Predictive Value of Genomic Classifier Scores and Transcriptomic Data for Prostate Cancer Distant Metastasis Risk: A Multicenter Retrospective Study

PURPOSE/OBJECTIVE(S)

Prostate-specific membrane antigen (PSMA) positron emission tomography (PET) has a greater specificity and sensitivity for detection of extraprostatic prostate cancer than conventional imaging. The Decipher genomic classifier is an established prognostic biomarker being evaluated for its ability to predict systemic treatment intensification. The relationship between Decipher scores and PSMA-based spread remains unknown, as do differences in transcriptomic patterns of PSMA PET-based spread in the de novo vs. recurrent setting.

MATERIALS/METHODS

We retrospectively identified patients who (a) had undergone staging with a PSMA PET prior to treatment or for evaluation of recurrence post-radical prostatectomy (RP) at two institutions and (b) had transcriptomic data available from the Genomics Resource for Intelligent Discovery (GRID) database from either biopsy or RP specimens. We classified the PSMA PET pattern of spread using molecular imaging (mi) staging as localized (miT+N0M0), node-positive (miN1M0), distant metastasis (miM1a-c), or negative/non-diagnostic. We used logistic regression to calculate the odds ratios (OR) with 95% confidence intervals (CI) for distant metastasis risk based on Decipher score both pre-treatment and post-RP. As an exploratory analysis, we compared each of the staging groups for differences in important transcriptomic signatures. Kruskal-Wallis and Pearson chi-squared tests were used for continuous and categorical variables, respectively.

RESULTS

A total of 315 patients were included in this analysis (n = 164 pre-treatment, n = 151 post-RP). Eighty PSMA PET scans were negative, while 147 were miT+N0M0, 45 were miN1M0, and 43 were miM1a-c. A higher Decipher score was associated with distant metastasis (miM1a-c) on PSMA PET both pre-treatment (OR 1.3 [95% CI: 1.0-1.7] per 0.1 increase in Decipher score, P = 0.05) and post-RP (OR 1.2 [1.0-1.4] per 0.1 increase in Decipher score, P = 0.04). There were higher TP53 mutation (P = 0.01) and cell cycle progression (P = 0.04) signature scores in miM1a-c patients compared to miN1M0 or miT+N0M0 patients. Basal subtype was more prevalent per PAM50 in miM1a-c or miN1M0 patients (36%) than miT+N0M0 patients (19%, P=0.01). Patients with de novo miN1M0 or miM1a disease (n = 19) had higher Decipher scores (0.85 vs 0.57, P = 0.10) and IFNa response (P = 0.08) than patients with recurrent miN1M0 or miM1a disease (n = 35).

CONCLUSION

Higher Decipher scores were associated with distant metastasis on PSMA PET in both the de novo and recurrent setting. Transcriptomic differences in pathways related to proliferation, p53 status, and PAM50 classification were seen when comparing localized, node-positive, and distant metastatic disease. Patients with de novo miN1M0 or miM1a disease may harbor more aggressive disease than those with miN1M0 or miM1a disease at recurrence.

Oncolytic DNX-2401 virotherapy plus pembrolizumab in recurrent glioblastoma: a phase 1/2 trial

Immune-mediated anti-tumoral responses, elicited by oncolytic viruses and augmented with checkpoint inhibition, may be an effective treatment approach for glioblastoma. Here in this multicenter phase 1/2 study we evaluated the combination of intratumoral delivery of oncolytic virus DNX-2401 followed by intravenous anti-PD-1 antibody pembrolizumab in recurrent glioblastoma, first in a dose-escalation and then in a dose-expansion phase, in 49 patients. The primary endpoints were overall safety and objective response rate. The primary safety endpoint was met, whereas the primary efficacy endpoint was not met. There were no dose-limiting toxicities, and full dose combined treatment was well tolerated. The objective response rate was 10.4% (90% confidence interval (CI) 4.2-20.7%), which was not statistically greater than the prespecified control rate of 5%. The secondary endpoint of overall survival at 12 months was 52.7% (95% CI 40.1-69.2%), which was statistically greater than the prespecified control rate of 20%. Median overall survival was 12.5 months (10.7-13.5 months). Objective responses led to longer survival (hazard ratio 0.20, 95% CI 0.05-0.87). A total of 56.2% (95% CI 41.1-70.5%) of patients had a clinical benefit defined as stable disease or better. Three patients completed treatment with durable responses and remain alive at 45, 48 and 60 months. Exploratory mutational, gene-expression and immunophenotypic analyses revealed that the balance between immune cell infiltration and expression of checkpoint inhibitors may potentially inform on response to treatment and mechanisms of resistance. Overall, the combination of intratumoral DNX-2401 followed by pembrolizumab was safe with notable survival benefit in select patients (ClinicalTrials.gov registration: NCT02798406).

Abstract 238: Comprehensive study of gene expression outliers and their regulation mechanisms in pan-cancer

Cancer is a disease characterized by remarkable heterogeneity, with many molecular features significantly associated with tumor progression in specific subsets of patients. Gene expression varies drastically between tumors and within cells of a single tumor. This variability in gene expression can be caused by gene-regulatory mechanisms such as DNA copy number changes, extrachromosomal DNA, or aberrant methylation, amongst many others. These mechanisms sometimes generate extreme outliers: transcripts that show atypically high or low gene expression in a small percentage of cancers. These outliers increase the molecular and phenotypic diversity between individuals, contributing to tumor heterogeneity. Gene expression in cancer has been well studied with many reports of differential gene expression patterns between specific cancer types or subtypes. Importantly, many of these differences were strongly associated with tumorigenesis and tumor progression. For example, the BCR-ABL fusion was discovered in chronic myeloid leukemia with drugs targeting this fusion gene dramatically increasing the survival rate. The EML-ALK fusion gene is another example of a gene-expression outlier and drug target. It occurs in about 4% of non-small-cell lung carcinomas and has been routinely screened for. These examples demonstrate the critical role gene expression outliers play in cancer progression and highlight their potential as biomarkers for diagnostics and identifying novel drug targets. Despite their importance, there has not yet been a comprehensive pan-cancer study of gene expression outliers and their general properties. We lack the answers to fundamental questions such as how many outliers exist in a typical tumor, whether this differs across cancer types, what mechanisms generate the most outliers, whether specific clinical or somatic mutational features correlate with the number or type of outliers, and how many recurrent outliers exist. To answer these questions, we performed a comprehensive and systematic analysis of cancer gene-expression outliers using molecular data from multiple cancer genomics projects. We have created a new statistical outlier detection method and applied it to transcriptomics and proteomics data across 33 cancer types. We used this resource to describe the fundamental landscape of gene-expression outliers, including the most likely genetic and epigenetic mechanisms driving them. The resulting outliers will be further studied for their impact on cancer progression and validated hits will serve as clinically relevant biomarkers and targets for future functional and therapeutic investigations.

Citation Format: Jee Yun Han, Stefan Eng, Jaron Arbet, Paul Boutros. Comprehensive study of gene expression outliers and their regulation mechanisms in pan-cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 238.

Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-ribose polymerase inhibitors and low-dose alkylating chemotherapy

Loss-of-function mutations in genes encoding the Krebs cycle enzymes Fumarate Hydratase (FH) and Succinate Dehydrogenase (SDH) induce accumulation of fumarate and succinate, respectively and predispose patients to hereditary cancer syndromes including the development of aggressive renal cell carcinoma (RCC). Fumarate and succinate competitively inhibit αKG-dependent dioxygenases, including Lysine-specific demethylase 4A/B (KDM4A/B), leading to suppression of the homologous recombination (HR) DNA repair pathway. In this study, we have developed new syngeneic Fh1- and Sdhb-deficient murine models of RCC, which demonstrate the expected accumulation of fumarate and succinate, alterations in the transcriptomic and methylation profile, and an increase in unresolved DNA double-strand breaks (DSBs). The efficacy of poly ADP-ribose polymerase inhibitors (PARPis) and temozolomide (TMZ), alone and in combination, was evaluated both in vitro and in vivo. Combination treatment with PARPi and TMZ results in marked in vitro cytotoxicity in Fh1- and Sdhb-deficient cells. In vivo, treatment with standard dosing of the PARP inhibitor BGB-290 and low-dose TMZ significantly inhibits tumor growth without a significant increase in toxicity. These findings provide the basis for a novel therapeutic strategy exploiting HR deficiency in FH and SDH-deficient RCC with combined PARP inhibition and low-dose alkylating chemotherapy.

Abstract 3621: 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma

Treatment failure in glioblastoma, the most common and lethal primary brain tumor in adults, is often attributed to intratumoral heterogeneity as it fosters tumor evolution and selection of resistant clones. Sources of intratumoral heterogeneity may include genomic alterations, such as single-nucleotide and structural variants, and epigenomic alterations, such as changes in chromatin structure and transcriptional regulation. The relative extent and functional significance of these contributors to intratumoral heterogeneity in glioblastoma have yet to be elucidated. In collaboration with neurosurgeons and neuro-imaging experts, we have established a novel approach towards characterizing intratumoral heterogeneity in three-dimensional (3D) space. For patients undergoing tumor resection, we utilize 3D surgical neuronavigation to safely acquire ~10 samples representing maximal anatomical diversity. Samples are mapped by 3D spatial coordinates and integrated with patient MRI scans for 360º visualization of sample location in context of the brain. We have now conducted whole-exome sequencing (Exome-Seq), assay for transposase-accessible chromatin (ATAC-Seq), and RNA-sequencing (RNA-Seq) for 83 spatially mapped samples obtained from 8 patients with primary IDH-WT glioblastoma. Integrative data analysis provides unprecedented insight into sources of intratumoral heterogeneity in glioblastoma and their 3D spatial patterning. We find that tumor cells show aberrant transcription factor activity, activation of fetal brain programs, and variable chromatin accessibility at CTCF-binding loop anchors indicating plasticity in higher-order chromatin structure. Chromosome conformation capture analysis by Hi-C extends these findings and reveals intratumoral differences in long-range chromatin interactions due to structural variants and enhancer hijacking. Further, we use deconvolution to identify microenvironmental contributors to epigenomic intratumoral heterogeneity including neural, glial, and immune populations. We define chromatin signatures associated with microenvironmental cell types and states, revealing their 3D spatial patterning, and validate these findings by single-cell ATAC-Seq. Our work thus establishes both tumor and microenvironmental sources of intratumoral heterogeneity in glioblastoma, revealing their chromatin programs and 3D spatial patterning. As a resource for further investigation, we have developed an interactive data sharing platform that enables visualization of brain tumor intratumoral heterogeneity in 360 degrees.

Citation Format: Radhika Mathur, Qixuan Wang, Patrick Schupp, Ana Nikolic, Takafumi Yamaguchi, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa LaFontaine, Joanna Phillips, Susan Chang, Yan Li, Janine Lupo, Paul Boutros, Marco Gallo, Michael Oldham, Feng Yue, Joseph Costello. 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3621.

Refining the definition of biochemical failure in the era of stereotactic body radiation therapy for prostate cancer: The Phoenix definition and beyond

BACKGROUND AND PURPOSE

The Phoenix definition for biochemical failure (BCF) after radiotherapy uses nadir PSA (nPSA) + 2 ng/mL to classify a BCF and was derived from conventionally fractionated radiotherapy, which produces significantly higher nPSAs than stereotactic body radiotherapy (SBRT). We investigated whether an alternative nPSA-based threshold could be used to define post-SBRT BCFs.

MATERIALS AND METHODS

PSA kinetics data on 2038 patients from 9 institutions were retrospectively analyzed for low- and intermediate-risk PCa patients treated with SBRT without ADT. We evaluated the performance of various nPSA-based definitions. We also investigated the relationship of relative PSA decline (rPSA, PSA_18month/PSA_6month) and timing of reaching nPSA + 2 with BCF.

RESULTS

Median follow-up was 71.9 months. BCF occurred in 6.9% of patients. Median nPSA was 0.16 ng/mL. False positivity of nPSA + 2 was 30.2%, compared to 40.9%, 57.8%, and 71.0% for nPSA + 1.5, nPSA + 1.0, and nPSA + 0.5, respectively. Among patients with BCF, the median lead time gained from an earlier nPSA + threshold definition over the Phoenix definition was minimal. Patients with BCF had significantly lower rates of early PSA decline (mean rPSA 1.19 vs. 0.39, p < 0.0001) and were significantly more likely to reach nPSA + 2 ≥ 18 months (83.3% vs. 21.1%, p < 0.0001). The proposed criterion (rPSA ≥ 2.6 or nPSA + 2 ≥ 18 months) had a sensitivity and specificity of 92.4% and 81.5%, respectively, for predicting BCF in patients meeting the Phoenix definition and decreased its false positivity to 6.4%.

CONCLUSION

The Phoenix definition remains an excellent definition for BCF post-SBRT. Its high false positivity can be mitigated by applying additional criteria (rPSA ≥ 2.6 or time to nPSA + 2 ≥ 18 months).

Dimensional reduction based on peak fitting of Raman micro spectroscopy data improves detection of prostate cancer in tissue specimens

SIGNIFICANCE

Prostate cancer is the most common cancer among men. An accurate diagnosis of its severity at detection plays a major role in improving their survival. Recently, machine learning models using biomarkers identified from Raman micro-spectroscopy discriminated intraductal carcinoma of the prostate (IDC-P) from cancer tissue with a ≥85  %   detection accuracy and differentiated high-grade prostatic intraepithelial neoplasia (HGPIN) from IDC-P with a ≥97.8  %   accuracy.

AIM

To improve the classification performance of machine learning models identifying different types of prostate cancer tissue using a new dimensional reduction technique.

APPROACH

A radial basis function (RBF) kernel support vector machine (SVM) model was trained on Raman spectra of prostate tissue from a 272-patient cohort (Centre hospitalier de l'Université de Montréal, CHUM) and tested on two independent cohorts of 76 patients [University Health Network (UHN)] and 135 patients (Centre hospitalier universitaire de Québec-Université Laval, CHUQc-UL). Two types of engineered features were used. Individual intensity features, i.e., Raman signal intensity measured at particular wavelengths and novel Raman spectra fitted peak features consisting of peak heights and widths.

RESULTS

Combining engineered features improved classification performance for the three aforementioned classification tasks. The improvements for IDC-P/cancer classification for the UHN and CHUQc-UL testing sets in accuracy, sensitivity, specificity, and area under the curve (AUC) are (numbers in parenthesis are associated with the CHUQc-UL testing set): +4  %   (+8  %  ), +7  %   (+9  %  ), +2  %   (6%), +9 (+9) with respect to the current best models. Discrimination between HGPIN and IDC-P was also improved in both testing cohorts: +2.2  %   (+1.7  %  ), +4.5  %   (+3.6  %  ), +0  %   (+0  %  ), +2.3 (+0). While no global improvements were obtained for the normal versus cancer classification task [+0  %   (-2  %  ), +0  %   (-3  %  ), +2  %   (-2  %  ), +4 (+3)], the AUC was improved in both testing sets.

CONCLUSIONS

Combining individual intensity features and novel Raman fitted peak features, improved the classification performance on two independent and multicenter testing sets in comparison to using only individual intensity features.

Using the Movember Foundation's GAP3 cohort to measure the effect of active surveillance on patient-reported urinary and sexual function-a retrospective study in low-risk prostate cancer patients

BACKGROUND

Active surveillance (AS) for low-risk prostate cancer (PCa) is intended to overcome potential side-effects of definitive treatment. Frequent prostate biopsies during AS may, however, impact erectile (EF) and urinary function (UF). The objective of this study was to test the influence of prostate biopsies on patient-reported EF and UF using multicenter data from the largest to-date AS-database.

METHODS

In this retrospective study, data analyses were performed using the Movember GAP3 database (v3.2), containing data from 21,169 AS participants from 27 AS-cohorts worldwide. Participants were included in the study if they had at least one follow-up prostate biopsy and completed at least one patient reported outcome measure (PROM) related to EF [Sexual Health Inventory for Men (SHIM)/five item International Index of Erectile Function (IIEF-5)] or UF [International Prostate Symptom Score (IPSS)] during follow-up. The longitudinal effect of the number of biopsies on either SHIM/IIEF-5 or IPSS were analyzed using linear mixed models to adjust for clustering at patient-level. Analyses were stratified by center; covariates included age and Gleason Grade group at diagnosis, and time on AS.

RESULTS

A total of 696 participants completed the SHIM/IIEF-5 3,175 times, with a median follow-up of 36 months [interquartile range (IQR) 20-55 months]. A total of 845 participants completed the IPSS 4,061 times, with a median follow-up of 35 months (IQR 19-56 months). The intraclass correlation (ICC) was 0.74 for the SHIM/IIEF-5 and 0.68 for the IPSS, indicating substantial differences between participants' PROMs. Limited heterogeneity between cohorts in the estimated effect of the number of biopsies on either PROM were observed. A significant association was observed between the number of biopsies and the SHIM/IIEF-5 score, but not for the IPSS score. Every biopsy was associated with a decrease in the SHIM/IIEF-5 score of an average 0.67 (95% CI, 0.47-0.88) points.

CONCLUSIONS

Repeated prostate biopsy as part of an AS protocol for men with low-risk PCa does not have a significant association with self-reported UF but does impact self-reported sexual function. Further research is, however, needed to understand whether the effect on sexual function implies a negative clinical impact on their quality of life and is meaningful from a patient's perspective. In the meantime, clinicians and patients should anticipate a potential decline in erectile function and hence consider incorporating the risk of this harm into their discussion about opting for AS and also when deciding on the stringency of follow-up biopsy schedules with long-term AS.

Identification of intraductal carcinoma of the prostate on tissue specimens using Raman micro-spectroscopy: A diagnostic accuracy case-control study with multicohort validation

BACKGROUND

Prostate cancer (PC) is the most frequently diagnosed cancer in North American men. Pathologists are in critical need of accurate biomarkers to characterize PC, particularly to confirm the presence of intraductal carcinoma of the prostate (IDC-P), an aggressive histopathological variant for which therapeutic options are now available. Our aim was to identify IDC-P with Raman micro-spectroscopy (RμS) and machine learning technology following a protocol suitable for routine clinical histopathology laboratories.

METHODS AND FINDINGS

We used RμS to differentiate IDC-P from PC, as well as PC and IDC-P from benign tissue on formalin-fixed paraffin-embedded first-line radical prostatectomy specimens (embedded in tissue microarrays [TMAs]) from 483 patients treated in 3 Canadian institutions between 1993 and 2013. The main measures were the presence or absence of IDC-P and of PC, regardless of the clinical outcomes. The median age at radical prostatectomy was 62 years. Most of the specimens from the first cohort (Centre hospitalier de l'Université de Montréal) were of Gleason score 3 + 3 = 6 (51%) while most of the specimens from the 2 other cohorts (University Health Network and Centre hospitalier universitaire de Québec-Université Laval) were of Gleason score 3 + 4 = 7 (51% and 52%, respectively). Most of the 483 patients were pT2 stage (44%-69%), and pT3a (22%-49%) was more frequent than pT3b (9%-12%). To investigate the prostate tissue of each patient, 2 consecutive sections of each TMA block were cut. The first section was transferred onto a glass slide to perform immunohistochemistry with H&E counterstaining for cell identification. The second section was placed on an aluminum slide, dewaxed, and then used to acquire an average of 7 Raman spectra per specimen (between 4 and 24 Raman spectra, 4 acquisitions/TMA core). Raman spectra of each cell type were then analyzed to retrieve tissue-specific molecular information and to generate classification models using machine learning technology. Models were trained and cross-validated using data from 1 institution. Accuracy, sensitivity, and specificity were 87% ± 5%, 86% ± 6%, and 89% ± 8%, respectively, to differentiate PC from benign tissue, and 95% ± 2%, 96% ± 4%, and 94% ± 2%, respectively, to differentiate IDC-P from PC. The trained models were then tested on Raman spectra from 2 independent institutions, reaching accuracies, sensitivities, and specificities of 84% and 86%, 84% and 87%, and 81% and 82%, respectively, to diagnose PC, and of 85% and 91%, 85% and 88%, and 86% and 93%, respectively, for the identification of IDC-P. IDC-P could further be differentiated from high-grade prostatic intraepithelial neoplasia (HGPIN), a pre-malignant intraductal proliferation that can be mistaken as IDC-P, with accuracies, sensitivities, and specificities > 95% in both training and testing cohorts. As we used stringent criteria to diagnose IDC-P, the main limitation of our study is the exclusion of borderline, difficult-to-classify lesions from our datasets.

CONCLUSIONS

In this study, we developed classification models for the analysis of RμS data to differentiate IDC-P, PC, and benign tissue, including HGPIN. RμS could be a next-generation histopathological technique used to reinforce the identification of high-risk PC patients and lead to more precise diagnosis of IDC-P.

Abstract 2908: Mesothelioma phylogeny reveal MTAP as a solitary clonal deletion, exposing vulnerability to the PRMT5 perturbagen, quinacrine

Background: Malignant Pleural Mesothelioma (MPM) remains an incurable cancer that is caused by asbestos, and for which there is a paucity of effective therapy. Stratified medicine for MPM is in its infancy. We hypothesized that deciphering the phylogenetic architecture of mesothelioma would yield a census of recurrent clonal homozygous copy number losses as potential therapeutic vulnerabilities.

Methods and Results: We prospectively enrolled 125 patients with MPM undergoing radical pleurectomy decortication, into the MEDUSA (Mesothelioma Evolution: DrUgging Somatic Alterations) study. Multi-region whole exome sequencing was conducted on 106 tumours from 20 patients (Medusa20 cohort). Up to 5 consistent regions were sampled: apex, pericardium, anterior/ posterior costophrenic angles, and the oblique fissure. For each patient, matching whole blood DNA was also whole exome sequenced to allow identification of tumour- specific somatic variations. Somatic copy number alterations (SCNAs) in each tumour region were called using SEQUENZA. We inferred phylogeny for each patient’s tumour using the SCNA calls by maximum parsimony (TUMULT), which revealed branched evolution in all MPMs. The total number of SCNAs ranged from 78 to 380 across the cohort with biphasic MPMs exhibiting a significantly larger total and clonal SCNA burden compared to epithelioid MPMs (p=0.024) . Only 9p21 which harbours CDKNA and methylthioadenosine phosphorylase (MTAP), exhibited clonal homozygous loss in 3 patients (15%). Clonal heterozygous loss was seen in 2 patients (10%). A further 5 patients showed with evidence of parallel evolution involving MTAP loss in distant MPM regions (25%), with one patient's MPM having late homozygous deletion in a single branch (5%). MTAP loss was validated by array based SCNA analysis and was found to be negatively prognostic in an independent cohort. Protein arginine methyltransferase 5 (PRMT5) has been recently identified as a vulnerability in MTAP deleted cancer. We found that siRNA silencing of PRMT5, caused MTAP selective loss of clonogenicity with proliferative arrest. Utilizing the connectivity map, quinacrine was validated as a PRMT5 perturbagen, which suppressed c-jun-dependent PRMT5 expression without inhibiting its methyltransferase activity. Quinacrine phenocopied PRMT5 siRNA, reducing global symmetrical arginine dimethylation of histone H4 (H4R3me2S). Finally, exogenous wild-type PRMT5 rescued quinacrine-mediated cell arrest in MTAP-negative cells, an effect not seen using the PMRT5 E444Q methyltransferase dead mutant.

Conclusion: MTAP deletion is a clonal homozygous event in mesothelioma, with potential as a therapeutically tractable Achilles heel, via PRMT5 silencing using a repurposed small molecule, quinacrine.

Citation Format: Sara Busacca, Lee Brannan, Apostolos Nakas, Annabel Sharkey, Chiara Riganti, David Waller, Cathy Richards, Iris Salaroglio, Vladan Milosevic, Peter Wells-Jordan, Alan Dawson, Michael Sheaff, John LeQuesne, Aarti Gaba, Robert Hastings, Luke Martinson, Jin-Li Lo, Amrita Bajaj, Paul Boutros, Tom John, Bibhusal Thapa, Gareth Wilson, Jacqui Shaw, Charles Swanton, Frank Dudbridge, Edward Hollox, Dean A. Fennell. Mesothelioma phylogeny reveal MTAP as a solitary clonal deletion, exposing vulnerability to the PRMT5 perturbagen, quinacrine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2908.

Long non-coding RNA urothelial carcinoma associated 1 (UCA1) mediates radiation response in prostate cancer

Radioresistance remains a significant obstacle in the treatment of Prostate Cancer (PCa). To simulate the clinical scenario of irradiation resistance (IRR), we created DU145-IRR PCa cell lines by treatment with 2 Gy daily IR for 59 fractions. DU145-IRR cells acquired an aggressive phenotype as evidenced by increased clonogenic survival, tumorigenic potential and invasiveness. We performed transcriptome profiling to discover dysregulated genes in DU145-IRR cells and identified the long non-coding RNA (lncRNA), Urothelial carcinoma-associated 1 (UCA1). We first investigated the role of UCA1 in radiation response and found that UCA1 abundance was significantly higher in DU145-IRR cells compared to control cells. UCA1 siRNA-knockdown reversed the aggressive phenotype and significantly increased sensitivity to IR. UCA1 depletion inhibited growth, induced cell cycle arrest at the G2/M transition and decreased activation of the pro-survival Akt pathway. We then studied the clinical significance of UCA1 expression in two independent cohorts of PCa patients: MSKCC (130 patients) and CPC-GENE (209 patients). UCA1 over-expression was associated with decreased 5-year disease-free survival in MSKCC patients (HR = 2.9; p = 0.007) and a trend toward lower biochemical recurrence-free survival in CPC-GENE patients (HR = 2.7; p = 0.05). We showed for the first time that UCA1 depletion induces radiosensitivity, decreases proliferative capacity and disrupts cell cycle progression, which may occur through altered Akt signaling and induced cell cycle arrest at the G2/M transition. Our results indicate that UCA1 might have prognostic value in PCa and be a potential therapeutic target.

Abstract 830: MiRNA-106a and LITAF are novel modulators of prostate cancer radioresistance

Prostate cancer (PCa) is the second most prevalent cancer affecting men worldwide, with radiotherapy being a primary treatment modality. PCa recurrence is a major clinical problem with up to a 40% biochemical recurrence rate at five years after external beam radiotherapy (ionizing radiation, IR). Therefore, there is an unmet need to characterize radioresistance in order to improve therapy and patient outcomes. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. MiRNAs are aberrantly expressed in cancer, specifically, miR-106a has been found to be overexpressed in various cancer types. The purpose of this study is to determine whether miR-106a confers IR resistance and tumor aggression in PCa.

Utilizing The Cancer Genome Atlas Data Portal, bioinformatics analysis discovered that miR-106a was significantly overexpressed in PCa samples relative to normal prostate. This suggests that miR-106a is involved in prostate carcinogenesis. Clonogenic survival assays revealed that cells overexpressing miR-106a had increased survival after IR treatment compared to control cells. Proliferation assays showed that miR-106a cells had a higher proliferation rate than control cells in both unirradiated and IR-treated cells. Affymetrix gene array analysis was used to identify possible targets of miR-106a. Combining results from the gene array, in silico prediction algorithms, and in vitro analyses, we identified lipopolysaccharide-induced TNFα factor (LITAF) as a target of miR-106a. In addition, LITAF knockdown lead to increased proliferation and clonogenic survival following IR, recapitulating the phenotype of miR-106a overexpression. Cells were stained for β-galactosidase expression following IR to assess senescence, as a mode of cell death. We found that both miR-106a overexpression and LITAF knockdown resulted in significantly fewer senescent cells post-IR. Upon examination of critical DNA damage response genes, we found that miR-106a overexpression and LITAF knockdown increased expression of ATM mRNA and protein. Upregulation of ATM is associated with IR resistance, elucidating the mechanism by which miR-106a overexpression and LITAF knockdown are involved in radioresistance. Tumor xenograft experiments, using a PCa cell line stably overexpressing miR-106a, confirmed that miR-106a increases proliferation compared to control tumors before and after IR.

Thus, our results strongly suggest that miR-106a is involved in PCa aggression and confers a radiation-resistant phenotype, by targeting the novel radiation response gene LITAF.

Note: This abstract was not presented at the meeting.

Citation Format: Christianne Hoey, Jessica Ray, Paul Boutros, Stanley K. Liu. MiRNA-106a and LITAF are novel modulators of prostate cancer radioresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 830. doi:10.1158/1538-7445.AM2017-830

Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants

Whole-exome sequencing studies have transformed our understanding of recurrent somatic mutations that contribute to cancer pathogenesis; however, these studies limit our ability to identify cancer-associated mutations to those that cause protein-coding changes. To more comprehensively catalogue cancer-associated gene alterations, we have extensively characterized tumor transcriptomes from 1,220 donors with matched whole-genome sequence data to identify recurrent RNA-level aberrations. Specifically, we created a unified RNA-Seq analysis pipeline including sequence alignment and quality control and subsequently identified gene alterations through outlier detection from estimated gene expression levels, alternative splicing, alternative transcription starts, and allele-specific expression and through identified RNA-edited sites and gene fusions. Our data represent an extensive catalog of RNA aberrations for each gene across 27 cancer types. We have also tested for genetic associations with these RNA phenotypes. Using an integrative analysis approach, we have mapped genome-wide cis and trans effects on individual RNA phenotypes, considering both common germline variants as well as somatic SNVs in gene promoters, enhancers, and intronic and other regions. Many of the regulatory associations we identify are not accessible by exome sequencing, underlining the importance of whole-genome sequence data. Utilizing this RNA-centric view, we have identified genes that are recurrently altered, yet have not been previously characterized as cancer genes or identified through DNA-level driver gene analysis. To identify further supporting evidence that these recurrent alterations are potential drivers, we identified genes with mutually exclusive RNA-level alterations. Our findings reveal new insights into selective advantages of somatic changes and molecular mechanisms of cancer. This work is by the Transcriptome Working Group of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and authors are listed in alphabetical order.

Citation Format: Samirkumar Amin, Philip Awadalla, Andrew Biankin, Paul Boutros, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, David Chang, Aurélien Chateigner, Ken Chen, Zechen Chong, Brian Craft, Chad Creighton, Deniz Demircioğlu, Nuno Fonseca, Milana Frenkel-Morgenstern, Gad Getz, Jonathan Göke, Mary Goldman, Liliana Greger, Syed Haider, Yao He, Katherine Hoadley, Yuan Ji, Andre Kahles, Ekta Khurana, Jan Korbel, Kjong Lehmann, Han Liang, Fenglin Liu, Maximillian Marin, Matthew Meyerson, Akinyemi Ojesina, Francis Ouellette, Chandra Pedamallu, Marc Perry, Gunnar Rätsch, Roland Schwarz, Yuichi Shiraishi, Cameron Soulette, Oliver Stegle, Patrick Tan, Alfonso Valencia, Linda Xiang, Christina Yung, Junjun Zhang, Fan Zhang, Zemin Zhang, Jingchun Zhu. Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr SY10-02. doi:10.1158/1538-7445.AM2017-SY10-02

Abstract 4339: Prognostic significance of copy number alteration burden in unfavorable intermediate-risk prostate cancers harboring intraductal carcinoma and cribriform architecture

Aim: Men with intermediate-risk prostate cancer represent a heterogeneous group of patients with varying prognoses. Intraductal carcinoma (IDC), cribriform architecture (CA), and high copy number alteration burden are novel pathological and genomic indices that predict aggressive disease and inferior clinical outcomes in patients with localised prostate cancer. We aimed to test the independent prognostic effect of these indices in a cohort of intermediate-risk prostate cancers.

Experimental methods: We defined a set of clinical and genomic indices to test for their prognostic significance in a cohort of individuals with NCCN-defined intermediate-risk prostate cancer, who were treated with radical prostatectomy (RadP) or radiotherapy (RT) (N = 173, RadP; N = 358, RT). Clinical indices include primary T-category, pre-treatment PSA level, Gleason's score and pattern, and presence of IDC and/or CA. Pathological features were reviewed centrally by two expert pathologists. Copy number alteration burden was assessed in 215 tumours of the cohort using SNP array profiling (Affymetrix Oncoscan), and reported as percent genome aberration (PGA). Our primary endpoint was to test if a model incorporating IDC/CA and PGA stratifies patients with intermediate-risk disease for risk of biochemical relapse after primary treatment.

Results: Biochemical relapse was associated with PGA on univariable and multivariable analysis for the sub-cohort of 215 patients (HR of High vs Low PGA defined by median = 1.61, 95% CI = 1.04-2.49, Wald's p = 0.033). Based on modelling of the clinical indices, presence of IDC/CA was associated with biochemical relapse-free rate (bRFR) on univariable and multivariable analyses (HR = 1.90, 95% CI = 1.34-2.69, p = 0.00034), along with PSA level. Risk stratification considering both IDC/CA and PGA indicated an additive prognostic effect of IDC/CA to PGA for early biochemical relapse, with 18-month bRFR of 83% in High PGA, present IDC/CA vs 94% in Low PGA, absent IDC/CA subgroups (HR = 2.55, 95% CI = 1.49-4.39, p = 0.00069). A comparison of risk stratification models revealed that inclusion of PGA to IDC/CA yielded the strongest model for predicting 18-month bRFR in patients with intermediate-risk prostate cancer following treatment (area under the curve, AUC = 0.580, 95% CI = 0.456-0.675 [T-category, PSA, and IDC/CA] vs 0.649, 95% CI = 0.476-0.776 [T-category, PSA, IDC/CA, and PGA]).

Conclusions: We herein demonstrate for the first time a novel risk stratification model integrating pathological (IDC/CA) and genomic (PGA) indices to identify patients with unfavourable intermediate-risk prostate cancer, who may benefit from intensification to conventional definitive treatment.

Citation Format: Melvin Lee Kiang Chua, Jure Murgic, Melania Pintilie, Emilie Lalonde, Charlotte Kweldam, Winnie Lo, Alejandro Berlin, Alan Dal Pra, Michele Orain, Valerie Picard, Helene Hovington, Alain Begeron, Yves Fradet, Bernard Tetu, Julie Livingstone, Alice Meng, Jun Yan Zhang, Gaetano Zafarana, Neil Fleshner, Mike Fraser, Paul Boutros, Robert Bristow, Theodorus van der Kwast. Prognostic significance of copy number alteration burden in unfavorable intermediate-risk prostate cancers harboring intraductal carcinoma and cribriform architecture. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4339.

PD-L1 and Tumor Infiltrating Lymphocytes as Prognostic Markers in Resected NSCLC

Introduction

Immune checkpoint inhibition has shifted treatment paradigms in non-small cell lung cancer (NSCLC). Conflicting results have been reported regarding the immune infiltrate and programmed death-ligand 1 (PD-L1) as a prognostic marker. We correlated the immune infiltrate and PD-L1 expression with clinicopathologic characteristics in a cohort of resected NSCLC.

Methods

A tissue microarray was constructed using triplicate cores from consecutive resected NSCLC. Immunohistochemistry was performed for CD8, FOXP3 and PD-L1. Strong PD-L1 expression was predefined as greater than 50% tumor cell positivity. Matched nodal samples were assessed for concordance of PD-L1 expression.

Results

Of 522 patients, 346 were node-negative (N0), 72 N1 and 109 N2; 265 were adenocarcinomas (AC), 182 squamous cell cancers (SCC) and 75 other. Strong PD-L1 expression was found in 24% cases. In the overall cohort, PD-L1 expression was not associated with survival. In patients with N2 disease, strong PD-L1 expression was associated with significantly improved disease-free (DFS) and overall survival (OS) in multivariate analysis (HR 0.49, 95%CI 0.36–0.94, p = 0.031; HR 0.46, 95%CI 0.26–0.80, p = 0.006). In this resected cohort only 5% harboured EGFR mutations, whereas 19% harboured KRAS and 23% other. KRAS mutated tumors were more likely to highly express PD-L1 compared to EGFR (22% vs 3%). A stromal CD8 infiltrate was associated with significantly improved DFS in SCC (HR 0.70, 95%CI 0.50–0.97, p = 0.034), but not AC, whereas FOXP3 was not prognostic. Matched nodal specimens (N = 53) were highly concordant for PD-L1 expression (89%).

Conclusion

PD-L1 expression was not prognostic in the overall cohort. PD-L1 expression in primary tumor and matched nodal specimens were highly concordant. The observed survival benefit in N2 disease requires confirmation.

Abstract P3-06-03: Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Background: Meta-analyses performed by the Early Breast Cancer Trialists Collaborative Group demonstrated a significant increase in disease free and overall survival through the addition of anthracyclines to polychemotherapy. Anthracyclines have, however, significant toxicities including cardiotoxicity and leukaemia. It is, therefore, imperative to identify those patients who will benefit from adjuvant anthracycline treatment; other patients could then be spared unnecessary toxicities and be considered for alternative adjuvant therapy. Several markers that may predict anthracycline benefit have been explored in patient cohorts (HER2, TOP2A, Ch17CEP and TIMP1) with limited success.

Methods: To identify markers that are clinically-relevant, we generated MDA-MB-231, MCF7, SKBR3 and ZR-75-1 breast cancer cell lines sensitive and resistant to epirubicin to identify pathways contributing to anthracycline resistance. A complementary approach including gene expression analyses to identify molecular pathways involved in resistance, and small-molecule inhibitors to reverse resistance were performed. RNA was extracted from patients in the BR9601 adjuvant trial evaluating the addition of epirubicin (E) to CMF and analysed through Nanostring technology. Log-rank analyses explored the predictive values of the signatures on distant relapse-free survival (DRFS). Cox-regression models tested independent predictive value on DRFS in the presence of treatment, age, tumour size, nodal status, ER status and grade, and treatment by marker interactions.

Results: Gene expression analysis identified upregulaton of a histone gene module in all four cell lines which was validated by qRT-PCR. Histone deacetylase small-molecule inhibitors reversed resistance and were cytotoxic for epirubicin-resistant cell lines, with IC50's ranging from 0.1-3.69µM, confirming that histone pathways are associated with epirubicin resistance. Gene expression analysis of the 18-gene histone module in the BR9601 clinical cohort revealed that patients whose tumour had low expression had an increased DRFS (HR: 0.35, 95%CI 0.17-0.73, p=0.005) when treated with E-CMF compared with patients treated with CMF alone. Conversely, there was no apparent benefit of E-CMF vs CMF in patients with high histone module expression (HR: 0.96, 95%CI 0.58-1.59, p=0.87). After multivariate analysis and adjustment for HER2 status, nodal status, age, grade and ER status, the treatment by marker interaction was 0.35 (95%CI 0.13-0.96, p=0.042) for DRFS.

Conclusion: Histone gene expression was an independent predictor of anthracycline benefit in terms of DRFS. In vitro data demonstrated that resistance could be reversed with histone deacetylase small-molecule inhibitors. The histone signature identified could be a potential theranostic candidate for patients with early breast cancer.

Citation Format: Spears M, Braunstein M, Liao L, Yao C, Lyttle N, Lobo N, Taylor KJ, Krzyzanowski PM, Kalatskaya I, Marcellus R, Stein L, Boutros P, Twelves CJ, Bartlett JMS. Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. [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 P3-06-03.

Copy number alterations of DNA mismatch repair (MMR) genes as novel prognostic markers in localised prostate cancer (CaP)

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Background: To investigate the prognostic significance of CNA of genes involved in the MMR pathway in localised CaP. Methods: We studied CNA of genes involved in MMR, namely MSH2, MSH3, MSH6, MLH1, PMS2, in 284 patients with intermediate-risk CaP (Toronto cohort), and compared our findings against three public databases (MSKCC and Cambridge cohorts) that included 375 low- to high-risk CaP. The Toronto cohort comprised of 143 and 141 individuals who underwent image-guided radiotherapy (IGRT) and radical prostatectomy (RadP), respectively, while all patients from the public databases underwent RadP. Information on genome-wide copy number alterations (Toronto) was obtained using Affymetrix Oncoscan array. Biochemical relapse-free survival (bRFS) was assessed for clinical outcome. Results: CNA of MSH2, MSH3, MSH6, MLH1, PMS2 were observed in 3.9% (n = 11), 7.7% (n = 22), 3.9% (n = 11), 4.6% (n = 13) and 13.0% (n = 37) of the Toronto cohort, respectively. Distinct patterns of allelic gain and loss were observed for the gene set; gains only for MLH1 and PMS2, and losses only, in all but 1 case, for MSH2, MSH3 and MSH6. In the Toronto cohort, allelic losses of MSH2, MSH3 and MSH6 were determined to be prognostic for poorer bRFS in IGRT patients (HR 2.04, 95% CI 1.01, 4.12, p = 0.048), but not for patients who underwent RadP (HR 1.08, 95% CI 0.49, 2.39, p = 0.84); while gains in MLH1 and PMS2 were not prognostic in either IGRT or RadP patients. A pooled analysis of these genes for all RadP patients from the Toronto and public databases (n = 516) did however indicate that allelic losses of MSH2, MSH3 and MSH6 were significant predictors of poorer bRFS (HR 2.48, 95% CI 1.64-3.77, p < 0.001), but not MLH1 and PMS2 gains. On multi-variable modelling that includes percent genome aberration and pre-treatment PSA levels, allelic losses of MSH2, MSH3 and MSH6remained significant predictors of bRFS for the pooled RadP cohort (HR 1.96, 95% CI 1.27, 3.01, Wald's p < 0.001), but not for IGRT patients (HR 1.50, 95% CI 0.72, 3.12, p = 0.28). Conclusions: We identified a distinct pattern of copy number loss of MSH2, MSH3 and MSH6 genes in localised CaP that appears to be a novel biomarker of failure to definitive treatment.

Prognostic value of copy-number alterations of the Cohesin complex in intermediate-risk prostate cancer recurrence

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Background: The Cohesin complex plays a critical role in mitotic progression and post-replicative DNA damage repair. It serves to bring together sister chromatids both in metaphase and in homologous recombination repair following ionizing radiation. The complex has also been shown to be phosphorylated in the ATM/BRCA1 pathway. The expression of various proteins in the complex are dysregulated in many cancers: breast, prostate, etc. Interestingly, in breast cancer cell lines, Cohesin is required for MYC activation in response to estrogen. Our study sought to correlate copy number alterations in this pivotal complex with biochemical relapse in prostate cancer patients. Methods: Our cohort consists of 284 patients with D’ Amico-classified intermediate-risk prostate cancer, treated with image-guided radiotherapy (IGRT, N = 143) or radical prostatectomy (RadP, N = 141). Pre-treatment biopsies and prostatectomy samples were analyzed using the Affymetrix Oncoscan array. The Phoenix and AUA criteria was used to define biochemical relapse for RadP and IGRT patients respectively. Results: Copy number alterations of RAD21, SMC1B, and STAG1 were observed in 18% (n = 52), 6.3% (n = 18), and 12% (n = 35) of the cohort respectively. They were predominantly losses in SMC1B, but gains in RAD21 and STAG1. All three genes in the Cohesin complex were associated with increased risk of biochemical relapse: RAD21 on chromosome 8 (HR = 1.93, 95% CI 1.23, 3.02, Wald’s p = 0.004), SMC1B on chromosome 22 (HR = 3.37, 95% CI 1.91, 5.94, Wald’s p < 10-4), and STAG1 on chromosome 3 (HR = 1.74, 95% CI 1.04, 2.89, Wald’s p < 0.05). However, when controlled for percent genome alteration and pre-treatment serum PSA levels, only copy number loss of SMC1B was a significant predictor of biochemical relapse (HR = 2.95, 95% CI 1.62, 5.38, Wald’s p < 10-3). Conclusions: We identified a novel association of copy-number alterations in members of the Cohesin complex with biochemical recurrence following radical prostatectomy or image-guided radiotherapy. This points to the central role of Cohesin in cell-cycle and DNA damage pathways promoting prostate cancer progression.

Copy number alterations of P53, RB1, and MDM2 as prognostic markers in intermediate-risk prostate cancer

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Background: We interrogated copy number alternations (CNA) of p53, Rb1 and MDM2 as prognostic determinants of biochemical failure in localized intermediate-risk prostate cancer. Methods: Using Affymetrix Oncoscan array technology, we characterized copy number alterations (CNA) for 284 D’Amico-classified intermediate-risk prostate cancers. Of the 284 patients, 143 underwent image-guided radiotherapy (IGRT), while 141 underwent radical prostatectomy (RadP). Biochemical-relapse free survival (bRFS) was assessed as a clinical end-point, with biochemical failure defined using the Phoenix and AUA criteria for IGRT and RadP patients, respectively. Results: We observed allelic losses ofp53 and Rb1 in 23.9% (n = 68) and 31.0% (n = 88) and allelic gains of MDM2 in 3.17% (n = 9) in our cohort, respectively. 7.7% (n = 22), 1.1% (n = 3) and 0.4% (n = 1) of all cases exhibited concurrent losses of p53 and Rb1, p53 loss and MDM2 gain, and concurrent p53/Rb1 loss and MDM2 gain, respectively. Patients with allelic losses of p53, Rb1 and allelic gain of MDM2 loci exhibited increased percent genome aberration (PGA) (Mean 9.2 vs. 6.1 p < 0.001; 10.1 vs. 5.4 p < 0.001; 18.1 vs. 6.5 p < 0.001 respectively). Rb1 loss and MDM2 gain were not significant predictors of bRFS, independent of treatment modality. Allelic loss of p53 was predictive of poor bRFS in the RadP cohort (HR = 1.86, 95% CI 1.10-3.16, p = 0.022), but not for IGRT patients (HR = 1.16, 95% CI 0.63-2.12, p = 0.629). Additionally, patients in the RadP cohort with concurrent losses of p53 and Rb1 also had a higher likelihood of poorer bRFS (HR = 2.32, 95% CI 1.1-4.93, p = 0.029). On multivariate analysis, incorporating PGA and pre-treatment PSA, concurrent p53/Rb1 losses, but not single p53 loss, was prognostic for bRFS in patients who underwent RadP (p53/Rb1 losses, HR = 2.16, 95% CI 1.0-4.65, Wald's p = 0.05; p53loss, HR = 1.62, 95% CI 0.94-2.79, Wald's p = 0.08). Conclusions: In a cohort of men with intermediate-risk prostate cancers, we identified an unfavourable subgroup of patients harbouring concurrent copy number losses of p53 and Rb1 that was associated with an adverse prognosis of biochemical failure following radical prostatectomy.

Abstract A10: The myc post-translational landscape: How novel gain-of-function mutants are revealing new stability and functional regulatory systems

The c-MYC (MYC) oncogene plays an important role in tumorigenesis and is implicated in &gt;50% of all human cancers. Deregulation of MYC can occur through abnormally high expression levels, but also through oncogenic lesions in upstream signaling cascades. The study of these signaling pathways have provided an alternative approach for the development of MYC-targeted therapeutics. For example, the study of post-translational modifications (PTMs) of MYC, such as P-T58 and the T58A gain-of-function mutant, identified FBXW7 as a tumor suppressor and the deubiquitinating enzyme USP28 as a therapeutic target.

We considered that MYC is highly modified post-translationally and that unknown mechanistic pathways may be modifying residues, in addition to T58, in order to control MYC stability and/or function. These undiscovered pathways may therefore provide additional opportunities for the development of MYC-targeted therapeutics. These considerations led to recent work in the Penn lab that uncovered clusters of negatively regulating residues of MYC function. These residues include S71/S81, a cluster of residues referred to as MYC-4 (T343, S344, S347 and S348) and a cluster of 6 lysine residues (6K) at the C-terminal end of MYC (K298, K317, K323, K326, K341 and K355). These negatively regulating residues were characterized using alanine (S71/S81 and 340 cluster) and arginine (C-terminal lysines) substitution mutants in our established transformation assays. The S71/S81A and MYC-4A mutants scored with having gain-of-function activity in comparison to wild-type MYC in multiple transformation assays including growth in soft agar and the disruption of regular acini formation using a normal, immortalized MCF10A cell line. In addition, these mutants were shown to regulate additional genes compared to wild-type MYC using genome-wide mRNA expression analysis of MCF10A acini, suggesting that these MYC proteins have gained additional transcriptional targets. Additionally, substitution of the C-terminal lysine residues with arginine (6KR) also revealed gain-of-function activity. 6KR expressing MCF10A and SH-EP cells had increased anchorage-independent growth compared to cells expressing wild-type MYC and was also more potent in promoting xenograft tumor growth of Rat1A and SH-EP cells. Interestingly, all three mutants do not have extended half-lives as seen with T58A, suggesting that functional activity and not stability is contributing to these transformative phenotypes.

The above mutants reveal that each of S71/S81, MYC-4 and C-terminal 6K residues are critically important for the negative regulation of MYC-induced transformation. To further explore these regions of MYC, we used mass spectrometry to identify post-translational modifications that occurred on MYC in growing cells. These data confirm phosphorylation events on S71/81 as well as at MYC-4A. Strikingly, three modifications were directly observed on three of the six lysine residues; acetylation of lysine 323, ubiquitylation of lysine 355 and SUMOylation of lysine 326. The importance of these modifications and the roles that these modifications have in regulating MYC activity are currently under investigation using our established transformation assays. I now aim to understand the contribution of single or multiple modifications within the indicated clusters and how these modifications modulate MYC activity.

Citation Format: Corey Lourenco, Amanda Wasylishen, Michelle Chan-Seng-Yue, Christina Bros, Dharmendra Dingar, William Tu, Manpreet Kalkat, Pak-Kei Chan, Peter Mullen, Brian Raught, Paul Boutros, Linda Penn. The myc post-translational landscape: How novel gain-of-function mutants are revealing new stability and functional regulatory systems. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A10.

Abstract 2490: Integrative systems analysis of HPV+ and HPV- oropharyngeal carcinomas

BACKGROUND: Over half of oropharyngeal carcinomas (OPCs) are linked to high-risk human papillomavirus (HPV) infection. As compared to their HPV-positive (HPV+) counterparts, HPV-negative (HPV-) OPCs are associated with significantly worse survival, inferior treatment response and a distinct molecular expression profile. There are currently considerable efforts underway to personalize treatment based on HPV status; however, this remains challenging as the current understanding of the different biological mechanisms in HPV+ vs. HPV- OPCs is limited. Hence, a comprehensive proteomic analysis was performed, utilizing archival OPC tissues, in order to acquire greater insights into the distinct biological pathways.

METHODS: Global protein expression profiling was conducted on 26 HPV- and 27 HPV+ pre-treatment formalin-fixed paraffin-embedded (FFPE) OPCs using an automated 5-step Multidimensional Protein Identification Technology (MudPIT) procedure on a LTQ-Orbitrap XL. Protein quantification was achieved by adjusted spectral counting. Differentially expressed proteins (p&lt;0.05) were classified into functionally enriched categories and interaction networks using GeneMania. Finally, differential expression of 4 proteins was evaluated by immunohistochemistry (IHC) on an independent cohort of 17 HPV- and 12 HPV+ pre-treatment FFPE OPC biopsies.

RESULTS: Among the 2633 high confidence protein groups identified, 174 were significantly differentially expressed in HPV+ vs. HPV- OPCs. Functional enrichment analysis of these proteins demonstrated enrichment of cell cycle, DNA repair, cytokine signaling, apoptosis, DNA packaging, and metabolism proteins. These results were in concordance with a previous publication of pooled OPCs (Slebos et al, 2012). In addition, utilizing The Cancer Genome Atlas (TCGA) data, we determined that the relative expression levels of many of these proteins could be attributed to changes in copy number, methylation, mRNA, or mutation profiles. Next, the top 4 proteins were selected for verification based on concordance with these datasets and reported biological relevance. Selected proteins are involved in actin assembly, purine metabolism, differentiation, and cell migration and invasion. As a result, the differential expression of 2 proteins was successfully validated by IHC, while 2 additional proteins exhibited the same trend as in the discovery cohort.

CONCLUSION: This study provides the most in-depth and integrated protein-centric view of HPV+ and HPV- OPC. As a key finding, we highlight the identification of an actin assembly oncoprotein reported to be involved in a targetable radioresistance pathway. We hypothesize that this pathway is preferentially activated in HPV- OPCs. Hence, future experiments will focus on validating the in vivo observed expression pattern of this protein in vitro, and manipulating its expression to overcome radioresistance in OPC models.

Citation Format: Lusia Sepiashvili, Angela Hui, Wei Shi, Wei Xu, Daryl Waggot, Paul Boutros, Alex Ignatchenko, Vladimir Ignatchenko, Shao Hui (Sophie) Huang, John Waldron, Brian O'Sullivan, Jonathan C. Irish, Fei-Fei Liu, Thomas Kislinger. Integrative systems analysis of HPV+ and HPV- oropharyngeal carcinomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2490. doi:10.1158/1538-7445.AM2014-2490

A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing

Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the genetic changes in a human papillomavirus- (HPV-)positive and an HPV-negative head and neck tumor. Methods. DNA was extracted from the blood and primary tumor of a patient with an HPV-positive tonsillar cancer and those of a patient with an HPV-negative oral tongue tumor. Exome enrichment was performed using the Agilent SureSelect All Exon Kit, followed by sequencing on the ABI SOLiD platform. Results. Exome sequencing revealed slightly more mutations in the HPV-negative tumor (73) in contrast to the HPV-positive tumor (58). Multiple mutations were noted in zinc finger genes (ZNF3, 10, 229, 470, 543, 616, 664, 638, 716, and 799) and mucin genes (MUC4, 6, 12, and 16). Mutations were noted in MUC12 in both tumors. Conclusions. HPV-positive HNSCC is distinct from HPV-negative disease in terms of evidence of viral infection, p16 status, and frequency of mutations. Next-generation sequencing has the potential to identify novel therapeutic targets and biomarkers in HNSCC.

Abstract 2311: microRNA-196b regulates HOXB7 in cervical cancer

Introduction: microRNAs (miRNAs) have been shown to play an important biological role in many human malignancies. The down-regulation of miR-196b has been previously reported in cervical cancer (CaCx), but its contribution to tumor progression remains unelucidated. Materials and Methods: miRNA expression was measured in frozen tissues from CaCx biopsies (n=79) and normal cervix (n=11), plus three CaCx cell lines (ME-180, SiHa and HT-3) using a quantitative real-time PCR (qPCR) approach simultaneously measuring 377 miRNAs. SiHa and ME-180 cells were transfected with 30 nmol/L of pre-miR-196b, pre-miR Negative Control (NC), siHOXB7, siVEGF, or Negative Control siRNA. Cell viability, clonogenicity and migration/invasion were analyzed using the Trypan blue exclusion assay, clonogenic assay and trans-well migration assays, respectively. Protein levels of HOXB7 and VEGF were measured by immunoblotting and ELISA, respectively. To determine candidate mRNA targets of miR-196b, a tri-modal approach was utilized by combining: a) all predicted targets from five target prediction databases; b) genes upregulated in CaCx patients; and c) genes down-regulated after in vitro miR-196b over-expression. A luciferase reporter assay was used to confirm the binding of miR-196b to the HOXB7 3′ UTR. Tumor formation was monitored in xenograft tumors in SCID mice; CD31 and Ki67 immunostaining were performed on tumors 25 days after implantation. Results: Significant down-regulation of miR-196b was observed in the CaCx cells lines and tissues. Patients with low miR-196b expression (n=39) experienced worse disease-free survival compared to those with high (n=39) miR-196b expression (p=0.02, HR=0.39). Pre-miR-196b transfection reduced cell viability (25% after 48h; 41% after 72h), clonogenicity (57%) and invasion (32% vs. 63% for cells treated with NC). In vivo, pre-miR-196b slightly decreased tumor growth, but associated with significantly reduced CD31 (69%) and Ki-67 expression (46% vs. 53% for NC cells). The luciferase reporter assay verified that HOXB7 is a direct and specific target of miR-196b. Decreased VEGF mRNA (43%) and protein (78%) levels after HOXB7 knockdown demonstrated that VEGF was a downstream mediator of HOXB7 activation. siRNA knockdown of HOXB7 or VEGF recapitulated the biological effects of miR-196b over-expression, including reduced cell viability (66% for siHOXB7 at 72h; 60% for VEGF at 72h), clonogenicity (69% for siHOXB7; 78% for siVEGF) and invasion (52% for siHOXB7 and 42% for siVEGF vs. 74% for Negative Control cells); thus corroborating the miR-196b/HOXB7/VEGF axis in CaCx progression. Conclusion: We have newly identified the miR-196b/HOXB7/VEGF pathway as an important dysregulated axis contributing to human CaCx progression; hence therapeutic targeting of this pathway could potentially improve patient outcome.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2311. doi:1538-7445.AM2012-2311

Abstract 3184: Whole genome sequencing of low-input fresh frozen prostate cancer biopsies

Prostate cancer is the most commonly diagnosed malignancy among men in the United States. Due to an aging population, prostate cancer incidence has been increasing, with an estimated 200,000 men being diagnosed in 2010 and more than 32,000 deaths resulting from this disease. Better predictors of patient prognosis and treatment outcome are required to individualize prostate cancer treatment. High-throughput genomic sequence-based approaches offer a unique opportunity to identify biomarkers of disease-progression, thereby enabling more individualized therapy. The Canadian Prostate Cancer Genome Network (CPC-GENE) is an outcomes-based initiative that will sequence 500 specimens from 350 prostate cancer patients over a 5-year time span. Previously, whole genome sequencing efforts from biopsy specimens have been hindered by insufficient quantities of extracted DNA required as input for sequencing library construction. As a proof of concept to demonstrate the ability to sequence low input amounts of DNA from prostate biopsies, whole genome sequencing has been initiated for 50 prostate tumor biopsy samples along with their matched blood-derived reference sample. An on-bead sample preparation protocol was optimized using decreasing quantities of input DNA and used to construct sequencing libraries from as low as 100ng of DNA derived from macrodissected fresh frozen prostate biopsies (&gt;70% cellularity). Sequencing is performed on the Illumina HiSeq 2000 platform to generate coverage depths of 50x for tumor samples and 30x for reference samples. Following alignment using NovoAlign and variant-calling using GATK, we compared our results to genotyping-array results generated using the Affymetrix OncoScan platform. Single-nucleotide variants detected using arrays were validated &gt;99% of the time by sequence data, confirming that the use of a low-input library did not hinder mutation detection. Sequencing does not exhibit significant genome-wide coverage biases, and CNV calls were compared between the genotyping arrays and the next-generation sequencing data. Outcomes from the sequencing and analysis of the initial 50 sample sets will similarly be applied over a 5-year period to characterize an additional 450 prostate specimens. The ability to whole genome sequence specimens where minimal amounts of extracted DNA exist presents new opportunities to sequence many samples previously deemed unusable, while also providing encouraging prospects for whole genome sequencing applications for future studies using biopsy specimens.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3184. doi:1538-7445.AM2012-3184

Role of nitric oxide in the attenuated pressor responses of pregnant or sodium-deplete sheep

Reduced pressor responsiveness to angiotensin II (Ang II) during pregnancy and sodium depletion is a well-known but little understood phenomenon; whether the same mechanisms are involved in both situations is unclear. In pregnant humans, altered vascular reactivity to norepinephrine (NE) has also been demonstrated. Nitric oxide (NO) has been implicated in the modulation of blood pressure (BP) and the maintenance of vascular tone and may be involved in these attenuated responses. We examined the role of NO in the pressor responses to (a) Ang II (5, 10, 25, 50 micrograms/h) and NE (0.32, 0.65, 1.62, 3.24 mg/h) in pregnant and postpartum sheep, and (b) to Ang II (5, 7, 5, 10, 25, 50 micrograms/h) in sodium-replete sheep and sheep made sodium deplete by 24 h of parotid salivary drainage. Vascular NO production was inhibited by pretreatment with N omega-nitro-L-arginine (NOLA 10 mg/kg), a NO-synthase inhibitor. Pregnancy significantly reduced (p < 0.001) pressor responses to Ang II, which ranged from 5.1 +/- 0.2-30.6 +/- 1.2 mm Hg as compared with postpartum increases of 10.3 +/- 0.5-52.2 +/- 3.4 mm Hg. Pretreatment with NOLA partially restored Ang II responses to postpartum levels. Pregnancy did not alter pressor responses to NE. Sodium depletion also significantly reduced responses to Ang II by the same amount as in pregnancy, and these responses returned to normal with pretreatment with NOLA. NO thus has a role in modulating the attenuated pressor responses to Ang II in pregnant and sodium-deplete sheep.

Bacteriuria localization and response to single-dose therapy in women

One hundred women with bacteriuria had the infection localized by the "bladder-washout" technique. Thirty-six of the 39 with infection confined to the bladder were cured with a single intramuscular injection of 500 mg of kanamycin sulfate, whereas 47 of the 65 patients with infection originating from their upper tract relapsed almost immediately. None of the seven patients with abnormal pyelograms and associated upper tract infection was cured with kanamycin. These results suport the hypothesis that bladder infections in women can be readily cured with a very short course of therapy. Women who relapse after a single injection of kanamycin almost always have renal infection.

A comparison of trimethorprim-sulfamethoxazole with sulfamethoxazole alone in infections localized to the kidneys

Ninety patients with urinary tract infections were treated in a randomized double-blind study with either a combination of trimethoprim and sulfamethoxazole (TMP-SMX) or sulfamethoxazole alone (SMX). Thirty of 42 patients treated with TMP-SMX were cured by the time of follow-up compared with 26 of 48 treated with SMX alone. Of the 29 patients infected with SMX-resistent organisms, the combination TMP-SMX cured 12 of 17, whereas SMX alone cured 2 of 12. Of the 61 patients infected with SMX-sensitive organisms, TMP-SMX cured 18 of 25; SMX alone cured 24 of 36. In 50 women the infection was found localized to The upper urinary tract by the use of the Fairley bladder washout technique. TMPsmx cured 16 or 24 of these patients with proved upper tract infections and SMX alone cured 11 of 26. Although none of these differences were significant, TMP-SMX appears to be an effective drug combination for the therapy of proved upper tract infection and is also effective in eradicating sulfonamide-resistant organisms.