “Mother Theresa,” Skopje, Republic of Macedonia in the period from January 2014 until June 2015. Informed consent for the use of these samples for research purposes was obtained from the patients in accordance with the Declaration of Helsinki. The study has been approved by the Ethics Committee of the Macedonian Academy of Sciences and Arts (Code: 011/2014). We analyzed 32 urine samples from patients with prostate cancer (PCa), benign prostate hyperplasia (BPH), bladder cancer (BC), and renal cancer (RC). The samples from the three cancer groups (PCa, BC, and RC) were collected Proteomes 2018, 6, 1 3 of 25 from patients prior prostate, bladder, or kidney biopsy or prior surgery. The samples from non-cancer subjects (BPH Group) were collected prior to needle biopsy of the prostate gland or transurethral resection of the prostate (TURP). Patients that were diagnosed with BPH were followed in the course of one year, during which repeat biopsy was performed to exclude the possibility of developing cancer. The diagnosis of all individuals whose samples were included in this study was based on histological evaluation of the tissues obtained by biopsy or surgical procedure (Supplementary Document 1). The preselection of the urine samples from PCa was made according to the patient’s histological records documenting tumor grade, stage as well as pre-procedure PSA level. The preselection of the BPH patients was made solely by pre-procedure PSA level in order to match with the PCa group. The mean pre-operative PSA serum level was 7.4 ± 2.1 and 6.8 ± 1.8 (ng/mL) of PCa and BPH group, respectively. The Gleason score of PCa patients was 6.9 ± 1.1 (mean ± SD). All of the BC and RC patients were at stage I or II at the time of sample collection. All the patients were male and were matched for age (group mean 61.1–69.8 years). 2.2. Sample Preparation The first morning urine (3–10) mL was collected from the patients prior to clinical intervention and was stored on ice for a short period (<1 h). Samples were centrifuged at 1000× g, for 10 min to remove cell debris, aliquoted in 1.5 mL tubes and stored at −80 ◦C until use. 2-D DIGE/MS analysis: Urine proteome was isolated from 100 µL urine in five or more replicates per sample using 2-D Clean-UP Kit (GE Healthcare, Little Chalfont, UK), according to the manufacturer’s instructions. The pellets from each replicate were dissolved in 10 µL of UTC buffer (8 M Urea, 2 M Thiourea, 4% CHAPS) and pooled together.

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