Prostate cancer (PC) is the second leading cause of cancer-related deaths in US men, and progression to androgen-independent PC (AIPC) typically results in metastasis and is lethal. However, the mechanisms whereby PC progresses from androgen dependence to androgen independence are not completely understood. Mutagenesis screens to identify novel genes involved in the progression to AIPC have been performed using replication-incompetent lentiviral vectors (LVs). In this approach the LV acts both as a mutagen and as molecular tag to identify nearby genes that may have been dysregulated by the vector provirus, and are candidate AIPC genes. Here we describe protocols for generation of replication-incompetent LV preparations and performing a mutagenesis screen to identify AIPC genes in vitro.

Replication-incompetent gammaretroviral (γRV) and lentiviral (LV) vectors have both been used in insertional mutagenesis screens to identify cancer drivers. In this approach the vectors stably integrate in the host cell genome and induce cancers by dysregulating nearby genes. The cells that contain a retroviral vector provirus in or near a proto-oncogene or tumor suppressor are preferentially enriched in a tumor. γRV and LV vectors have different integration profiles and genotoxic potential, making them potentially complementary tools for insertional mutagenesis screens. We performed screens using both γRV and LV vectors to identify driver genes that mediate progression of androgen-independent prostate cancer (AIPC) using a xenotransplant mouse model. Vector transduced LNCaP cells were injected orthotopically into the prostate gland of immunodeficient mice. Mice that developed tumors were castrated to create an androgen-deficient environment and metastatic tumors that developed were analyzed. A high-throughput modified genomic sequencing PCR (MGS-PCR) approach identified the positions of vector integrations in these metastatic tumors. OR2A14, FER1L6, TAOK3, MAN1A2, MBNL2, SERBP1, PLEKHA2, SPTAN1, ADAMTS1, SLC30A5, ABCC1, SLC7A1 and SLC25A24 were identified as candidate prostate cancer (PC) progression genes. TAOK3 and ABCC1 expression in PC patients predicted the risk of recurrence after androgen deprivation therapy. Our data shows that γRV and LV vectors are complementary approaches to identify cancer driver genes which may be promising potential biomarkers and therapeutic targets.

Hematopoietic stem-cell gene therapy is a promising treatment of X-linked severe combined immunodeficiency disease (SCID-X1), but currently, it requires recipient conditioning, extensive cell manipulation, and sophisticated facilities. With these limitations in mind, we explored a simpler therapeutic approach to SCID-X1 treatment by direct IV administration of foamy virus (FV) vectors in the canine model. FV vectors were used because they have a favorable integration site profile and are resistant to serum inactivation. Here, we show improved efficacy of our in vivo gene therapy platform by mobilization with granulocyte colony-stimulating factor (G-CSF) and AMD3100 before injection of an optimized FV vector incorporating the human phosphoglycerate kinase enhancerless promoter. G-CSF/AMD3100 mobilization before FV vector delivery accelerated kinetics of CD3+ lymphocyte recovery, promoted thymopoiesis, and increased immune clonal diversity. Gene-corrected T lymphocytes exhibited a normal CD4:CD8 ratio and a broad T-cell receptor repertoire and showed restored γC-dependent signaling function. Treated animals showed normal primary and secondary antibody responses to bacteriophage immunization and evidence for immunoglobulin class switching. These results demonstrate safety and efficacy of an accessible, portable, and translatable platform with no conditioning regimen for the treatment of SCID-X1 and other genetic diseases.

BackgroundPrevious studies have shown that foamy viral (FV) vectors are a promising alternative to gammaretroviral and lentiviral vectors and also that insulators can improve FV vector safety. However, in a previous analysis of insulator effects on FV vector safety, strong viral promoters were used to elicit genotoxic events. In the present study, we developed and analyzed the efficacy and safety of a high-titer, clinically relevant FV vector driven by the housekeeping promoter elongation factor-1 and insulated with an enhancer blocking A1 insulator (FV-EGW-A1). MethodsHuman CD34(+) cord blood cells were exposed to an enhanced green fluorescent protein expressing vector, FV-EGW-A1, at a multiplicity of infection of 10 and then maintained in vitro or transplanted into immunodeficient mice. Flow cytometry was used to measure engraftment and marking in vivo. FV vector integration sites were analyzed to assess safety. ResultsFV-EGW-A1 resulted in high-marking, multilineage engraftment of human repopulating cells with no evidence of silencing. Engraftment was highly polyclonal with no clonal dominance and a promising safety profile based on integration site analysis. ConclusionsAn FV vector with an elongation factor-1 promoter and an A1 insulator is a promising vector design for use in the clinic.

X-linked combined immunodeficiency disease (XSCID) is caused by mutation in the common gamma chain, γC (interleukin-2 receptor subunit gamma, IL2RG) in both humans and canines. It is characterized by the inability of T-cell development leading to absence of T-cells in peripheral blood, lack of T-cell mediated immune response, low IgA and IgG levels, and early infant mortality. In the 1990s, human XSCID clinical trials utilizing gamma-retroviral vectors to deliver the IL2RG gene caused leukemia in 5 out of 20 patients due to vector integration in or near proto-oncogenes. Recent studies showed Foamy virus based vectors as an excellent alternative for in vivo gene-therapy because it is non-pathogenic in humans while exhibiting increased serum stability and favorable integration pattern. Previously, we have demonstrated CD3+ T-cell reconstitution in the canine model via intravenous injection of foamy virus expressing human elongation factor-1 alpha promoter (Ef1α)-yC. Unfortunately, the treated animals contained a low number of gene corrected progenitors at a sub-therapeutic level. Here, we achieved long-term therapeutic immune-reconstitution by intravenous delivery of a human phosphoglycerate kinase promoter (Pgk)-mediated γC foamy viral vector into XSCID neonatal canines. Long-term (2 years) post-injection follow-up demonstrated therapeutic levels of CD3+ T-cell expansion. Within the T-cell population, gene correction with Pgk-γC stabilized at ~80%. We validated T-cell functionality by using spectratyping analysis, which exhibited a diverse repertoire of receptor gene rearrangement. Retroviral integration site analysis (RIS) indicated polyclonal contribution to the reconstituted T-cells. Immunoglobulin ELISA assays showed that IgA and IgG levels in peripheral blood are comparable to normal healthy controls. We immunized the gene-corrected canine recipients with bacteriophage ϕx174 and confirmed production of specific IgG antibodies, showing the ability for isotype switching in B-lymphocytes. Currently, the gene-corrected canines exhibit comparable health and physical attributes to normal controls. Furthermore, semen from the gene-corrected male canine was used via artificial insemination to produce a litter of viable offsprings. In summary, our data demonstrate that Pgk-γC foamy viral vector delivered long-term therapeutic gene correction in a large-animal model for XSCID gene therapy. Most importantly, these results indicate that in vivo Pgk-γC foamy vector administration is a viable option for long-term immune reconstitution in future XSCID human clinical trials.

Lentiviral vectors (LVs) pseudotyped with vesicular stomatitis virus envelope glycoprotein (VSV-G) have demonstrated great promise in gene therapy trials employing hematopoietic stem cell and T-cells. The VSV-G envelope confers broad tropism and stability to the vector but is toxic when constitutively expressed, which has impeded efforts to generate stable producer cell lines. We previously showed that cocal pseudotyped LVs offer an excellent alternative to VSV-G vectors because of their broad tropism and resistance to human serum inactivation. In this study, we demonstrate that cocal LVs transduce CD34(+) and CD4(+) T-cells more efficiently than VSV-G LVs and share the same receptor(s) for cell entry. 293T-cells stably expressing the cocal envelope produced significantly higher LV titers than VSV-G expressing cells. We developed cocal pseudotyped, third-generation, self-inactivating LV producer cell lines for a GFP reporter and for a WT1 tumor-specific T-cell receptor, which achieved concentrated titers above 10(8) IU/ml and were successfully adapted for growth in suspension, serum-free culture. The resulting LVs were at least as effective as standard LVs in transducing CD34(+) and CD4(+) T-cells. Our stable cocal LV producer cell lines should facilitate the production of large-scale, high titer clinical grade vectors.

In both humans and canines, X-linked severe combined immunodeficiency disease (XSCID) is caused by mutations in the interleukin-2 receptor gamma chain gene (IL2RG) which results in a lack of response to common gamma-chain (gammaC) dependent cytokines and abnormal development of T and B lymphocytes, and natural killer (NK) cells. Death from infections usually occurs before 1 year of age unless allogeneic hematopoietic cell transplantation (HCT) is performed. While HCT is successful if an HLA-matched sibling donor is available, transplants from mismatched and unrelated donors are associated with greater morbidity and overall survival can be as low as 50%. To circumvent these complications, several clinical trials are testing the possibility of utilizing blood and marrow stem cells from the patient for ex vivo gene therapy to treat X-SCID. Although these trials show promising results, they require expensive GMP cell manufacturing that are not accessible to many patients, and may also necessitate low level of conditioning to improve engraftment of gene-corrected cells. With these limitations in mind, we have explored in vivo gene therapy as a treatment for X-SCID. We previously showed that foamy virus vectors (FVs), exhibit a potentially more favorable integration profile compared to lenti- and gamma-retroviral vectors. In vivo delivery of a gammaC-FV in dogs resulted in immune reconstitution with gene-corrected T cells in dogs but the treated animals still developed infections and had low levels of immunoglobulin levels. We hypothesized that an increased transduction of hematopoietic stem/progenitor cells in vivo might result in more rapid and sustained immune reconstitution. Thus, in the current study, we used cG-CSF and AMD3100 to mobilize hematopoietic stem/progenitor cells into the peripheral blood prior to in vivo injection with a FV expressing the gammaC gene driven by a PGK promoter (PGK-gammaC-FV). We mobilized two X-SCID dogs at ~3 weeks of age with 5ug/kg of cG-CSF bi-daily from day -4 to -1 prior to FV injection, and with 4mg/kg of AMD3100 on the morning of the injection with 4x10e8 IU of PGK-gammaC-FV. Our mobilization protocol resulted in a 10-fold increase in CD34+ cells in the peripheral blood of mobilized X-SCID dogs as compared to a unmobilized normal littermate control (Figure 1 A). Lymphocyte recovery and gene marking in the mobilized animals was significantly improved as compared to animals that were previously injected with similar doses of either PGK-gammaC-FV or EF1a-gammaC-FV but without mobilization. As illustrated in Figure 1B-C, lymphocyte counts expanded to ~3000 cells/uL with ~75% gene marking in the mobilized animals treated with PGK-gammC-FV within 30 days, as compared to <1500 cells/uL with <5% gene marking in unmobilized dogs treated with EF1a-gammaC-FV and to <1000 cells/uL with <50% gene marking in unmobilized dogs treated with PGK-gammaC-FV at all time points post-therapy. The expansion of CD3+ T-cells at 6 weeks post injection for the mobilized dogs was about 2700 cells/uL, as compared to <380 cells/uL in the PGK-gammaC-FV and <210 cells/uL in the EF1a-gammaC-FV unmobilized dogs. Notably, in human clinical trials, CD3 T cell counts were <250 cells/uL following transplantation with autologous CD34+ cells modified with EF1a-gammaC-SIN gamma-retrovirus (Hacein-Bey-Abina, NEJM, 2014). In conclusion, mobilization with cG-CSF and AMD3100 prior to in vivo injection of PGK-gammaC-FV substantially improved the lymphocyte expansion and immune reconstitution in X-SCID dogs and resulted in a higher level of gene marking in myeloid cells (about 1%) at one-month post injection than seen in our previous studies in unmobilized dogs. These results suggest remarkable potential for an accessible and portable approach for treatment of human X-SCID clinical trials using combination of hematopoietic stem/progenitor cells mobilization and in vivo foamy viral vector delivery.

X-linked severe-combined immune deficiency (SCID-X1) results from inactivating mutations in the gene encoding the common gamma chain (γc), a cytokine receptor subunit required for lymphoid development and function. In humans, SCID-X1 is characterized by the absence of T cells and natural killer cells, non-functional B cells, and is fatal within the first year of life if left untreated. Although HLA matched allogenic stem cell transplants yield survival rates exceeding 90%, such donors are often unavailable. Thus, gene replacement therapy offers a promising alternative treatment for patients lacking suitable donors. Clinical trials using gamma-retroviral vectors demonstrated efficacy; however, adverse events highlighted the need for improved safety. While adverse events have been eliminated using SIN-gamma-retroviral vectors, we hypothesized that foamy viruses (FV) that lack native pathogenicity and boast an integration site profile much less focused on either active genes or promoter regions than lentiviruses or gamma-retroviruses might provide an improved and safer therapeutic platform. We determined whether a candidate clinical FV vector containing the human phosphoglycerate kinase 1 (PGK) promoter driving human γc expression could safely and effectively rescue lymphocyte development and function in SCID-X1 mice. Our promoter choice was based upon ongoing studies using FV vectors in parallel in a canine model of SCID-X1 where the PGK promoter outperforms the EF1α promoter currently in use in SIN-retro and lentiviral-based SCID-X1 clinical trials. We report here the combined results of 66 primary and 130 secondary transplant mice that demonstrate significant and sustained immune reconstitution. SCID-X1 mice were transplanted with 2×10^6 FV- or LV-transduced, or WT or SCID-X1 lineage negative HSCs. Animals were sacrificed at ~25 weeks post-transplant; bone marrow, spleen and thymus were collected for analysis and secondary recipients were also established. Primary FV gene therapy recipients showed significantly greater B and T lymphoid numbers compared to SCID-X1 controls, with output viral copy numbers of ~1-4 in all tissues. Splenocytes from primary treated animals proliferated in response to CD3/CD28 and also demonstrated γc dependent intracellular pSTAT signaling in response to IL-7 and IL-21. FV and LV gene therapy-treated mice displayed comparable lymphocyte reconstitution and output copy number. Secondary recipients revealed sustained partial rescue of lymphoid compartments and viral marking, indicating the transduction of long-term repopulating HSCs. RIS analysis demonstrated polyclonal marking in splenic lymphoid populations with 3508 unique FV and 2441 unique LV integrations detected (3 experiments/3 animals per experiment). Further, analysis of individual mice from a primary transplant experiment demonstrated polyclonal marking with 588-1060 and 651-895 unique integration sites in FV- and LV-treated animals, respectively. Analysis to determine detailed integration site profile and potential proximity to protooncogenes is ongoing. Together, these data suggest FV gene therapy may provide an effective alternative treatment option for SCID-X1.

The Berlin patient and successes in retroviral hematopoietic stem cell (HSC) gene therapy suggest that gene therapy may provide a functional cure for HIV. However, retroviral-HSC gene therapy has resulted in serious adverse side effects due to vector mediated genotoxicity, including leukemia. Foamy virus (FV) vectors have a promising integration profile and may be safer than retroviral vectors. FV vectors also can efficiently deliver anti-HIV transgenes that can reduce the titer of HIV-1 based lentiviral vectors. We report a novel combinatorial anti-HIV FV vector that uses a housekeeping elongation factor 1 alpha (EF1α) promoter but still potently blocks HIV infection. We first evaluated the relative potency of various previously described anti-HIV transgenes, including the C46 fusion inhibitor, the F12-Vif derivative Chim3, lens epithelium derived growth factor-integrase binding domain (LIBD) and TRIM5α-CyclophilinA fusion (TCypA) in a FV vector background. We found that C46 was the most potent anti-HIV transgene, followed by TCypA and LEDGF-IBD. Next, we hypothesized that using a less-genotoxic internal promoter to drive the transgenes would reduce vector-mediated genotoxicity. Therefore, a direct comparison was made between the efficacy of housekeeping gene promoters (EF1α and Ubiquitin C; UbC) and a highly genotoxic SFFV promoter in expressing the C46 transgene and subsequently blocking HIV replication. We observed that C46 EF1α had ~2 to 4 fold higher anti-HIV effect than C46 driven by either SFFV or UbC promoters, respectively. Based on these results, we designed a novel combinatorial FV vector expressing three anti-HIV transgenes: C46, TcypA and LIBD. The gene cassette was driven by an EF1α promoter and also has mCherry as a reporter gene (FV-E C46TLmC-W). This vector can be produced at high titer, 1.4 × 107 transducing units/ml which is critical for clinical translation. This novel combinatorial anti-HIV FV vector showed a higher potency in blocking HIV replication than C46 alone at a late time point, 21 days post HIV infection (Figure 1). An in vitro competitive survival advantage assay indicated that cells transduced with our novel combinatorial anti-HIV FV vectors are highly resistant to HIV infection compared to cells transduced with FV expressing a control EGFP reporter gene alone (FV-EG-W) (Figure 2). Further studies will be focused on the efficacy of our novel combinatorial anti-HIV FV vector in human CD34+ cells transplanted in a mouse xenotransplant in vivo model. Our goal is to develop a safe and potent combinatorial FV vector for clinical studies.

Lentiviral vectors (LVs) are routinely used for stable gene transfer and have demonstrated great promise in hematopoietic stem cell gene therapy and also immunotherapy using genetically modified T cells. LVs are commonly pseudotyped with vesicular stomatitis virus envelope glycoprotein (VSV-G), which confers broad tropism to the vector and allows for vector concentration by centrifugation. However, the use of VSV-G has several limitations, such as susceptibility to inactivation by human serum complement making it unsuitable for in vivo delivery. Furthermore, VSV-G is toxic when constitutively expressed, which has impeded efforts to generate stable producer cell lines. In this study, we first validate the use of cocal vesiculovirus envelope to pseudotype LVs by demonstrating that cocal LVs transduce hematopoietic stem cells and CD4+ T cells more efficiently than VSV-G LVs. We also provide evidence that cocal and VSV-G envelopes use the same receptor for cell entry. We then describe the development of two high-titer, cocal-pseudotyped, LV producer cell lines for a GFP reporter and for a WT1 tumor-specific T cell receptor (TCR). The different 3rd generation lentiviral helper genes were sequentially introduced in HEK293T cells by co-transfection with plasmids encoding antibiotic resistance genes followed by selection to allow for stable protein expression. Cells expressing the cocal envelope produced over 10-times more infectious LV particles as compared to VSV-G expressing cells. High-titer cocal producer cells were isolated by screening for best single clones, which were capable of generating concentrated titers above 108 infectious units per mL. We found that these producer cells were stable after serial passages for over 3 months, with no drop in titer detected over time. The resulting GFP and WT1-TCR vectors performed at least as well as identical vectors made with our standard transient transfection protocol for the transduction of CD34+ and CD4+ T cells, respectively. Cocal LV producer cells were also adapted for growth in suspension, serum-free culture, which will facilitate efforts for the scaling up of vector production. In summary, we have successfully developed two independent LV producer cells lines with clinically usable titers. The broad applicability of our cocal packaging cell line offers a promising tool toward the generation of large-scale, clinical grade LV.

Retroviral gene therapy offers immense potential to treat many genetic diseases and has already shown efficacy in clinical trials. However, retroviral vector mediated genotoxicity remains a major challenge and clinically relevant approaches to reduce integration near genes and proto-oncogenes are needed. Foamy retroviral vectors have several advantages over gammaretroviral and lentiviral vectors including a potentially safer integration profile and a lower propensity to activate nearby genes. Here we successfully retargeted foamy retroviral vectors away from genes and into satellite regions enriched for trimethylated histone H3 at lysine 9 by modifying the foamy virus Gag and Pol proteins. Retargeted foamy retroviral vectors integrated near genes and proto-oncogenes less often (p < 0.001) than controls. Importantly, retargeted foamy retroviral vectors can be produced at high, clinically relevant titers (>107 transducing units/ml), and unlike other reported retargeting approaches engineered target cells are not needed to achieve retargeting. As proof of principle for use in the clinic we show efficient transduction and retargeting in human cord blood CD34+ cells. The modified Gag and Pol helper constructs we describe will allow any investigator to simply use these helper plasmids during vector production to retarget therapeutic foamy retroviral vectors.

Retroviral vector gene therapy is a promising approach to treating HIV-1. However, integrated vectors are mutagens with the potential to dysregulate nearby genes and cause severe adverse side effects. Leukemia has already been a documented severe adverse event in gene therapy clinical trials for the treatment of primary immunodeficiencies. These side effects will need to be reduced or avoided if retroviral vectors are to be used clinically for HIV-1 treatment. The addition of chromatin insulators to retroviral vectors is a potential strategy for reducing adverse side effects. Insulators have already been effectively used in retroviral vectors to reduce genotoxicity in pre-clinical studies. Here, we will review how insulators function, genotoxicity in gene therapy clinical trials, the design of insulated retroviral vectors, promising results from insulated retroviral vector studies, and considerations for the development of insulated retroviral treatment vectors for HIV-1 gene therapy.

Hematopoietic stem cell (HSC) gene therapy using retroviral vectors is a powerful and promising approach to permanently correct many hematopoietic disorders. Increasing the transduction of quiescent HSCs and reducing genotoxicity are major challenges in the field. Retroviral vectors, including lentiviral and foamy vectors, have been extensively modified resulting in improved safety and efficacy. This review will focus on recent advances to improve vector entry, transduction efficiency, control of transgene expression and approaches to improve safety by modifying the retroviral integration profile.

Abstract Breast cancer (BC) is a heterogeneous disease and the second leading cause of malignancy among women in the U.S.. Metastasis of the primary tumor results in poor prognosis and increased mortality and the molecular mechanisms by which metastatic tumors occur are not well understood. Identifying the genes that drive the metastatic process could provide targets for improved therapy and biomarkers to improve outcomes for BC patients. Here, we utilized a replication-incompetent gammaretroviral vector (γRV) to perform a forward insertional mutagenesis screen to identify genes involved in BC metastasis. In this approach, BC cells mutagenized with a γRV were xenotransplanted into the mammary fat pad of immunodeficient mice, and primary tumors and metastases were allowed to develop. Metastatic lesions were collected and analyzed for proviral integration sites to identify vector integration sites and nearby candidate metastasis genes. The γRV has a bacterial origin of replication and kanamycin resistance gene that allows for rescue in bacteria and rapid identification of vector integration sites. Using this approach, we identified the previously described metastasis gene WWTR1, and several other novel candidate metastasis genes including SHARPIN. SHARPIN was then independently validated as a BC metastasis gene in vivo using RNAi. Analysis of patient data showed that SHARPIN expression predicts metastasis-free survival after adjuvant chemotherapy (p < 0.005, Concordance Index = 55.3, Risk Groups Hazard Ratio = 1.87). Our replication-incompetent γRV approach is efficient and has broad potential to identify genes involved in oncogenic processes for BC and other cancers. Keywords Insertional mutagenesis screen, Gammaretroviral vector (γRV), Metastasis, Inducible shRNA, Prognostic biomarker. Citation Format: Bii VM, Rae DT, Trobridge GD. A novel mutagenesis screen identifies SHARPIN as a breast cancer metastasis gene that predicts survival of breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-05-13.

Retroviral vector-mediated stem cell gene therapy is a promising approach for the treatment of hematopoietic disorders. However, genotoxic side effects from integrated vector proviruses are a significant concern for the use of retroviral vectors in the clinic. Insulated foamy viral (FV) vectors are potentially safer retroviral vectors for hematopoietic stem cell gene therapy. We evaluated two newly identified human insulators, A1 and A2, for use in FV vectors. These insulators had moderate insulating capacity and higher titers than previously developed insulated FV vectors. The A1-insulated FV vector was chosen for comparison with the previously described 650cHS4-insulated FV vector in human cord blood CD34+ repopulating cells in an immunodeficient mouse model. To maximize the effects of the insulators on the safety of FV vectors, FV vectors containing a highly genotoxic spleen focus forming virus promoter were used to elicit differences in genotoxicity. In vivo, the A1-insulated FV vector showed an approximate 50% reduction in clonal dominance compared with either the 650cHS4-insulated or control FV vectors, although the transduction efficiency of the A1-insulated vector was higher. This data suggests that the A1-insulated FV vector is promising for future preclinical and clinical studies.

Prostate cancer (PC) is the second leading cause of cancer related deaths in US men. Androgen deprivation therapy (ADT) improves clinical outcome, but tumors often recur and progress to androgen independent prostate cancer (AIPC) which no longer responds to ADT. The progression to AIPC is due to genetic alterations that allow PC cancer cells to grow in the absence of androgen. Here we performed an insertional mutagenesis screen using a replication‐incompetent lentiviral vector (LV) to identify the genes that promote AIPC in an orthotopic mouse model. Androgen sensitive PC cells, LNCaP, were mutagenized with LV and injected into the prostate of male mice. After tumor development, mice were castrated to select for cells that proliferate in the absence of androgen. Proviral integration sites and nearby dysregulated genes were identified in tumors developed in an androgen deficient environment. Using publically available datasets, the expression of these candidate androgen independence genes in human PC tissues were analyzed. A total of 11 promising candidate AIPC genes were identified: GLYATL1, FLNA, OBSCN, STRA13, WHSC1, ARFGAP3, KDM2A, FAM83H, CLDN7, CNOT6, and B3GNT9. Seven out the 11 candidate genes; GLYATL1, OBSCN, STRA13, KDM2A, FAM83H, CNOT6, and B3GNT6, have not been previously implicated in PC. An in vitro clonogenic assay showed that knockdown of KDM2A, FAM83H, and GLYATL1 genes significantly inhibited the colony forming ability of LNCaP cells. Additionally, we showed that a combination of four genes, OBSCN, FAM83H, CLDN7, and ARFGAP3 could significantly predicted the recurrence risk in PC patients after prostatectomy (P = 5.3 × 10−5). © 2015 Wiley Periodicals, Inc.