Translational Oncogenomics - Rob Bristow

Rob obtained his BSc in 1986 at the University of Toronto, where he went on to complete his Medical Degree in 1992 and later his PhD in Medical Biophysics in 1997. He has since been a Clinician-Scientist and Professor within the Departments of Radiation Oncology and Medical Biophysics at the University of Toronto. As a Senior Scientist at the Princess Margaret Cancer Centre he treated genitourinary cancers. Rob is twice a Canadian Foundation for Innovation (CFI) awardee. He was made a Canadian Cancer Society Research Scientist in 2004 and an ESTRO Honorary Fellow in 2011.

He became the Director of the Manchester Cancer Research Centre (MCRC) in August 2017 to develop a new cancer strategy and lead the continued growth of the MCRC.

Introduction


Control of genome stability requires careful coordination between cell cycle checkpoint control and DNA repair mechanisms. Defects in the repair of DNA double-stranded breaks have been associated with acquiring genetic instability, particularly in genes responsible for homologous recombination (HR) such as BRCA1 and BRCA2. Defects in these genes lead to an increased risk of ovarian and breast cancer in women and prostate cancer in men. BRCA2- associated prostate cancers have a particular poor outcome with more than 50% of men dead at 5 years after local therapy. More recently, other DNA repair gene mutations or dysfunction have been linked to aggressive prostate cancer leading to castrate resistance and the metastatic phenotype.


Our group is therefore interested in the mechanisms through which hypoxia and defects or mutations in DNA repair genes lead to prostate cancer aggression.

Figure: Prostate tumour bearing germline mutation of DNA repair genes.

Overview

 

Almost 50,000 men living in the UK will be diagnosed with prostate cancer every year, and since the 1990’s the trend has been one of increasing incidence. Localised prostate cancer represents a broad spectrum of disease, and high-risk cancers have a 10- to 15-fold increased probability of prostate cancer specific mortality and harbouring metastases, which may go undetected at the point of diagnosis. Yet despite the use of stringent clinical criteria to place patients into prognostic groups, 30-50% of men can still fail precision radiotherapy or surgery due to local resistance and/or systemic spread. Clearly, there is a need to develop new biomarkers that give an insight into heterogeneity of outcomes in prostate cancer patients.

There is growing interest in the potential of genes involved in maintenance of genome fidelity to form the basis of new biomarkers. In addition, tumour-associated hypoxia represents an endogenous stress that is associated with genome instability and understanding the mechanistic basis for this correlation is a key aim of our research. In recent years, there has been a growing appreciation of the role of DNA repair genes in the biology of prostate cancer (PCa). In depth analyses of the prostate cancer genome have shown that somatic mutations in DNA repair genes are relatively frequent and are more common in incurable, castrate-resistant disease (mCRPC) than in primary cancers. Concordantly, it has been shown that men carrying germline mutations in such genes are at a higher risk of developing prostate cancers that progress to become metastatic. The presence of hypoxia in PCa is also correlated with a poor prognosis and several factors may contribute to this observation, including resistance to radiotherapy leading to failure of local control, impaired DNA repair, and adaptive responses that promote metastasis. As hypoxia is tightly correlated with levels of genome instability across a range of cancer types, we also wish to understand the interaction between the tumour microenvironment (TME) and the mutator phenotype. Our lab therefore studies genotype-phenotype interactions using primary or ex vivo human prostate cancer models for multi-omic and functional genomic studies.

 

Models for Chromosomal Instability: TME and Genetics

We are driving translational studies in prostate cancer - local and systemic aggression - within the PCUK-funded HYPROGEN trial in Manchester at the Christie NHS Foundation Trust (Figure 1). The biomarker assessments of this trial are designed to answer the question as to how hypoxia can drive LOH and chromosomal instability in the primary and metastases. We use a small molecule marker of hypoxia (Pimonidazole), which is administered to prostate cancer patients prior to their treatment with local and systemic treatment for metastatic hormone sensitive, M1 disease or high-risk localised prostate cancer. This allows assessment of hypoxia in biopsy or radical prostatectomy specimens collected as part of their standard treatment. Detailed analyses with Prof David Wedge (Genomics, Division of Cancer Sciences) and Dr Pedro Oliveira (Pathology, Christie NHS Foundation Trust) will clarify the relationships between levels of oxygenation and DNA repair, genome instability and metastatic spread. Parallel studies are studying mutations and methylation in ctDNA and CTCs to determine whether aggressive clones can be detected at diagnosis using a liquid biopsy in collaboration with Prof Caroline Dive (CRUK MI Cancer Biomarker Centre). Such studies will allow us to better understand the potential use of hypoxia as a biomarker to predict prognosis and to guide improved treatment strategies in prostate cancer.

Figure 1: The HYPROGEN trial aims to characterise the role of hypoxia in driving the early metastatic spread of tumours. Patients with oligo-metastatic disease are recruited to the study prior to receiving any treatment. Hypoxia can be assessed by means of the tracer molecule, pimonidazole, which is administered before biopsies are taken from both the primary tumour and selected bone metastases. Genomics and transcriptomics will then be applied to provide insights into the relationship between hypoxia, genomic instability and metastatic spread.

 

Increasing genetic instability leads to increased organoid size and resistance to experimental radiotherapy based on our work with hTERT-immortalised primary prostate cancer cells with activated oncogenes (cMYC) or inactivated tumour suppressor genes (TP53, PTEN). In other work, we have shown that prolonged treatment of hypoxia in vitro can give rise to new genetic clones with varying growth in autonomy and invasion. This suggests that hypoxia can modify chromosomal instability and current efforts are underway to delineate the mechanistic reason behind this observation using a multi-omic approach combining whole genome sequencing with transcriptomics, proteomics and metabolomics (Figures 2 and 3).

Figure 2: A. Next-generation sequencing has revealed increased levels of genome instability in cells exposed to hypoxia. Clones with high rates of genomic alteration are being assessed for tumourigenicity and invasive phenotypes. B. Studies for mechanisms of chromosomal instability in hypoxic in vitro models.

 

Hereditary Syndromes and Prostate Cancer

Prostate cancer tumours that harbour BRCA2 mutations for example, are more likely to respond to PARP inhibitors or to Cisplatin compared with non-BRCA mutated tumours. On the other hand, tumours deficient in mismatch repair genes, in addition to showing great sensitivity to androgen blockade, may also be targetable by immune checkpoint inhibitors. There is great excitement in the potential clinical utility of genetic testing in prostate cancer and the current challenge is to consolidate prior studies with further evidence, both to support biomarker development and to provide a mechanistic framework for clinical observations. Although mutations in MMR genes are rare in PCa, the presence of mutations in one of the MMR genes (MSH2, MSH6, EPCAM, MLH1 or PMS2) has been correlated with MSI and adverse pathology in PCa – and overall, patients with Lynch syndrome are at two-fold higher risk of developing prostate cancer. Furthermore, given that the use of PD-1 inhibitors has been approved for treatment of gastro-intestinal tumours with MSI, the detection of MMR-deficient prostate cancers could have therapeutic implications, and there is great interest in developing new biomarkers that assess mismatch repair along with other metrics of genome stability.

Figure 3: Gradients of hypoxia can be detected in tumour biopsy material by monitoring the expression of GLUT-1, which is increased in hypoxic areas. The hypoxic phenotype can then be further explored by monitoring the expression of other genes in these areas –for example the DNA repair gene Rad51 as shown here. This technique can also be combined with the latest spatial transcriptomic techniques to provide detailed insights into the hypoxic tumour environment.

 

Our aim is to comprehensively characterise clinical material sampled from patients with germline DNA repair defects, and to develop matching pre-clinical models that allow experimental approaches. By collaborating with research collaborators at Manchester University NHS Foundation Trust and in Melbourne, we have assembled a unique collection of BRCA2 and MMR-deficient specimens for further study. We are carrying out a detailed interrogation of these samples including next-generation sequencing studies and spatial transcriptomics to define the relationship between LOH, secondary and tertiary genomic rearrangements, patterns of gene expression and risk status. We hope to better define the role of BRCA2 deficiency in driving aggressive disease and to uncover new possibilities for personalised therapy for this group of patients.

In addition, we are developing models of hereditary prostate cancer ex vivo by hTERT-immortalisation of normal prostate epithelium from germline carriers that undergo radical prostatectomy for prostate cancer (Figure 4). As these models form prostaspheres, 2D culture and 3D organoid phenotypes can be interrogated following additional activation of prostate cancer-related oncogenes (e.g. cMYC) or CRISPR knock-out of tumour suppressor genes (e.g. TP53, PTEN).

Figure 4: Our approach involves working with clinical specimens isolated from patient with high-risk prostate cancers such as those arising in men with germlines defects in DNA repair. We aim to identify the genetic drivers of high risk disease by undertaking a range of functional genomics approaches, and to explore novel treatment options for this group of patients.

 

Prostate Cancer Genomics and Chromosomal Gains

Many human disorders result from unbalanced chromosome abnormalities, in which there is a net gain or loss of genetic material amongst the 23 pairs of chromosomes. The resulting phenotypes are caused by the imbalance of one or more dosage-sensitive genes in a particular chromosomal segment. Somatic chromosomal imbalance instability leads to cancer initiation and progression and the gain of a single chromosomal unit can activate or inhibit cell proliferation, immune system activation and metastatic capacity. An exemplar is the chromosomal gain of the right arm of 8q (Chr.8q) in prostate, ovarian and breast cancer; this gain is associated with poor clinical outcome.

Up to 20% of prostate cancer cases present with Chr. 8q, which harbours the c-Myc oncogene with co-amplification of up to 30-40 other genes. This usually is detected by sequencing techniques based on bulk DNA from a tumour section, but whether sub-clones exist at a cellular level showing cell-to-cell heterogeneity for gains is not known. We are currently using molecular pathology approaches (in situ FISH, chromosomal instability assays, genomics and spatial transcriptomics) to understand the intra-prostatic cell heterogeneity of chromosomal gains using spatial ‘omics on tumour foci within individual patients’ prostate glands removed at surgery. We hypothesise that chromosomal gains are focal within the prostate cancers in which co-amplified genes work together to drive genetic instability with subsequent clonal selection and adaption into aggressive phenotypes. A better understanding of cell-to-cell heterogeneity could drive new therapies against aggressive subclones.

Functional genomic studies to validate pathology findings is an option using prostate epithelial cells (PrEC) transfected with engineered Human Artificial mini-Chromosomes (HACs). These HAC-Chr. 8q cells would mirror the genetics of Chr. 8q gains (e.g. a mini-chromosome, with c-Myc and other co-amplified genes) to inform upon genetic instability, mutations and cell growth autonomy. The work will be completed primarily in the Translational Oncogenomics laboratory in collaboration with Prof Patrick Cai (HAC systems; FSE-Manchester Institute of Biotechnology), Prof David Wedge and Dr Pedro Oliveira.

Publications

 

Bhandari V, Li CH, Bristow RG, Boutros PC; PCAWG Consortium. (2020)
Divergent mutational processes distinguish hypoxic and normoxic tumours. 
Nature Communication 11(1):737. PubMed abstract

Bhandari V, Hoey C, Liu LY, Lalonde E, Ray J, Livingstone J, Lesurf R, Shiah YJ, Vujcic T, Huang X, Espiritu SMG, Heisler LE, Yousif F, Huang V, Yamaguchi TN, Yao CQ, Sabelnykova VY, Fraser M, Chua MLK, van der Kwast T, Liu SK, Boutros PC, Bristow RG. (2019)
Molecular landmarks of tumor hypoxia across cancer types.
Nature Genetics 51(2):308-318. PubMed abstract

Hopkins JF, Sabelnykova VY, Weischenfeldt J, Simon R, Aguiar JA, Alkallas R, Heisler LE, Zhang J, Watson JD, Chua MLK, Fraser M, Favero F, Lawerenz C, Plass C, Sauter G, McPherson JD, van der Kwast T, Korbel J, Schlomm T, Bristow RG, Boutros PC. (2017)
Mitochondrial mutations drive prostate cancer aggression.
Nature Communications 8(1):656. PubMed abstract

Kron KJ, Murison A, Zhou S, Huang V, Yamaguchi TN, Shiah YJ, Fraser M, van der Kwast T, Boutros PC, Bristow RG, Lupien M. (2017)
TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer.
Nature Genetics 49(9):1336-1345. PubMed abstract

Chua MLK, Lo W, Pintilie M, Murgic J, Lalonde E, Bhandari V, Mahamud O, Gopalan A, Kweldam CF, van Leenders GJLH, Verhoef EI, Hoogland AM, Livingstone J, Berlin A, Dal Pra A, Meng A, Zhang J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Reuter VE, Fleshner N, Fraser M, Boutros PC, van der Kwast TH, Bristow RG. (2017)
A Prostate Cancer "Nimbosus": Genomic instability and SChLAP1 dysregulation underpin aggression of intraductal and cribriform subpathologies.
European Urology 72(5):665-674. PubMed abstract

Chua MLK, van der Kwast TH, Bristow RG. (2017)
Intraductal carcinoma of the prostate: anonymous to ominous.
European Urology 72(4):496-498. PubMed abstract

Murphy DG, Risbridger GP, Bristow RG, Sandhu S. (2017)
The evolving narrative of DNA repair gene defects: distinguishing indolent from lethal prostate cancer.
European Urology 71(5):748-749. PubMed abstract

Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, Huang V, Shiah YJ, Yousif F, Lin X, Masella AP, Fox NS, Xie M, Prokopec SD, Berlin A, Lalonde E, Ahmed M, Trudel D, Luo X, Beck TA, Meng A, Zhang J, D'Costa A, Denroche RE, Kong H, Espiritu SM, Chua ML, Wong A, Chong T, Sam M, Johns J, Timms L, Buchner NB, Orain M, Picard V, Hovington H, Murison A, Kron K, Harding NJ, P'ng C, Houlahan KE, Chu KC, Lo B, Nguyen F, Li CH, Sun RX, de Borja R, Cooper CI, Hopkins JF, Govind SK, Fung C, Waggott D, Green J, Haider S, Chan-Seng-Yue MA, Jung E, Wang Z, Bergeron A, Dal Pra A, Lacombe L, Collins CC, Sahinalp C, Lupien M, Fleshner NE, He HH, Fradet Y, Tetu B, van der Kwast T, McPherson JD, Bristow RG, Boutros PC. (2017)
Genomic hallmarks of localized, non-indolent prostate cancer.
Nature 541(7637):359-364. PubMed abstract

Taylor RA, Fraser M, Livingstone J, Espiritu SM, Thorne H, Huang V, Lo W, Shiah YJ, Yamaguchi TN, Sliwinski A, Horsburgh S, Meng A, Heisler LE, Yu N, Yousif F, Papargiris M, Lawrence MG, Timms L, Murphy DG, Frydenberg M, Hopkins JF, Bolton D, Clouston D, McPherson JD, van der Kwast T, Boutros PC, Risbridger GP, Bristow RG. (2017)
Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories.
Nature Communications 8:13671. PubMed abstract

Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MH, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG. (2015)
Spatial genomic heterogeneity within localized, multifocal prostate cancer.
Nature Genetics 47(7):736-45. PubMed abstract

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Postdoctoral Fellows
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Clinical Fellow
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Graduate Students
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