Julie Livingstone

Spatial genomic heterogeneity within localized, multifocal prostate cancer

Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer to delineate new oncogenes or tumor suppressors. We initially determined the copy number aberration (CNA) profiles of 74 patients with index tumors of Gleason score 7. Of these, 5 patients were subjected to whole-genome sequencing using DNA quantities achievable in diagnostic biopsies, with detailed spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity in focal genomics. Multifocal tumors are highly heterogeneous for single-nucleotide variants (SNVs), CNAs and genomic rearrangements. We identified and validated a new recurrent amplification of MYCL, which is associated with TP53 deletion and unique profiles of DNA damage and transcriptional dysregulation. Moreover, we demonstrate divergent tumor evolution in multifocal cancer and, in some cases, tumors of independent clonal origin. These data represent the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcome and inform the development of novel biomarkers that reflect individual prognosis.

Genomic hallmarks of localized, non-indolent prostate cancer

Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this heterogeneity. Here we analysed 200 whole-genome sequences and 277 additional whole-exome sequences from localized, non-indolent prostate tumours with similar clinical risk profiles, and carried out RNA and methylation analyses in a subset. These tumours had a paucity of clinically actionable single nucleotide variants, unlike those seen in metastatic disease. Rather, a significant proportion of tumours harboured recurrent non-coding aberrations, large-scale genomic rearrangements, and alterations in which an inversion repressed transcription within its boundaries. Local hypermutation events were frequent, and correlated with specific genomic profiles. Numerous molecular aberrations were prognostic for disease recurrence, including several DNA methylation events, and a signature comprised of these aberrations outperformed well-described prognostic biomarkers. We suggest that intensified treatment of genomically aggressive localized prostate cancer may improve cure rates.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimers disease. The Alzheimers disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state‐of‐the‐art in predicting cognitive outcomes in Alzheimers disease based on high dimensional, publicly available genetic and structural imaging data. This meta‐analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.

Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories

Germline mutations in the BRCA2 tumour suppressor are associated with both an increased lifetime risk of developing prostate cancer (PCa) and increased risk of aggressive disease. To understand this aggression, here we profile the genomes and methylomes of localized PCa from 14 carriers of deleterious germline BRCA2 mutations (BRCA2-mutant PCa). We show that BRCA2-mutant PCa harbour increased genomic instability and a mutational profile that more closely resembles metastastic than localized disease. BRCA2-mutant PCa shows genomic and epigenomic dysregulation of the MED12L/MED12 axis, which is frequently dysregulated in metastatic castration-resistant prostate cancer (mCRPC). This dysregulation is enriched in BRCA2-mutant PCa harbouring intraductal carcinoma (IDC). Microdissection and sequencing of IDC and juxtaposed adjacent non-IDC invasive carcinoma in 10 patients demonstrates a common ancestor to both histopathologies. Overall we show that localized castration-sensitive BRCA2-mutant tumours are uniquely aggressive, due to de novo aberration in genes usually associated with metastatic disease, justifying aggressive initial treatment.

Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities

The mammary epithelium depends on specific lineages and their stem and progenitor function to accommodate hormone-triggered physiological demands in the adult female. Perturbations of these lineages underpin breast cancer risk, yet our understanding of normal mammary cell composition is incomplete. Here, we build a multimodal resource for the adult gland through comprehensive profiling of primary cell epigenomes, transcriptomes, and proteomes. We define systems-level relationships between chromatin–DNA–RNA–protein states, identify lineage-specific DNA methylation of transcription factor binding sites, and pinpoint proteins underlying progesterone responsiveness. Comparative proteomics of estrogen and progesterone receptor–positive and –negative cell populations, extensive target validation, and drug testing lead to discovery of stem and progenitor cell vulnerabilities. Top epigenetic drugs exert cytostatic effects; prevent adult mammary cell expansion, clonogenicity, and mammopoiesis; and deplete stem cell frequency. Select drugs also abrogate human breast progenitor cell activity in normal and high-risk patient samples. This integrative computational and functional study provides fundamental insight into mammary lineage and stem cell biology.

Abstract B100: High-risk pathologic and genomic features of BRCA2-mutant prostate cancer

Germline BRCA mutations are associated with an increased risk of developing aggressive prostate cancer with poor clinical outcomes. However, the mechanisms by which BRCA mutations contribute to clinical aggressiveness are not completely understood. Previously, we showed that BRCA2-mutant prostate cancers often have intraductal carcinoma of the prostate (IDC-P), a distinct growth pattern of prostate cancer that is associated with adverse clinical features. Despite this, IDC-P is not routinely reported in pathology and its functional significance remains poorly understood. Thus, we investigated the clinical relevance of IDC-P as well as the underlying molecular features of localised BRCA2-mutant prostate cancers with and without IDC-P. To define the prevalence of IDC-P across cohorts of sporadic and familial prostate cancer, we conducted a systematic review in accordance with PRISMA guidelines. This analysis of over 7,000 patient specimens revealed that the prevalence of IDC-P rises from 2.1% in low-risk cohorts to 56% in cohorts with metastatic/recurrent disease. Since these data showed that IDC-P is a prominent feature of high-risk prostate cancer, we next studied the biologic features of IDC-P using patient-derived xenografts (PDXs). PDXs were established from three patients with germline BRCA mutations and compared to PDXs from four high-risk sporadic cases. IDC-P was successfully grown within the PDXs, maintaining its characteristic morphologic features for up to 800 days. Using classical castration-hormone regeneration experiments, we showed that IDC-P contains a subset of “castrate-tolerant” cells that persist after androgen deprivation and subsequently regenerate the tumor. Notably, we found that PDXs derived from BRCA-mutant tumors have the same response to androgen deprivation as sporadic cases. To further investigate the aggressiveness of BRCA2-mutant tumors, we profiled the genomes and methylomes of localized prostate cancers from 14 germline BRCA2-mutation carriers and compared them to 200 sporadic prostate cancers. BRCA2-mutant prostate cancers had elevated genomic instability and global hypomethylation compared to sporadic tumors. In addition, some genomic features of BRCA2-mutant tumors more closely resembled metastatic than localized disease. Importantly, negative prognostic factors were enriched in BRCA2-mutant prostate cancers harboring IDC-P. Sequencing of macrodissected IDC-P and invasive carcinoma revealed that these two pathologies arise from a common tumor clone and diverge later in tumor evolution. In summary, this work demonstrates that IDC-P pathology and genomic instability are two high-risk features of localized BRCA2-mutant prostate cancers. Given the high prevalence of IDC-P in high-risk patient cohorts, including BRCA2-mutation carriers, IDC-P warrants greater recognition and reporting as this may improve patient risk stratification. Citation Format: Laura H. Porter, Mitchell G. Lawrence, Carmel Pezaro, Heather Thorne, Dragan Ilic, Melissa Papargiris, Michael Fraser, Julie Livingstone, Declan G. Murphy, Mark Frydenberg, Damien Bolton, Daniel Moon, David Clouston, Theo van der Kwast, Paul C. Boutros, Robert G. Bristow, Renea A. Taylor, Gail P. Risbridger. High-risk pathologic and genomic features of BRCA2-mutant prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr B100.

Abstract A28: Mutational landscape of TP53 in localized prostate cancer

Background: We performed a comprehensive interrogation of the mutational landscape of TP53 in the context of localized prostate cancer using a large clinical/molecular-paired dataset from the Canadian Prostate Cancer Gene Network (CPC-GENE). We further test the associations of TP53 mutations with outcomes post-image-guided radiotherapy (IGRT) or radical prostatectomy (RadP). Methods: Copy number status (N = 284), single nucleotide variants (SNV) (N = 123), methylation status (N = 117), and mRNA abundance profiling (N = 115) were assessed using the Affymetrix Oncoscan FFPE express v3.0 assay, whole genome sequencing (up to 100-200x), Illumina 450K methylation array, and Affymetrix HuGene 2.0 array, respectively. Patient cohort comprised of NCCN-defined intermediate-risk prostate cancer who underwent either IGRT (N = 146) or RadP (N = 137). Biochemical-relapse free rate (bRFR) was assessed as the primary clinical end-point. Results: We identified 65 cases (22.9%) with mono-/bi-allelic copy number alteration (CNA) of TP53, and 7 cases (5.7%; 6 non-synonymous and 1 splice variant) with TP53 SNV in our cohort, which was comparable with the TCGA (30% CNA, 7% SNV) and MSKCC (17% CNA, 2.9% SNV) cohorts of low to high-risk localized prostate cancers. Epigenomic profiling revealed specific sites of DNA hypermethylation (β-value >0.7) within the body and 59 UTR gene-regions, while the TSS gene-region was unaffected. Genomic mutations (CNA and/or SNV) of TP53 were associated with global genomic instability (percent genome aberration of 9.5 vs 6.4, p = 0.001) and reduced mRNA levels (mRNA abundance Z-Score: -0.58 vs 0.22, p-value = 0.0011), but methylation status had no consequence on these indices. Neither TP53 genomic mutations (HR = 1.35, 95% CI 0.91-2.00, Wald9s p = 0.14) nor mRNA abundance (HR = 1.39, 95% CI 0.71-2.75, Wald9s p = 0.34) was associated with bRFR on multivariable analyses. However, stratification by combinatorial genomic and mRNA abundance indices identified an unfavorable subgroup that was associated with poorer bRFR on multivariable analysis (HR = 2.95, 95% CI 1.42-6.12, Wald9s p = 0.004). Conclusions: This is the first comprehensive interrogation of the mutational landscape of TP53 in localized prostate cancer. Our findings suggest that functional TP53 loss at both the copy number and transcription level accounts for a subset of non-indolent localized prostate cancer. Citation Format: Osman Mahamud, Melvin L.K Chua, Stephane Supiot, Emilie Lalonde, Alan Dal Pra, Alejandro Berlin, Michele Orain, Valerie Picard, Helene Hovington, Alain Bergeron, Yves Fradet, Bernard Tetu, Gaetano Zafarana, Alice Meng, Julie Livingstone, Melania Pintilie, Michael Fraser, Theodorus van der Kwast, Paul C. Boutros, Bristow G. Robert. Mutational landscape of TP53 in localized prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr A28.

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

96 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 obse...

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

117 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 los...

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

Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA 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, Gleasons 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, Walds 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.