Supplemental Table 1: SEREX identified antigens used on the antigen array. Name Symbol UniGene # Functional Significance Antigens identified by SEREX screening of a prostate cancer library in this study: Chloride channel, nucleotide-sensitive, 1A CLNS1A Hs.430733 Involved in small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization U3 small nucleolar ribonucleoprotein, homolog UTP15 Hs.406703 Nucleolar processing Bromodomain containing 9 BRD9 Hs.449278 DNA repair and/or cell cycle regulation TBC1 domain family, member 4 TBC1D4 Hs.210891 Insulin signaling Switch-associated protein 70 SWAP-70 Hs.153026 B-cell signaling Makorin, ring finger protein, 1 MKRN1 Hs.490347 E3 ligase involved in telomere length homeostasis Host cell factor C2 HCFC2 Hs.506558 Interacts with herpes simplex virus VP16 Kinesin family member 11 KIF11 Hs.8878 Involved in spindle dynamics during mitosis SWI/SNF-related matrix-associated actin- SMARCA4 Hs.327527 Member of chromatin remodeling complex dependent regulator of chromatin a4 isoform D involved in transcriptional activation. Tumor suppressor. Hydroxymethylbilane synthase HMBS Hs.82609 Metabolic enzyme. Mutations associated with porphyria malonyl-CoA decarboxylase precursor MLYCD Hs.644610 Metabolic enzyme Cofilin 1 (non-muscle) CFL1 Hs.170622 Intracellular actin-modulating protein Growth factor receptor-bound protein 2 GRB2 Hs.444356 Signaling- binds EGFR RNA exonuclease 4 homolog REXO4 Hs.438409 Unknown function. Possible transcription factor Chondroitin sulfate synthase 1 CHYS1 Hs.110488 Acts as a galactosyltransferase Disrupted in renal carcinoma protein 2 DIRC2 Hs.477346 Member of the major facilitator superfamily of transporters NADH dehydrogenase (ubiquinone) Fe-S protein NDUFS1 Hs.471207 Mitochondrial membrane Complex I protein 1, 75kDa (NADH-coenzyme Q reductase) Mof4 family associated protein 1 MRFAP1 Hs.701277 Influences transcription through chromatin remodeling Antigens identified in a SEREX screen of an ovarian cancer library: Matrilin-2 MATN2 Hs.189445 Adaptor protein of the extracellular matrix Cancer/testis antigen 1B NY-ESO-1 Hs.721615 Cancer/testis antigen expressed in variety of malignant tumors Tumor protein p53 p53* Hs.654481 Tumor suppressor. Regulates cell cycle arrest, apoptosis and senescence Hexamethylene bis-acetamide inducible 1 His1* Hs.15299 Transcriptional regulator Antigens identified in previous SEREX screens of a prostate cancer and testis library (12): Centrosomal protein 78 CEP78 Hs.374421 Cell cycle regulation Zinc finger protein 707 ZNF707 Hs.521922 Possible regulator of transcription Poly (ADP-ribose) polymerase family, member 1 PARP1 Hs.177766 DNA repair Outer dense fiber of sperm tails 2 ODF-2 Hs.129055 Maintains the elastic structure and recoil of the sperm tail Serologically defined colon cancer antigen 1 SDCCAG1 Hs.388584 Nuclear export RalA binding protein 1 RALBP1 Hs.334603 Signaling and drug transport Synaptonemal complex protein 65 SC65 Hs.446459 Cell cycle regulation WD repeat domain 36 WDR36 Hs.533237 Signaling Dihydrolipoamide dehydrogenase DLD Hs.131711 Metabolic enzyme Son DNA binding protein SON Hs.517262 Possible MYC family oncoprotein Recombining binding protein suppressor of RBPSUH Hs.479396 Notch signaling hairless F-box only protein 38 FBXO38 Hs.483772 Regulator of gene expression during differentiation * Reported previously (20) Supplemental Table 2: Antigens recognized by autoantibodies prior to treatment. vaccine EBRT (no Cancer-free ADT+EBRT WW +EBRT vaccine) Controls (n=15) (n=9) (n=33) (n=8) (n=15) Common to patients and controls: CLNS1A 4 0 1 0 1 UTP15 1 3 1 0 1 BRD9 2 1 0 0 2 TCB1B4 2 1 0 1 3 SC65 3 0 0 0 1 SON 3 2 0 0 1 RBPSUH 5 5 0 0 4 Unique to prostate cancer patients: SWAP-70 4 1 1 0 0 MKRN1 2 1 1 0 0 HCFC2 4 0 0 0 0 DLD 1 0 1 0 0 FBX038 0 1 1 1 0 NY-ESO-1 2 0 1 0 0 SDCCAG1 1 0 1 0 0 KIF1 1 0 0 0 0 SMARCA4 1 0 0 0 0 HMBS/SC65 1 0 0 0 0 MLYCD 1 0 0 0 0 DIRC2 1 0 0 0 0 NDUFS1 1 0 0 0 0 MATN2 1 0 0 0 0 MRFAP1 1 0 0 0 0 EBRT: External Beam Radiation Therapy; ADT: Androgen Deprivation Therapy; WW: Watchful Waiting = Active surveillance Supplemental Table 3: Comparison of treatment-induced T cell and autoantibody responses. Antigen Treatment-induced autoantibody Patient PSA T cell Treatment spreading T cell responses ID responses* responses* By Western By Array NIH-31 Vx + EBRT Yes Yes No No NIH-32 Vx + EBRT N/A N/A Yes No NIH-33 Vx + EBRT N/A N/A Yes No NIH-36 Vx + EBRT N/A N/A No No NIH-35 Vx + EBRT N/A N/A No Yes NIH-37 Vx + EBRT N/A N/A Yes No NIH-38 Vx + EBRT Yes Yes No No NIH-39 Vx + EBRT N/A N/A No No NIH-41 Vx + EBRT Yes Yes No No NIH-43 Vx + EBRT Yes N/A Yes Yes NIH-03 Vx + EBRT No N/A Yes Yes NIH-04 Vx + EBRT Yes N/A Yes No NIH-006 Vx + EBRT Yes Yes Yes Yes NIH-7 Vx + EBRT Yes No No Yes NIH-9 Vx + EBRT Yes No No No NIH-10 Vx + EBRT Yes Yes No No NIH-12 Vx + EBRT Yes Yes No No NIH-11 Vx + EBRT No N/A Yes Yes NIH-14 Vx + EBRT Yes N/A No No NIH-15 Vx + EBRT No Yes No No NIH-17 Vx + EBRT No Yes Yes No NIH-21 Vx + EBRT Yes N/A Yes No NIH-23 Vx + EBRT Yes N/A No No NIH-24 Vx + EBRT Yes N/A No No NIH-25 Vx + EBRT Yes N/A No No NIH-28 Vx + EBRT Yes N/A Yes Yes NIH-29 Vx + EBRT Yes Yes Yes No NIH-40 Vx + EBRT N/A N/A No No NIH-44 Vx + EBRT No N/A No No NIH-45 Vx + EBRT No N/A Yes No NIH-46 Vx + EBRT Yes No No No NIH-47 Vx + EBRT Yes No Yes No NIH-48 Vx + EBRT N/A N/A Yes No NIH-02 EBRT No N/A Yes No NIH-8 EBRT No N/A No No NIH-13 EBRT No N/A No No NIH-16 EBRT No N/A No No NIH-18 EBRT No N/A No No NIH-19 EBRT No N/A No No NIH-22 EBRT No N/A No No NIH-27 EBRT No N/A No No * T cell responses to PSA or to antigens not contained in the vaccine (i.e., antigen spreading to PSMA, PAP, PSCA, MUC-1, XAGE-1 and PAGE-4) were previously published (Gulley 2005; Lechleider 2008). N/A= Not Available Supplemental Table 4: Clinical characteristics of the 7 patients with autoantibody responses against the panel of 4 antigens. Age at PSA at Biochemical Patient Dose IL-2 ADT Gleason Stage Risk Treatment Diagnosis Failure/Recurrence NIH-03 4 MIU/M2 53 10.6 Yes 6 T2a Intermediate Yes NIH-006 4 MIU/M2 56 63 Yes 8 T2c High Yes NIH-7 4 MIU/M2 51 94.5 Yes 7 T2b High No NIH-11 4 MIU/M2 64 14.7 Yes 8 T1c High Yes NIH-28 4 MIU/M2 63 206 Yes 7 T3b High Yes NIH-35 0.6 MIU/M2 73 5.7 No 6 T1c Low No NIH-43 0.6 MIU/M2 67 123 No 6 T2a High No .