Supplemental Table 1: Primers Utilized for QPCR Analysis and Examination for TMPRSS2:ERG Fusion

Supplemental Table 1: Primers utilized for QPCR analysis and examination for TMPRSS2:ERG fusion.

Target Gene Primers PSMA/ FOLH1 CAAGCAGCCACAACAAGTATGC GAAGGGTCCACTTTGCTTTCAA CD10/ MME ACAGCAACTTGGAGACGTTGTGC CTCCAGCAAATGCTGCTTCCACAT ERG GACGACTTCCAGAGGCTCAC TGAAGTCAAATGTGGAAGAGGA HOXC4 CCCACCCCTATCGTGGTTAT GGGCATTTCACATCGACACT HOXC5 GCGCATAGAGATCGCCAACAACTT TCTTCCACTTCATCCTGCGGTTCT Hepsin AGAATACATCCAGCCTGTGTGCCT TCAGCGCCATTGCAGACATCATTG AMACR CTCAACTGCCGTTCAACAATCGCA ATCACTGAGGCGCTAAGGGAAACA FASN CAAATTGCTGCTTGGATTTTGA TTAATTGTGGGAGGCTGAGAGC SPOCK AGCTGGCCCAGATACAAGTACCAA CTTGCTTGGGTGGCTGATTCTGAT Myosin VI TGACACCGGAACAAATGGCCAAAG AGCTGCCAGGAGCTCAATATCACA EZH2 CAGTTTGTTGGCGGAAGCGTGTAA AGGATGTGCACAGGCTGTATCCTT RPL13A CCTGGAGGAGAAGAGGAAAGAGA TTGAGGACCTCTGTGTATTTGTCAA TMPRSS2:ERG fusion AGCTAAGCAGGAGGCGGA CGACTGGTCCTCACTCACAA

Supplemental Table 2: Gene sets analyzed through GSEA.

Genes Increased in Prostate Cancer Genes Decreased in Prostate Cancer Gene Gene Name Gene Symbol Gene Name Symbol NME1 Nonmetastatic cells 1 MEIS1 MEIS1, mouse homolog of, 1 ST14 Suppression of tumorgenicity 14 VCL Vinculin PPP3CA Protein phosphatase 3, alpha isoform LAMA4 Laminin, alpha 4 SND1 EBNA2 coactivator p100 SPARCL1 SPARC-like protein 1 PRSS8 Serine protease 8 GSN Gelsolin FASN Fatty acid synthase PRKCB1 Protein kinase C, beta-1 ARMET Arginine-rich protein mutated in early tumors RCAN2 Regulator of calcineurin 2 AMACR Alpha-methylacyl-CoA racemase FBN1 Fibrillin 1 PDLIM5 PDZ and LIM domain 5 GJA1 Gap junction protein, alpha 1 BRP44 Brain protein 44 GPM6B Glycoprotein M6B BDH1 3-alphahydroxybutyrate dehydrogenase 1 PMP22 Peripheral myelin protein 22 HPN Hepsin GATM L-arginine:glycine aminotransferase TSTA3 Tissue-specific transplantation antigen 3 TACC1 Transforming acidic coiled coil containing protein 1 APRT Adenine phosphoribosyl transferase HLF Hepatic leukemia factor TCRG T cell antigen receptor, gamma subunit NFU1 HIRA-interacting protein 5 GDF15 Growth/differentiation factor 15 PRNP Prion protein LIG3 DNA ligase 3 ITGA1 Integrin alpha-1 ABHD2 Abhydrolase domain-containing 2 TIMP3 Tissue inhibitor of metalloproteinase 3 TRAP1 TGFBR-associated protein 1 MGP Matrix gamma-carboxyglutamic acid TPD52 Tumor protein D52 MEIS2 MEIS1, mouse homolog of, 2 AHCY S-adenosylhomocysteine hydrolase CAV2 Caveolin 2 EBNA1BP EBNA1 binding protein 2 SEC23A SEC23, S. cerevisiae, homolog of, A 2 EIF3S2 Eukaryotic translation intiation factor 3, subunit 2 ITSN1 Intersectin 1 POLD2 DNA polymerase, delta 2 RND3 Rho family GTPase 3 TFF3 Trefoil factor 3 G6PD Glucose 6 phosphate dehydrogenase PAICS Phophoribosylaminoimidazole carboxylase MFGE8 Milk fat globule-EGF factor 8 UAP1 UDP-N-acetylglucosamine pyrophosphorylase 1 PRKAR2B Protein kinase, cAMP dependent, type II beta C6orf108 Deoxynucleoside 5'-monophosphate N- RAP1B Ras-related protein RAP1B glycosidase SOX4 SRY-box 4 DDR2 Discoidin domain receptor family, member 2 NFYC Nuclear transcription factor Y, gamma C7 Complement component 7 ATP6AP1 Vacuolar ATPase, subunit 1 PPAP2B Phosphatidic acid phosphatase type 2B SLC25A6 Solute carrier familly 25, member A6 PLP2 Proteolipid protein 2 PRDX4 Peroxiredoxin 4 TPM1 Tropomyosin 1 KRT18 Keratin 18 BTG3 B-cell translocation gene 3 ODC1 Ornithine decarboxylase 1 PKD2 Polycystic kidney disease 2 FAAH Fatty acid amide hydrolase ST5 Suppressor of tumorigenicity 5 DAP Death-associated protein HMGN4 HMG nucleosome binding protein 4 TRIM14 Tripartite motif containing protein 14 AKAP12 A-kinase anchor protein 12 KRT8 Keratin 8 IGFBP3 Insulin-like growth factor binding protein 3 MYC v-myc avian myelocytomatosis viral oncogene homolog

Supplemental Table 3: GSEA results

Increased in Enrichment Score Normalized ES P-value FDR (q-value) CABE (ES) Genes increased in 0.56 1.58 0.072 0.079 prostate cancer

Increased in Enrichment Score Normalized ES P-value FDR (q-value) BABE (ES) Genes decreased in 0.57 1.50 0.087 0.099 prostate cancer

Supplemental Table 4: Race of CABE Patient’s included in the study. The number corresponds to the numbered lane within the microarray heat map in Figure 1.

Patient Race CABE 1 White CABE 2 White CABE 3 White CABE 4 African American CABE 5 White CABE 6 African American CABE 7 White CABE 8 African American CABE 9 African American CABE 10 White CABE 11 White CABE 12 Pacific Islander CABE 13 White CABE 14 White CABE 15 White