Jenkins, Robert B.

Abstract Motivations: Gleason score is the most prognostic variable in prostate cancer pathology. Patients with high Gleason (8+) are the most likely to experience biochemical recurrence (BCR), clinical progression (CP) and prostate-cancer specific mortality (PCSM), whereas patients with Gleason ≤6 are expected to have excellent long-term outcomes. However, the majority of prostate cancer patients are diagnosed with Gleason score 7, a heterogeneous group in terms of patient outcomes. In the absence of adverse pathological factors (APF, such as preoperative PSA, SM+, ECE and SVI) most Gleason 7 patients will have excellent outcomes. In contrast, Gleason 7 patients with APF are considered at high-risk for recurrence and therefore are candidates for adjuvant therapy. In this study, we have investigated whether a classifier based on differentially expressed genomic features could be used to improve prognostication of Gleason 7 patients, independent of APF. Methods: Two whole-transcriptome (1.4 million feature) oligonucleotide microarray expression datasets from radical prostatectomy specimens were analyzed. The first one (GEO accession: GSE21032) consisted of 125 fresh frozen (FF) samples from the MSKCC Oncogenome Project and the second dataset had 545 formalin-fixed-paraffin- embedded (FFPE) samples from the Mayo Clinic tumor registry. For genomic feature selection, differential expression in the FF dataset between Gleason ≤6 (n=40) and ≥8 (n=15) was assessed with false discovery rate adjusted t-tests (p<0.05). Next, a k-nearest neighbor (KNN) classifier was trained and tuned using the selected features to predict clinical progression (i.e., positive bone or CT scans after BCR) in the FFPE dataset, again using samples with Gleason score ≤6 (n=63) and ≥8 (n=211). The KNN classifier was evaluated on Gleason score 7 (n=209) FFPE samples (not used for training) using multivariable logistic regression. Results: The KNN classifier segregated the Gleason 7 samples into high and low risk CP groups. The KNN odds ratios were 2.9 (p<0.005), 2.1 (p<0.05) and 2.8 (p<0.05) for BCR, CP and PCSM end-points, respectively when comparing high and low risk groups. Multivariable analysis revealed that the KNN classifier was independently prognostic. Conclusions: A KNN classifier developed using differentially expressed genomic features significantly stratified Gleason score 7 patients for several clinically relevant endpoints. Future validation studies will address the utility of this classifier in predicting pathological Gleason score from biopsy specimens, which may be particularly useful for evaluation of biopsy Gleason 6 cases. In these patients, deferring prostatectomy in favour of active surveillance is an appealing treatment option unless the ‘true’ Gleason of the index lesion is in fact a Gleason 7 or higher, where immediate surgery is likely a life-saving procedure. Citation Format: Nicholas Erho, Thomas Sierocinski, Elai Davicioni, Robert B. Jenkins, Mercedeh Gadhessi, Christine Buerki, Ismael A. Vergara, Anamaria Crisan, Zaid Haddad, Benedikt Zimmermann, Anirban Mitra, Timothy J. Triche. Identification of biomarkers for stratification of Gleason score 7 patients using whole-transcriptome expression profiling [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr B46.

Purpose It has been suggested that PTEN, a negative regulator of PI3K/AKT signaling, is involved in tumor sensitivity to trastuzumab. We investigated the association between tumor PTEN protein expression and disease-free survival (DFS) of patients randomly assigned to receive chemotherapy alone (arm A) or chemotherapy with sequential (arm B) or concurrent trastuzumab (arm C) in the phase III early-stage human epidermal growth factor receptor 2 (HER2) –positive trial—North Central Cancer Treatment Group (NCCTG) N9831. Patients and Methods The intensity and percentage of invasive cells with cytoplasmic PTEN staining were determined in tissue microarray sections containing three cores per block (n = 1,286) or in whole tissue sections (WS; n = 516) by using standard immunohistochemistry (138G6 monoclonal antibody). Tumors were considered positive for PTEN (PTEN-positive) if any core or WS had any invasive cells with ≥ 1+ staining. Median follow-up was 6.0 years. Results Of 1,802 patients included in this analysis (of 3,505 patients registered to N9831), 1,342 (74%) had PTEN-positive tumors. PTEN positivity was associated with hormone receptor negativity (χ2 P < .001) and nodal positivity (χ2 P = .04). PTEN did not have an impact on DFS within the various arms. Comparing DFS of arm C to arm A, patients with PTEN-positive and PTEN-negative tumors had hazard ratios (HRs) of 0.65 (P = .003) and 0.47 (P = .005), respectively (interaction P = .16). For arm B versus arm A, patients with PTEN-positive and PTEN-negative tumors had HRs of 0.70 (P = .009) and 0.85 (P = .44), respectively (interaction P = .47). Conclusion In contrast to selected preclinical and limited clinical studies suggesting a decrease in trastuzumab sensitivity in patients with PTEN-negative tumors, our data show benefit of adjuvant trastuzumab for patients with HER2-positive breast cancer, independent of tumor PTEN status.

Abstract The determination of HER2 amplification is critical to selecting appropriate patients for HER2 targeted therapy in breast cancer. Dual in situ hybridization (DISH), an alternative to fluorescence in situ hybridization (FISH) and immunohistochemistry, is now available. To compare the FISH and DISH methods, we tested 251 samples enriched for common or difficult-to-assess HER2 anomalies. Seven samples failed DISH testing. There was a 64% (156/244) concordance between FISH and DISH by anomaly (κ = 0.58, 95% confidence interval, 0.51-0.65; P &lt; .0001) and an 83% (203/244) concordance by amplification status (κ = 0.58; 95% confidence interval, 0.47-0.69; P &lt; .0001). DISH resulted in lower estimates of HER2/ centromere 17 ratios than FISH, and many cases that were equivocal with FISH were normal with DISH. DISH did not detect any case with coamplification of HER2 and centromere 17. Using a cohort of difficult specimens, we observed less than 95% concordance between FISH and DISH. DISH may underestimate the HER2/chromosome 17 ratio, or FISH may overestimate this ratio.

Genomewide association studies (GWAS) and candidate‐gene studies have implicated single‐nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case‐control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate‐gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate‐gene studies was associated in the full case‐control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate‐gene approach lay in selecting both appropriate genes and relevant SNPs within these genes.

Purpose Anaplastic oligodendrogliomas, pure (AO) and mixed (anaplastic oligoastrocytoma [AOA]), are chemosensitive, especially if codeleted for 1p/19q, but whether patients live longer after chemoradiotherapy is unknown. Patients and Methods Eligible patients with AO/AOA were randomly assigned to procarbazine, lomustine, and vincristine (PCV) plus radiotherapy (RT) versus RT alone. The primary end point was overall survival (OS). Results Two hundred ninety-one eligible patients were randomly assigned: 148 to PCV plus RT and 143 to RT. For the entire cohort, there was no difference in median survival by treatment (4.6 years for PCV plus RT v 4.7 years for RT; hazard ratio [HR] = 0.79; 95% CI, 0.60 to 1.04; P = .1). Patients with codeleted tumors lived longer than those with noncodeleted tumors (PCV plus RT: 14.7 v 2.6 years, HR = 0.36, 95% CI, 0.23 to 0.57, P < .001; RT: 7.3 v 2.7 years, HR = 0.40, 95% CI, 0.27 to 0.60, P < .001), and the median survival of those with codeleted tumors treated with PCV plus RT was twice that of patients receiving RT (14.7 v 7.3 years; HR = 0.59; 95% CI, 0.37 to 0.95; P = .03). For those with noncodeleted tumors, there was no difference in median survival by treatment arm (2.6 v 2.7 years; HR = 0.85; 95% CI, 0.58 to 1.23; P = .39). In Cox models that included codeletion status, the adjusted OS for all patients was prolonged by PCV plus RT (HR = 0.67; 95% CI, 0.50 to 0.91; P = .01). Conclusion For the subset of patients with 1p/19q codeleted AO/AOA, PCV plus RT may be an especially effective treatment, although this observation was derived from an unplanned analysis.

Purpose There is increasing recognition of the existence of intratumoral heterogeneity of the human epidermal growth factor receptor (HER2), which affects interpretation of HER2 positivity in clinical practice and may have implications for patient prognosis and treatment. We determined the frequency and prognostic impact of heterogeneous HER2 gene amplification and polysomy 17 in patients with esophageal adenocarcinoma (EAC). Patients and Methods HER2 amplification (by fluorescence in situ hybridization) was examined in surgical EAC specimens (n = 675). HER2 heterogeneity was defined according to consensus guidelines as gene amplification (HER2/CEP17 ratio ≥ 2.0) in more than 5% but less than 50% of cancer cells. No patient received neoadjuvant or HER2-targeted therapy. Cox models were used to assess disease-specific survival (DSS) and overall survival (OS). Results Overall, 117 EACs (17%) demonstrated HER2 amplification, of which 20 (17%) showed HER2 heterogeneity. All HER2-heterogeneous tumors were amplified. Among HER2-amplified tumors, heterogeneous tumors had significantly higher frequency of poor histologic grade and polysomy 17. In multivariable models that included number of metastatic lymph nodes, grade, tumor stage, and polysomy 17, only HER2 heterogeneity and node number were prognostic among HER2-amplified tumors, with heterogeneity showing worse DSS (hazard ratio, 2.04; 95% CI, 1.09 to 3.79; P = .025) and OS (P = .026). Among HER2-nonamplified EACs, polysomy 17 was independently associated with worse DSS (P = .012) and OS (P = .023). Conclusion Among HER2-amplified EACs, 17% show HER2 heterogeneity, which independently predicts for worse cancer-specific death. Among HER2-nonamplified EACs, polysomy 17 is independently associated with worse survival. These novel findings demonstrate aggressive subgroups in HER2-amplified and -nonamplified EACs that have important implications for HER2 analysis and determination of benefit from HER2-targeted therapy.

Prostate cancer is the second leading cause of cancer death among United States men. However, disease aggressiveness is varied, with low-grade disease often being indolent and high-grade cancer accounting for the greatest density of deaths. Outcomes are also disparate among men with high-grade prostate cancer, with upwards of 65% having disease recurrence even after primary treatment. Identification of men at risk for recurrence and elucidation of the molecular processes that drive their disease is paramount, as these men are the most likely to benefit from multimodal therapy. We previously showed that androgen-induced expression profiles in prostate development are reactivated in aggressive prostate cancers. Herein, we report the down-regulation of one such gene, Sparcl1 , a secreted protein, acidic and rich in cysteine (SPARC) family matricellular protein, during invasive phases of prostate development and regeneration. We further demonstrate a parallel process in prostate cancer, with decreased expression of SPARCL1 in high-grade/metastatic prostate cancer. Mechanistically, we demonstrate that SPARCL1 loss increases the migratory and invasive properties of prostate cancer cells through Ras homolog gene family, member C (RHOC), a known mediator of metastatic progression. By using models incorporating clinicopathologic parameters to predict prostate cancer recurrence after treatment, we show that SPARCL1 loss is a significant, independent prognostic marker of disease progression. Thus, SPARCL1 is a potent regulator of cell migration/invasion and its loss is independently associated with prostate cancer recurrence.

Abstract Glioblastoma multiforme (GBM) is the most common and highly malignant primary brain tumor in adults with a median survival just over 1 year, and novel therapies are urgently needed. Deregulation of the p16 (INK4A)-CDK4/6-pRb pathway are commonly found in human GBM patients and selective inhibitors of CDK4/6 may be specifically useful to suppress proliferation associated with these alterations. PD0332991 is an orally active small molecule that specifically inhibits CDK4 and CDK6. Therefore, the efficacy of PD0332991 was evaluated in the Mayo panel of primary GBM xenograft lines using short-term explant cultures. We hypothesized that expression of p15 and/or p16, endogenous inhibitors of CDK4/6 activity, would suppress the response of GBM tumors to PD0332991 treatment. To test this hypothesis, 2 GBM xenograft cell lines with wild-type p16/p15 levels (GBM5 and 28) and 2 lines without detectable p16/p15 levels (GBM22 and 43) were selected for further analysis. Tumor cells were treated with graded concentrations (10 nanoM to1 microM) of PD0332991 for 5 days and subjected to CyQUANT cell proliferation assays. Consistent with our hypothesis, treatment with 1 microM PD0332991 effectively inhibited cell proliferation to 56.6±3.5% (P&lt;0.001) and 44.3±3.4% (P&lt;0.001) of control in GBM22 and GBM43 cells respectively, but did not affect cell proliferation in GBM5 and GBM28 cells (98.7±15.6% and 101.8±12.0% of control, respectively). In addition, 1 microM PD0332991 induced G1-phase cell cycle arrest in GBM22 (treated 79.7±0.8% vs. control 63.4±0.5% of cells in G1 phase, P&lt;0.001) and GBM43 (treated 70.6±1.1% vs. control 48.9±4.6% of cells in G1 phase, P&lt;0.001) but not in GBM5 and GBM28 (treated 52.3±2.7% vs. control 54.0±5.1%, treated 52.4±4.7% vs. control 54.6±2.6%, respectively). The status of p15 and p16 was confirmed by RT-PCR, which demonstrated readily detectable expression of p15 and p16 in GBM5 and GBM28, but not in GBM22 and GBM43 cells. Additional comparative genomic hybridization (CGH) data showed that CDKN2A and 2B (genes encode for p16 and p15 respectively) are homozygously deleted in GBM22 and 43, hemizygously deleted in GBM5 and normal in GBM28. We also examined the status of CDK4, CDK6, pRb and other molecules in the p16-CDK4/6-pRb pathway by Western, RT-PCR and CGH in these GBM lines and the data will be presented. We are now testing whether shRNA knockdown and/or re-expression of p15/p16 in the relevant cell lines alters their responsiveness to PD0332991. In conclusion, CDK4/6 inhibitor PD0332991 inhibits cell proliferation and induces G1 cell cycle arrest in p15/p16- null GBM tumors, but is less effective in p15/p16 expressing tumors. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C191.

Abstract Purpose: Glioblastoma is a devastating, incurable disease with few known prognostic factors. Here, we present the first genome-wide survival and validation study for glioblastoma. Experimental Design: Cox regressions for survival with 314,635 inherited autosomal single-nucleotide polymorphisms (SNP) among 315 San Francisco Adult Glioma Study patients for discovery and three independent validation data sets [87 Mayo Clinic, 232 glioma patients recruited from several medical centers in Southeastern United States (GliomaSE), and 115 The Cancer Genome Atlas patients] were used to identify SNPs associated with overall survival for Caucasian glioblastoma patients treated with the current standard of care, resection, radiation, and temozolomide (total n = 749). Tumor expression of the gene that contained the identified prognostic SNP was examined in three separate data sets (total n = 619). Genotype imputation was used to estimate hazard ratios (HR) for SNPs that had not been directly genotyped. Results: From the discovery and validation analyses, we identified a variant in single-stranded DNA-binding protein 2 (SSBP2) on 5q14.1 associated with overall survival in combined analyses (HR, 1.64; P = 1.3 × 10−6). Expression of SSBP2 in tumors from three independent data sets also was significantly related to patient survival (P = 5.3 × 10−4). Using genotype imputation, the SSBP2 SNP rs17296479 had the strongest statistically significant genome-wide association with poorer overall patient survival (HR, 1.79; 95% CI, 1.45-2.22; P = 1.0 × 10−7). Conclusion: The minor allele of SSBP2 SNP rs17296479 and the increased tumor expression of SSBP2 were statistically significantly associated with poorer overall survival among glioblastoma patients. With further confirmation, previously unrecognized inherited variations influencing survival may warrant inclusion in clinical trials to improve randomization. Unaccounted for genetic influence on survival could produce unwanted bias in such studies. Clin Cancer Res; 18(11); 3154–62. ©2012 AACR.