Epigenetic targeting in pancreatic ductal adenocarcinoma to overcome resistance to immunotherapies

Primary supervisor: Oliver Pearce, Queen Mary University of London

Secondary supervisor: David Propper, Queen Mary University of London, Gerard Evan, The Francis Crick Institute

Project

Pancreatic ductal adenocarcinoma (PDAC) is unresponsive to immunotherapy. This project aims to identify epigenetic modulating drugs that overcome this resistance and the fundamental mechanisms that these drugs perturb.

The unresponsiveness of PDAC to immune checkpoint blockade (ICB) is a product of interactions between cancer cells and cancer-associated fibroblasts (CAFs) which promote immunosuppression. Much evidence indicates that this immunosuppressed tumour microenvironment (TME) is epigenetically regulated [1]. The study will examine the ability of a panel of clinically tolerated drugs targeting various epigenetic processes to reverse features that correlate with immune unresponsiveness using 3D tissue culture models constructed to best represent the PDAC TME. The project will define the effects of epigenetic modification of the TME on transcription enhancers, gene transcription and downstream signalling pathways.

Background: There are now many clinically tolerated drugs that target various epigenetic processes that could be combined with immunotherapies to reverse the immune unresponsiveness of PDAC. A broad range of laboratory studies show that such approaches are effective in reversing immunosuppressed features. There are also 2 clinical studies that show this approach can work for some patients, although so far not in PDAC [2,3]. As there are many possible drugs, it is important to develop a preclinical 3D model of the immunosuppressed PDAC TME to test the relevant drugs.

Project: Establish immune exclusion reversal human model for PDAC. Tumours that have excluded immune effector cells – termed immune excluded- are generally resistant to ICB. Tumours with immune infiltration – termed immune inflamed phenotype – are often responsive to ICB. We have developed a decellularized tissue model that recreates the immune excluded phenotype and allows analysis of interventions that convert it to an immune inflamed phenotype [4.] We have developed this model for ovarian and breast cancers, optimised the removal of the cellular component whilst maintaining the composition and architecture of the extracellular matrix [5]. In this model we have established a co-culture of tumour cells and CAR-T cells where cell movement parameters including speed, direction and distance can be measured using spinning-disc confocal microscopy. The CAR-T cells are used as a surrogate to determine reversal of T cell exclusion. We have shown that T cell infiltration and tumour killing are enhanced by manipulating the extracellular matrix. Here, this model will be developed for PDAC:

1. Using a library of human PDAC tissues a decellularized model will be constructed using established protocols.
2. The decellularized model will be re-seeded with PDAC cancer cell lines, CAFs and a CAR-T cell line to produce an excluded model.
3. These cultures will be treated with epigenetic modifying drugs, after which CAR-T movement and location and ability to kill tumour cells will be measured. Increased T-cell contact with tumour cells will indicate whether the drug is reversing the excluded phenotype.
4. For drugs that reverse immunosuppression, underlying fundamental effects will be determined through measurements of changes in transcriptional enhancers, gene transcription and downstream signalling pathways.

References

1. Evan GI, Hah N, Littlewood TD, et al.: Re-engineering the Pancreas Tumor Microenvironment: A “Regenerative Program” Hacked. Clin Cancer Res 23:1647-1655, 2017
2. Saltos AN, Tanvetyanon T, Creelan BC, et al.: Phase II randomized trial of first-line pembrolizumab and vorinostat in patients with metastatic NSCLC (mNSCLC). Journal of Clinical Oncology 38:9567-9567, 2020
3. Rodriguez CP, Wu QV, Voutsinas J, et al.: A Phase II Trial of Pembrolizumab and Vorinostat in Recurrent Metastatic Head and Neck Squamous Cell Carcinomas and Salivary Gland Cancer. Clin Cancer Res 26:837-845, 2020
4. Puttock EH, Tyler EJ, Manni M, et al.: Extracellular matrix educates a tumor macrophage phenotype found in ovarian cancer metastasis. bioRxiv:2022.08.11.503568, 2022
5. Malacrida B, Pearce OMT, Balkwill FR: Building in vitro 3D human multicellular models of high-grade serous ovarian cancer. STAR Protoc 3:101086, 2022