The absolute number and frequency of each adverse event will be reported, and subdivided according to toxicity grade. A description of adverse events by treatment arm will also be reported. A particular adverse event occurring more than once in the same subject will be counted only once and at its worse grade . 8.3 Secondary Endpoints 8.3.2 Regulatory T cell (T reg) infiltration The method for quantifying T reg density from harvested prostate tissue is as described in Section 8.2.1 . This endpoint will be expressed as the mean staining percentage in tumor tissue, and will be reported separately for each treatment arm. 8.3.1 CD4+ T cell infiltration The method for quantifying CD4+ T cell density from harvested prostate tissue is as described in Section 8.2.1. This endpoint will be expressed as the mean staining percentage in tumor tissue, and will be reported separately for each treatment arm. 8.3.3 Tissue androgen concentrations Tissue concentrations of testosterone and 5α -dihydrotestosterone (DHT) will be measured using a highly sensitive liquid chromatography–electrospray ionization tandem mass spectrometry method using a high proton affinitive derivatiz ation of the 17β-hydroxyl group of testosterone and DHT with picolinic acid, and a mobile phase consisting of MeCN –MeOH – Androgen suppression with prostate GVAX and cyclophosphamide J1265 Johns Hopkins University 45 of 68 J1265 PROT (Vers) 1.4 113012 H2O–formic acid an d a conventional octadecylsilica (ODS) column (Yamashita et al 2009) . Purification of the derivatives will be carried out using solid- phase extraction with the ODS cartridge. By this method, testosterone and DHT will be determined simultaneously with limit s of quantification of 0.5 pg and 1 pg/3 mg of prostate tissue, respectively . Tissue androgen concentrations will be reported separately for each treatment arm. 8.3.4 Androgen receptor (AR) quantification The method for quantifying androgen receptor (AR) density from harvested prostate tissue is similar to that described in Section 8.2.1 , and will rely on immunohistochemical staining for the AR protein. This endpoint will be expressed as the mean staining percentage in tumor tissue, and will be reported s eparately for each treatment arm . 8.3.5 Markers of apoptosis TMAs from formalin -fixed tumor samples will be analyze d for the degree of tumor apoptosis using immunohistochemical staining for activated caspase 3 (Marcelli et al 2000) , or by using the method of terminal deoxynucleotidyl transferase (TdT) -mediated deoxyuridine triphosphate (dUTP) nick end labeling ( i.e. TUNEL assay) (Furuya et al 1995) . The in situ Cell Death Detection Kit (Roche, Indianapolis, IN) may be used to perform TUNEL reactions. Quanti fication of staining percentage will be achieved using the Aperio ScanScope® CS instrument (Aperio Technologies , Vista , CA) as describe d in Section 8.2 .1. This endpoint will be expressed as the mean staining percentage in tumor tissue, and reported separately for each treatment arm. Analyses will be performed in the laboratory of Dr Angelo DeMarzo . 8.3.6 Markers of cell proliferation TMAs from fixed tumor samples will be analyzed for the degree of tumor cell proliferation using the validated marker , Ki-67. This will be achieved by immu nohistochemical staining (Berges et al 1995; Rubin et al 2002) , using the Ki -67 monoclonal antibody (Dako North America, Carpineteria, CA). Quantification of staining percentage will be performed using the Aperio ScanSc ope ® CS instrument (Aperio Technologies , Vista , CA) as described in Section 8.2.1 . This endpoint will be expressed as the mean staining percentage in tumor tissue, and reported separately for each treatment arm. Assays will be performed in the laboratory o f Dr DeMarzo . 8.3.7 Pathological complete responses (pCR) This will be defined as the absence of tumor identification by the study pathologist on standard histological analysis of the resected prostate specimens. The proportion of men achieving a pCR will be reported separately for each treatment arm. 8.3.9 Novel anti -prostate antibodies Patient sera will be cryopreserved and archived at the Johns Hopkins Specimen Acquisition Core (SAC) facility . Novel induced ant ibody specificities will be investigated by interrogating patient sera using the high -throughput immunoblot (HTI) assay developed by our collaborator, Dr. Douglas McNeel , as previously de scribed (Smith et al 2011; Zabransky et al 2012). Briefly, λ -phage en coding 126 unique prostate -associated antigens will spotted in triplicate in a 16×24 array onto E. C oli bacterial lawns using a Biomek FX liquid handling robot. These individual antigens includ e 29 cancer -testis antigens , 40 antigens identified in pati ents with chronic prostatitis , and 57 antigens identified in individual patients, some of whom were t reated with androgen ablation or other immunomodula tory therapies . Encoded proteins will be transferred to nitrocellulose membranes, washed, blocked, and prob ed with sera from patients pre- or post -treatment, diluted 1:100 in isotonic buffer. Human IgG will then be detected with an IgG -specific secondary antibody conjugated to alkaline phosphatase and immunoreactivity will be detected by development with 0.3 mg/mL nitro blue tertazolium chloride (NBT) (Fisher Biotech , Hampton, NH) and 0.15 Androgen suppression with prostate GVAX and cyclophosphamide J1265 Johns Hopkins University 46 of 68 J1265 PROT (Vers) 1.4 113012 mg/mL 5 -bromo 4- chloro 3- indoylpho sphate (BCIP) (Fisher Biotech). Membranes will be digitally scanned and then assessed visually, with individual plaques scored “ positive ” or “not positive ” by 3 independent observers, blinded to the treatment arm , timing of sample acquisition , and membran e layout. Triplicate samples will be evaluated for each antigen, and immunoreact ivity to individual antigens will be scored positive if there is concordance among 2 of 3 observers, and if immunoreactivity is scored positive in at lea st two of the three replicates. Novel antibody specificities with potential biomarker and/or therapeutic potential will be independently co nfirmed by developing individual ELISA assays for those particula r antigens. 8.3.9 PSA response rates This will be defined as the proportion of patients who achieve an undetectable PSA (<0.1 ng/mL) by 3 months after prostatectomy. The proportion of men ach ieving a PSA response will be reported separately for each treatment arm. 8.3.10 Time to PSA recurrence This will be defined as the interval from the time of prostatectomy to the time when the serum PSA is ≥0.2 ng/ mL. PSA will be measured every 3 (±1) mon ths during the first post- operative year and every 6 (±2) months during the second and third post- operative years. For subjects who have not yet demonstrated PSA relapse at the time of censoring , patients will be censored at the date of the last assessment that shows a lack of PSA recurrence . This outcome will be expressed as a median for each treatment arm , and will be determined using the Kaplan- Meier method . 9. REGULATORY AND REPORTING REQUIREMENT S Contact details for personnel connected with this stu dy are provided on the title page at the front of this protocol. Patient registration procedures are described in Section 4. 9.1 Regulatory Responsibilities 9.1.1 Protocol c hair The protocol c hair (=PI) , Emmanuel Antonarakis is responsible for the following t asks: • Coordinating, developing, writing, submitting, and obtaining IRB -approval for the protocol as well as its subsequent amendments. • Assuring that a ll study personnel are using the correct version of the protocol. • Taking responsibility for the overall conduct of the study and for monitoring the progress of the study. • Reviewing and ensuring reporting of serious adverse events (SAEs). • Reviewing data from all patients . 9.1.2 Study Coordinator The study coordinator , Harry Cao , is responsible for the following tasks: • Ensuring that IRB approval has been obta ined prior to patient registration, and maintaining copies of IRB approvals (including approval of amendments) . • Managing patient registration. • Collecting a nd compiling data from each patient . • Establishing procedur es for documentation, reporting, and sub mission of AEs / SAEs to the p rotocol chair ( Charles G. Drake , MD PhD ) and other applicable parties. Androgen suppression with prostate GVAX and cyclophosphamide J1265 Johns Hopkins University 47 of 68 J1265 PROT (Vers) 1.4 113012 • Facilitating audits by securing selected source documents and research records from participati ng patients for audit . 9.1.3 Study personnel Study personnel (co -investigators, research nurses) are responsible for these tasks: • Following the protocol as written, and Good Clinical Practice (GCP) guidelines . • Submitting data to the project manager . • Regist ering all patie nts by submitting the patient reg istration form and signed informed consent form promptly . • Providing sufficient experienced clinical and administrative staff and adequate facilities and equi pment to conduct the trial according to the protocol. • Maint aining regulatory binders and providing copies of all required docu ments to the project manager . • Collecting/ submitting data according to the schedule specified by the protocol. 9.2 Data Management Data collected during this study will be e ntered into a secure database. The study coordinator will be responsible for the initial study configuration and setup of the database and for any future changes. 9.2.1 Case report forms Case report forms (CRFs) will be generated by the study coordinator for the collection of all study- related data. Investigators and study personnel will be res ponsible for ensuring that the CRFs are kept up -to-date. 9.2.2 Source documents Investigators and s tudy personnel will record clinical data in each patient’s source documents ( i.e., the patient’s medical record). Source documentation will be made avail able to support the patient research record. Study monitors will review entries on the CRFs at regular intervals, comparing the content with the source documents. 9.2.3 Record retention The investigator will maintain adequate and accurate records to enable the conduct of the study to be fully documented and the study data to be subsequently verified. After stud y closure, the investigator should maintain all source docume nts, study -related documents, and the CRFs. Because the length of time required for retaining records depends upon a number of regulatory and legal factors, documents should be stored until the investigator is notified that the documents may be destroyed . In this study, records are to be retained and securely stored for a minimum of 3 years after the completion of all study -related activities. 9.3 Study Monitoring and Quality Assurance This is a DSMP Level III study under the Johns Hopkins Sidney Kimmel Comprehensive Cancer Center (SKCCC) Data Safety Monitoring Plan (herein after referred to as either JHU SKCCC DSMP or DSMP; please see Appendix E for complete plan). The protocol will be internally monitored by the principal investigator. External data mon itoring will be performed by the SKCCC Clinical Research Office Quality Assurance Program (CRO QA) at least quarterly, but may occur more or less frequently depending on the rate of accrual (per the DSMP). Additional data and safety monitoring oversight will also be performed by the SKCCC Safety Monitoring Committee (SMC - as defined in the DSMP) and a Medical Expert Committee (MEC ) as detailed below. Androgen suppression with prostate GVAX and cyclophosphamide J1265 Johns Hopkins University 48 of 68 J1265 PROT (Vers) 1.4 113012 Authorized representatives of SKCCC are permitted to perform audits or inspections, including source data verification. The purpose of these audits or inspections is to systematically and independently examine all trial -related activities and documents to determine whether these activities were conducted and data were recorded, analyzed, and accurately reporte d according to the protocol, Good Clinical Practice (GCP) guidelines , and any applicable regulatory requirements. Regular ly scheduled registration reports will be gener ated to monitor patient accrual and the completeness of registration data. Routine data quality reports will be generated to assess missing data and inconsistencies. Accrual rates and the extent and accuracy of evaluations and follow -up will be monitored periodically throughout the study period, and potential problems will be brought to the attention of the principal investigator for discussion and action. The Medical Expert Committee (MEC) for th is clinical study contains two medical oncologists and one urologist (see below) from other disciplines who are not affiliated with this clinical tri al protocol. The MEC will review safety data on at least a semi -annual basis. The MEC will provide a written summary of each assessment to the IND Sponsor -Investigator after each meeting. In turn, the study team will forward these summaries to the JHU IRB and JHU SKCCC SMC. The operating plan of the MEC will be as follows: • Meetings will be held at least semi -annually, and potentially more frequently if needed. • Meetings will be conducted in -person or via video/teleconference, with a participant sign -in sheet collected at each meeting. • Approximately one week prior to each MEC meeting, the study team will submit the following items to MEC personnel for review and discus sion at the meeting (t he PI may join the MEC meeting in order to answer any questions the MEC might have):  A summary of the clinical trial’ s progress to date;  The latest IRB -approved consent document;  A summary of all AEs, SAEs , deaths, and withdrawals to date Note that the MEC reserves the right to halt trial accrual or all study activity if, after review, serious safety concerns warrant this action. If the MEC halts study accrual or all study activity, then the study team must notify the JHU SKCCC SMC, JHU IRB, FDA, and NIH RAC immediately. The MEC consists of the following members:  Dr Dung Le (medical oncology); phone : 443-287-0002; email : dle@jhmi.edu  Dr Evan Lipson (medical oncology); phone : 410-502-5977; email : elipson2@jhmi.edu  Dr Ronald Rodriguez (urology); phone : 410- 614-6662; email : rrodrig@jhmi.edu All clinical work conducted under this protocol is subject to Good Clinical Practice (GCP) guidelines. This includes inspection of study -related records by the principa l investigator, project manager , sponsor or its designee, or health authori ty representatives at any time.