Clinical utility of molecular subtyping of pancreatic cancer

Background: Pancreatic Cancer remains a dismal disease with the worst survival outcomes of any solid organ malignancy. The most common form is Pancreatic Ductal Adenocarcinoma (PDAC) which has a 5-year survival of only 5% and a median survival in the region of 6 months after diagnosis. The majority of patients present with metastatic or locally advanced disease that is unsuitable for surgical resection. The only potential curative treatment is surgery, yet only around 15 – 20% of patients undergo surgical resection. Of these, half of patients develop disease recurrence at 1 year, and only around 20% survive 5 years after surgery. These figures demonstrate that current treatment strategies are inadequate and better therapies and treatment selection tools are urgently needed. Recent large-scale next generation sequencing studies of pancreatic cancer have revealed a small set of consistent mutations found in most pancreatic cancer genomes, and beyond that a low prevalence of targetable mutations for current therapies. Transcriptomic analysis has revealed molecular subtypes with significant differences in gene expression and molecular pathways. This may explain the failure of conventional clinical trial designs to show any meaningful survival benefit, except in small and undefined patient sub-groups. With the development of next generation sequencing technology, genomic sequencing and analysis can be performed in a clinically meaningful turnaround time. This can identify therapeutic targets in individual patients and personalise treatment selection. Incorporating pre-clinical discovery and molecularly guided therapy into clinical trial design has the potential to significantly improve outcomes in this lethal malignancy. Aims: The aims of this PhD thesis are: 1. examine the clinical and pathological features of molecular subtypes of PDAC to identify novel biomarkers to select patients for surgical resection; 2. investigate therapeutic opportunities targeting DNA damage response machinery; and 3. develop clinical strategies to translate these findings into personalised clinical trials. Results: Early recurrence after surgery, particularly liver metastases, and metastatic presentation were strongly associated with gene expression sets that define the squamous subtype of PDAC (P < 0.001). Lung recurrence, localised disease and long-term survival were associated with the classical pancreatic subtype and an anti-tumour immune response (P < 0.001). Patients with tumours of the body and tail of pancreas had significantly worse survival than those with pancreatic head tumours (12.1 versus 22.0 months; P = 0.001). Location in the body and tail was associated with the squamous subtype of PDAC. Body and tail PDACs are enriched for gene programmes involved in tumour invasion and epithelial-to-mesenchymal transition, as well as features of poor antitumour immune response. In three independent PDAC cohorts (total participants = 1184) the relationship between aberrant expression of pro-metastatic proteins S100A2 and S100A4 and survival was assessed. High expression of either S100A2 or S100A4 were independent poor prognostic factors in a training cohort of 518 participants and two independent validation cohorts (Glasgow, n = 198; German, n = 468). A preoperative nomogram incorporating S100A2 and S100A4 expression predicted survival as well as nomograms derived using post-operative clinicopathological variables. DNA damage response (DDR) deficient cell lines and xenograft models were highly sensitive to Cisplatin and PARP inhibitors. A novel transcriptional signature of replication stress was generated and associated with the squamous subtype in both cell lines and bulk tumour samples. This signature predicted differential responses to cell cycle inhibitors of ATR, WEE1, CHK1, CDK4/6 and PLK4. Response to these inhibitors were independent of DDR status, but strongly associated with replication stress. These findings were used to inform the design of a phase Ib / II clinical trial targeting DDR deficiency and Replication Stress using PARP and ATR inhibitors in PDAC. A tissue acquisition protocol using endoscopic ultrasound guided biopsies for next generation sequencing was designed and allowed multi-omic characterisation of PDAC. This has been implemented within the PRECISION-Panc master protocol to allow molecular profiling of all patients, irrespective of disease stage, and facilitate precision medicine trials in PDAC. Conclusions: Significant phenotypic differences exist between molecular subtypes of PDAC and these differences informed the design of novel selection tools for surgical resection. Proof of concept data demonstrates DDR deficiency and increased Replication Stress to be attractive targets in PDAC. Therapeutic vulnerabilities extend beyond platinum chemotherapy and can be targeted with novel small molecule inhibitors, with independent biomarkers that predict response to agents targeting either DDR or replication stress. This has led to the design and development of personalised medicine trials via the PRECISION-Panc platform targeting DDR and Replication stress that will open in early 2019