Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy

BACKGROUND

Comprehensive molecular characterization of cancer that has metastasized to bone has proved challenging, which may limit the diagnostic and potential therapeutic opportunities for patients with bone-only metastatic disease.

METHODS

We describe successful tissue acquisition, DNA extraction, and whole-exome sequencing from a bone metastasis of a patient with metastatic, castration-resistant prostate cancer (PCa).

RESULTS

The resulting high-quality tumor sequencing identified plausibly actionable somatic genomic alterations that dysregulate the phosphoinostide 3-kinase pathway, as well as a theoretically actionable germline variant in the BRCA2 gene.

CONCLUSIONS

We demonstrate the feasibility of diagnostic bone metastases profiling and analysis that will be required for the widespread application of prospective 'precision medicine' to men with advanced PCa.

A phase II study of neoadjuvant chemotherapy with docetaxel and bevacizumab in patients (pts) with high-risk localized prostate cancer: A Prostate Cancer Clinical Trials Consortium trial

5060

Background: Treatment options for high-risk localized prostate cancer remain inadequate, with the majority of pts relapsing despite surgery or radiation therapy. We conducted a phase II multicenter trial of neoadjuvant docetaxel and bevacizumab prior to radical prostatectomy in pts with high risk localized prostate cancer. Methods: Eligibility included any of the following: PSA > 20 ng/ml or PSA velocity > 2 ng/ml/yr, cT3 disease, any biopsy Gleason 8–10, Gleason 7 with T3 disease by endorectal (er) MRI. Also, >50% biopsy cores involved and either Gleason 7 or PSA >10 or cT2 disease were eligible. Pts were treated with docetaxel 70 mg/m2 q 3weeks x 6 cycles and bevacizumab 15 mg/m2 q 3 weeks x 5 cycles. The primary endpoint was erMRI partial response (PR, defined here as >50% decrease in tumor volume) in a single target lesion after chemotherapy. Results: 42 pts were registered and treated with 220 cycles so far. Median age was 55 yrs (range 41–67). Median Gleason score was 8 (69% with Gleason 8–10 cancer). Median PSA was 10.5 ng/ml (range 2.1–72.5). Clinical stage was T2 in 46% and T3 in 32%. Of 23 evaluable pts to date, the median decline in the maximal tumor volume by erMRI was -45% (range -84% to 110%). 9/23 (39%) patients had PR, and only 1 pt had radiographic progression. Any PSA decline was noted in 22/34 (65%) evaluable pts, with 18% having a >50% decline. Treatment was well-tolerated: 2 pts had grade 3 allergic reactions requiring discontinuation, 3 had febrile neutropenia and 1 had grade 3 hyperglycemia. Mild fatigue was common. Only 1 pt stopped treatment because of a rising PSA. To date, 31 pts have had radical prostatectomy. One had intraoperative bladder neck injury and was treated instead with radiation + hormone therapy. A second pt had an intraoperative rectal injury but completed surgery. Conclusions: Neoadjuvant docetaxel and bevacizumab demonstrates clinical evidence of activity in men with high-risk localized prostate cancer, with a 39% PR rate by erMRI and PSA declines noted in 65%. Treatment was well-tolerated. The study is ongoing and updated data on response, toxicity and pathology will be presented.

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No association between a polymorphic variant of the IRS-1 gene and prostate cancer risk

OBJECTIVE

Insulin receptor substrate-1 (IRS-1) acts as a docking protein between the insulin-like growth factor-1 (IGF-1) receptor and intracellular signaling molecules in the IGF-1 signaling pathway. Accumulating data support a role of IGF-1 in prostate carcinogenesis. We assessed the influence of the most common IRS-1 gene polymorphism (Gly972Arg) on prostate cancer risk, alone and in combination with IGF-1 and other components in the IGF-1 signaling pathway.

MATERIALS AND METHODS

In a nested case-control study within the Physicians' Health Study, the IRS-1 polymorphism was assayed from prospectively collected samples from 564 incident prostate cancer cases and 758 controls matched on age and smoking. We calculated relative risks (RR) and 95% confidence intervals (CI) using conditional logistic regression.

RESULTS

Among the controls, 0.8% were homozygous (AA) and 12% were heterozygous (GA) for the polymorphic allele. There was no association between carriage of the A allele and total prostate cancer risk (RR = 1.1 95% CI = 0.8-1.5), advanced disease (stage C or D or lethal prostate cancer, RR = 1.3 95% CI = 0.8-2.3), or plasma IGF-1 levels. We explored possible interactions with body mass index and components in the IGF-1 pathway including IGFBP3, PI3k, and PTEN but none of these factors influenced the relation between IRS-1 genotype and prostate cancer risk.

CONCLUSIONS

Our data do not support an association between carriage of the variant IRS-1 gene and prostate cancer risk.

A genomic approach to identify mechanisms associated with chemotherapy resistance

2534

Background: Gene expression profiling has shown an ability to predict chemotherapeutic response (Potti et al. Nature Medicine 2006). Building on this work, we used a genomic strategy to explore the biology associated with the development of chemotherapy resistance and sought to determine if disease context impacted results. Methods: Gene set enrichment analysis (GSEA) was performed on expression data for NCI60 cell lines sensitive and resistant to specific chemotherapeutic agents (adriamycin, cyclophosphamide, docetaxel, etoposide, 5-fluoruracil, paclitaxel, topotecan). GSEA was additionally performed on a series of lung cancer cell lines with a defined sensitivity to cisplatin and docetaxel. Sensitive and resistant cell lines with individual mean and confidence intervals greater than 1SD from the mean across all samples were included. Adjusting for multiple hypothesis testing, gene sets with a false discovery rate (FDR) <0.25 were deemed statistically significant. In the discovery mode, gene sets with a nominal p-value <0.05 were also of interest. Finally, overlapping gene sets between agents were assessed. Results: Statistically-significant gene sets, representing biologic pathways associated with resistance, were identified for the various chemotherapeutic agents (i.e., cell death, erbb3, and bad pathways associated with docetaxel resistance). No gene sets with FDR <0.25 or nominal p-value <0.05 were common to all drugs. In assessing disease specific resistance, 22 lung cancer cell lines for cisplatin (15 sensitive, 7 resistant) and 14 lung cancer cell lines for docetaxel (10 sensitive, 4 resistant) were analyzed. GSEA identified the bcl-2 pathway (p<0.002) to be associated with cisplatin resistance. In contrast, the proteosome (p=0.01) and akt (p=0.02) pathways were associated with docetaxel resistance. Pathways involved in the production of V-H+-ATPase were enriched in cisplatin and docetaxel resistant lung cancer cell lines suggesting a global mechanism of resistance. Conclusions: These results support the use of a genomic approach to identify unique drug-specific and global therapeutic targets associated with the development of chemotherapy resistance. Interestingly, disease context appears important in identifying novel targets.

No significant financial relationships to disclose.

Immune signatures hold prognostic import across solids tumors

21041

Background: The host immune response can impact cancer growth, prognosis, and response to therapy. In colorectal cancer, the presence of cells involved with T-cell mediated adaptive immunity better predicts of survival than the current staging method. Immune signatures based on host response to cancer have the potential to predict prognosis and facilitate target specific therapy. Methods: We used the gene expression data associated with immune host response to colorectal cancer (Galon et al., Science 2006) to perform hierarchical clustering of solid tumors for which the clinical annotation were available. Specifically, prostate (n=79), breast (n=132), lung (n=37), and lymphoma (n=127) samples were clustered based upon expression of genes associated with host immune responses (Th1 mediated adaptive immunity (Th1), inflammation, and immune suppression (IS)). Kaplan-Meier survival analysis was then used to determine if major sample clusters had significantly different disease free survival. Results: Clusters with differential prognosis (disease free survival) were consistently seen across all tumors. Among adenocarcinomas, and similar to previously published colorectal data, the Th1 genes were consistently associated with better prognosis. Specifically, in breast cancer patients, increased expression of the Th1 genes was protective, but only in patients under 45 years of age (HR=0.42; p=0.05). In prostate cancer, patients with increased expression of the Th1 genes and inflammation genes had better prognosis when compared to those without the Th1 genes (HR=0.36; p=0.03) or inflammation genes (HR=0.37; p=0.03). Lung cancer patients expressing the Th1 genes and IS genes appear to have improved survival when compared to those without the IS genes (HR=0.33; p=0.08). In contrast, Th1 genes were associated with poorer prognosis in lymphoma patients. Patients with decreased Th1 genes and increased expression of inflammation genes had better prognosis than those expressing the Th1 genes (HR=0.43; p=0.013) or IS genes (HR= 0.35; p=0.002) only. Conclusions: Signatures of the host immune response to solid tumors hold prognostic significance. Future work will determine if immune signatures can be predictive of response to therapy and help guide management.

No significant financial relationships to disclose.

Systemic strategies for prostate cancer

Systemic therapy beyond hormonal therapy for advanced prostate cancer includes chemotherapy, antiangiogenic therapy, signal transduction inhibitors, immunomodulatory therapy, and other experimental therapeutics. This review will discuss the state of systemic therapy for advanced prostate cancer in 2007, with an emphasis on therapy in the neoadjuvant, adjuvant, and metastatic setting. As chemotherapy gains greater acceptance in the urologic oncology community for use in men with hormone-refractory disease, evaluating the role of systemic therapy in earlier disease states is essential given the success in other solid tumors for advancing cure rates. Current randomized phase III trials worldwide are addressing these questions in each disease state, and are anticipated to change the landscape of prostate cancer management for years to come. In this discussion, we will emphasize those agents that are currently being evaluated in phase II and III trials, with an emphasis on those trials that are likely to impact the standard of care in the near future. The collection of tumor or surrogate tissue is emphasized to define biomarkers that may predict for sensitivity to these systemic therapies.

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target

Glioblastoma is the most common primary malignant brain tumor of adults and one of the most lethal of all cancers. Patients with this disease have a median survival of 15 months from the time of diagnosis despite surgery, radiation, and chemotherapy. New treatment approaches are needed. Recent works suggest that glioblastoma patients may benefit from molecularly targeted therapies. Here, we address the compelling need for identification of new molecular targets. Leveraging global gene expression data from two independent sets of clinical tumor samples (n = 55 and n = 65), we identify a gene coexpression module in glioblastoma that is also present in breast cancer and significantly overlaps with the "metasignature" for undifferentiated cancer. Studies in an isogenic model system demonstrate that this module is downstream of the mutant epidermal growth factor receptor, EGFRvIII, and that it can be inhibited by the epidermal growth factor receptor tyrosine kinase inhibitor Erlotinib. We identify ASPM (abnormal spindle-like microcephaly associated) as a key gene within this module and demonstrate its overexpression in glioblastoma relative to normal brain (or body tissues). Finally, we show that ASPM inhibition by siRNA-mediated knockdown inhibits tumor cell proliferation and neural stem cell proliferation, supporting ASPM as a potential molecular target in glioblastoma. Our weighted gene coexpression network analysis provides a blueprint for leveraging genomic data to identify key control networks and molecular targets for glioblastoma, and the principle eluted from our work can be applied to other cancers.

USP2a is an oncogenic isopeptidase and a potential target in prostate cancer

14522

Background: De-ubiquitinating enzymes (isopeptidases) remove ubiquitin side chains prior to degradation by the proteosome thus stabilizing their protein targets. We have identified a novel androgen regulated isopeptidase, USP2a, and demonstrated that it binds and prolongs the half-life of fatty acid synthase (FAS), a key enzyme in lipid metabolism of tumor cells. Methods: We determined whether USP2a has oncogenic properties in vitro and in vivo. Wild-type and catalytically inactive USP2a were introduced in immortalized normal prostate epithelial cells (AR-iPrECs). Clonogenicity assays and apoptosis induction by chemotherapeutic agents were performed on these cells. Anti-USP2a siRNA were transfected in normal and transformed (LNCaP, DU145 and PC-3) prostate cell lines. Oncogenicity in vivo was shown by s.c. injection of NIH3T3-USP2a cells in nude mice. Furthermore, USP2a mRNA expression and gene microarrays were tested in 52 human prostate adenocarcinomas. Results: Wild-type USP2a overexpression in AR-iPrEC cells resulted in a significant increase in number and size of colonies compared to those obtained in parental cells. Growth in soft agar was significantly enhanced as well. Silencing of USP2a in LNCAP and DU145 cells resulted in a strong apoptotic effect, evaluated by FACS analysis and cleaved-PARP expression. The role of this isopeptidase in apoptosis regulation was confirmed on AR-iPrEC-USP2a cells, that showed resistance to apoptosis induced by cisplatin and taxol. Importantly, USP2a overexpression was able to transform NIH3T3 cells, generating greater than or equal to 0.5 cm subcutaneous tumors in 12/12 nude mice within 3 weeks, while none of the negative controls grew. USP2a mRNA was overexpressed in 39% of human prostate cancers, showing 1.6–104 (median 5.48) fold induction relative to normal tissues by qRT-PCR. Gene expression profiling of the same tumors revealed specific signatures in USP2a-overexpressing tumors. Conclusions: Our results demonstrate that USP2a behaves as an oncogene in vitro and in vivo and is overexpressed in organ-confined prostate cancer. These data strongly suggest that this isopeptidase is a potential drug target in prostate cancer.

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Finasteride and bicalutamide as primary hormonal therapy in patients with advanced adenocarcinoma of the prostate

BACKGROUND

Medical or surgical castration is effective in advanced prostate cancer but with profound side-effects, particularly on sexual function. Effective, less toxic therapies are needed. This study examined whether the addition of finasteride to high-dose bicalutamide enhanced disease control, as measured by additional decreases in serum prostate-specific antigen (PSA).

PATIENTS AND METHODS

Forty-one patients with advanced prostate cancer received bicalutamide (150 mg/day). Finasteride (5 mg/day) was added at first PSA nadir. Serum PSA was measured every 2 weeks until disease progression. Questionnaires were administered to assess sexual function.

RESULTS

Median follow-up is 3.9 years. At the first PSA nadir, median decrease in PSA from baseline was 96.5%. Thirty of 41 patients (73%) achieved a second PSA nadir and median decrease of 98.5% from baseline. Median time to each nadir was 3.7 and 5.8 weeks, respectively. Median time to treatment failure was 21.3 months. Toxicities were minor, including gynecomastia. Seventeen of 29 (59%) and 12 of 24 (50%) men had normal sex drive at baseline and at second PSA nadir, respectively. One-third of men had spontaneous erection at both time points.

CONCLUSION

Finasteride provides additional intracellular androgen blockade when added to bicalutamide. Duration of control is comparable to castration, with preserved sexual function in some patients.

The V89L polymorphism in the 5alpha-reductase type 2 gene and risk of prostate cancer

5alpha-Reductase type 2, the predominant prostatic isozyme of this protein, converts testosterone to dihydrotestosterone. It has been hypothesized that individuals with greater 5alpha-reductase activity are at increased risk for prostate cancer (CaP). A single nucleotide polymorphism of the 5alpha-reductase type 2 gene (SRD5A2) gives rise to a substitution of leucine (leu) for valine (val) at codon 89 (V89L), the presence of which may affect serum androstanediol glucuronide (AAG) levels. We studied the effect of this polymorphism on the risk of prostate cancer in a prospective, nested, case-control design within the Physicians' Health Study. In all controls (n = 799), the leu allele frequency was 0.30. Among the 386 controls with plasma AAG levels available, there was no significant association between AAG levels and V89L genotype. We also detected no significant association between risk for CaP and genotype [odds ratio: val/val = 1.0 (reference), leu/val = 0.96 (95% confidence interval, 0.76-1.20), and leu/ leu = 0.84 (95% confidence interval, 0.57-1.24)]. These data do not support a moderate to large effect of the SRD5A2 V89L polymorphism on plasma AAG levels or CaP risk in this predominantly Caucasian cohort, although a small effect cannot be completely excluded.

Debrisoquine hydroxylase (CYP2D6) and prostate cancer

The p450 hepatic microsomal enzyme system metabolizes exogenous drugs and carcinogens. Debrisoquine hydroxylase (CYP2D6), one member of the p450 hemoproteins, has polymorphic expression leading to poor metabolism of debrisoquine and similar compounds in approximately 7% of Caucasians. The genetic locus for this enzyme has been characterized, and the mutations responsible for the slowed metabolism have been identified. Epidemiological studies of the CYP2D6 phenotype suggest an association between the normal or rapid metabolism phenotype and increased risk of lung and bladder cancer. Preliminary data have also suggested an association with prostate cancer (CaP). We used a PCR-based assay to investigate possible associations between the CYP2D6 B allele, the most common genetic mutation responsible for the poor metabolism phenotype, and CaP. Using genomic DNA isolated from peripheral blood, we genetically typed 571 men with CaP and 767 matched controls, all participants in the Physician's Health Study. Relative to men homozygous for the wild-type allele, heterozygotes for the B allele have an odds ratio of 1.19 (95% confidence interval, 0.94-1.51) for CaP, and men homozygous for the B allele have an odds ratio of 1.37 (95% confidence interval, 0.86-2.20). When analyzed as a trend over zero, one, or two copies of the B allele, there emerges a possible association between the B allele and an increased risk of CaP of borderline statistical significance (P = 0.07).

A polymorphism of the 5 alpha-reductase gene and its association with prostate cancer: a case-control analysis

Prostate cancer (CaP) is the most commonly diagnosed, nondermatological cancer in the United States. The development and progression of CaP is influenced by androgens. 5 alpha-Reductase, type II, converts testosterone to dihydrotestosterone and is critical to the development of the prostate. A TA dinucleotide repeat polymorphism exists in the 3' untranslated region of the 5 alpha-reductase type II gene. 5 alpha-Reductase alleles with longer TA repeats are more common in African-Americans, the group with the highest incidence of CaP. It has been hypothesized that the longer TA repeat alleles might be associated with increased risk of CaP. We studied this potential association within the Physician's Health Study, a predominantly Caucasian cohort study. Using PCR we identified the TA genotype in 590 men with CaP and 802 age-matched controls. The frequency of each allele in the controls was TA(0), 0.87, TA(9), 0.13, and TA(18), 0.01. Homozygotes for the longer TA alleles, TA(9) and TA(18), were underrepresented among cases with an odds ratio of 0.47 (confidence interval, 0.20-1.12), but this was not statistically significant (P = 0.08, two tailed). Our analysis does not support the prior hypothesis that longer TA alleles confer an increased risk of CaP in a predominantly Caucasian population; in fact, longer TA alleles are more prevalent in men without CaP.