Supplementary Table 1: Non-proteomic studies to discover biomarkers of prostate cancer Biomarker(s) ‡: Samples† IL-18BP n = 67 cancer urine samples post DRE and n = 37 healthy controls. PCA3, TMPRSS2:ERG, and Annexin-A3 n = 86 untreated prostate cancer donors and n = 45 healthy controls. Engrailed-2 (EN2) n = 82 prostate cancer patients and n = 102 healthy controls-no need for DRE with this marker. c-MET receptor n = 75 localized prostate cancer donors, n = 81 metastatic prostate cancer donors. n = 16 prostate cancer urine samples, n = 15 healthy controls. δ-catenin N-telopeptide of type-I collagen n = 94 urine donors Study design and Diagnostic/Prognostic Utility‡ ELISA-based study. IL-18BP elevated in prostate cancer urine compared to controls. ROC AUC for IL-18 BP = 0.658. qRT-PCR (PCA3, TMPRSS2:ERG) and WB (Annexin-A3). Elevated levels of Annexin-A3 protein in urine from patients with PC, elevated levels of PCA3, TMPRSS2: ERG transcripts ROC AUC for panel = 0.84 (if PSA = 4-10 ng/ml) and 0.856 (all patients). ELISA/WB. EN2 elevated in prostate cancer. Detection of prostate cancer, sensitivity = 66%, specificity = 88.2%. Results confirmed at a second centre. ELISA. ROC AUC for detection of metastatic disease = 0.90 (95% CI = 0.840.95). WB-based study.. Increased δ-catenin detects prostate cancer with 87.5% specificity and 83.3% sensitivity. Increased levels in the urine of prostate cancer compared to controls (p<0.0005). ELISA-based study. Increased uNTX inversely correlated with overall patient survival Elevated urinary NTx HR = 2.2. (95% CI = 1.2-4.0). Reference(s): (1) (2) (3) (4) (5) (6) n = 411 urine donors. ELISA-based study: Increased uNTX inversely correlated with overall patient survival High NTx levels associated with a 4-6-fold increased risk of death, skeletal related events and disease progression compared to low levels (p < 0.001). (7) Alpha-methylacyl coenzyme-A racemase n = 26 urine donors. (8) Vascular Endothelial Growth Factor (VEGF) n = 100 prostate cancer patients. Thymosin-β15 n = 61 untreated prostate cancer patients, n = 46 prostatectomy samples, 14 with androgen deprivation therapy, and control groups (n = 52 normal patients, n = 15 with genitourinary diseases, n = 81 with non malignant prostate conditions and n = 73 with other urological conditions). WB-based study. AMACR detected in 12 out of 12 donors with biopsy confirmed adenocarcinoma, 5 out of 12 with no cancer detected on biopsy and in 1 out of 2 with atypia on biopsy. ELISA-study. Increased VEGF levels correlate with decreased survival (p = 0.024). If VEGF > 28 pg/ml 60% increased risk of death (HR = 1.62, p = 0.03). ELISA-based study. At 40 (ng/dl)/microgram protein/mg creatinine detection of PCa with 58% sensitivity and 94% specificity. Improves diagnostic specificity of PSA monitoring. ELISA-based study. Urinary prostatic inhibin-like peptide high in benign prostatic hyperplasia, and low in prostate cancer. ELISA-based study. CD105 elevated in urine from biopsy proven cases versus controls (p < 0.0014). ROC AUC = 0.72. Predicts PC with a sensitivity of 73% and a specificity of 63% WB-Based Study. Annexin-A3 levels drop within prostate cancer. Urine post DRE used. Annexin-A3 levels and PSA (11) Prostatic inhibin-like peptide Endoglin (CD105) Annexin-A3 n = 99 prostate cancer urine samples, n = 69 samples from radical prostatectomy donors and n=20 from patients classified as having low-risk of prostate cancer. n = 591 prostate cancer patients recruited. (9) (10) (12) (13) levels predicted prostate cancer with ROC AUC = 0.82 (PSA = 2-6 ng/ml), 0.83 (PSA = 4-10 ng/ml) and = 0.81 (all patients). †All samples are human and urine unless otherwise specified; n numbers refer to number with condition unless otherwise stated, ‡Abbreviations used for proteomic techniques are defined within the text and list of common abbreviations. 1. Fujita K, Ewing CM, Isaacs WB, Pavlovich CP. Immunomodulatory IL-18 binding protein is produced by prostate cancer cells and its levels in urine and serum correlate with tumor status. Int J Cancer. 2011 Jul 15;129(2):424-32. 2. Cao DL, Ye DW, Zhang HL, Zhu Y, Wang YX, Yao XD. A multiplex model of combining gene-based, protein-based, and metabolite-based with positive and negative markers in urine for the early diagnosis of prostate cancer. Prostate. 2011 May 15;71(7):700-10. 3. Morgan R, Boxall A, Bhatt A, Bailey M, Hindley R, Langley S, et al. Engrailed-2 (EN2): a tumor specific urinary biomarker for the early diagnosis of prostate cancer. Clin Cancer Res. 2011 Mar 1;17(5):1090-8. 4. Russo AL, Jedlicka K, Wernick M, McNally D, Kirk M, Sproull M, et al. Urine analysis and protein networking identify met as a marker of metastatic prostate cancer. Clin Cancer Res. 2009 Jul 1;15(13):4292-8. 5. Lu Q, Zhang J, Allison R, Gay H, Yang WX, Bhowmick NA, et al. Identification of extracellular deltacatenin accumulation for prostate cancer detection. Prostate. 2009 Mar 1;69(4):411-8. 6. Rajpar S, Massard C, Laplanche A, Tournay E, Gross-Goupil M, Loriot Y, et al. Urinary N-telopeptide (uNTx) is an independent prognostic factor for overall survival in patients with bone metastases from castration-resistant prostate cancer. Ann Oncol. 2010 Sep;21(9):1864-9. 7. Brown JE, Cook RJ, Major P, Lipton A, Saad F, Smith M, et al. Bone turnover markers as predictors of skeletal complications in prostate cancer, lung cancer, and other solid tumors. 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Endoglin (CD105) as a urinary and serum marker of prostate cancer. Int J Cancer. 2009 Feb 1;124(3):664-9. 13. Schostak M, Schwall GP, Poznanovic S, Groebe K, Muller M, Messinger D, et al. Annexin A3 in urine: a highly specific noninvasive marker for prostate cancer early detection. J Urol. 2009 Jan;181(1):343-53.