CRUK City of London Centre Development Fund
The CRUK City of London Centre brings together the discovery science of the Crick and the cross-disciplinary, translational and clinical expertise at UCL, KCL and QMUL and their healthcare partners. The Centre will provide a centre of excellence in cancer biotherapeutics, with an initial research focus on tumor heterogeneity, the microenvironment and immunotherapies, and a major interest in childhood cancer.
The annual City of London Centre Development Fund provides short-term, pump-priming funding to support innovative research projects and inspirational, proof-of-concept cancer research. The scheme offers funds for up to five £25,000 awards per year.
For general enquiries regarding the programme please email: firstname.lastname@example.org
The following projects have been selected for funding:
2022 Development Fund Projects
Combining molecular imaging with spatial transcriptomics to enable systematic research into radio-immunotherapy
Main applicant: Gilbert Fruhwirth (KCL)
Co-applicants: Kairbaan Hodivala-Dilke (Barts)
Radiotherapy is a treatment that uses high-energy X-rays to kill cancer cells. We know from research that radiotherapy can sometimes help the human immune system to fight cancer, but unfortunately, this effect of radiotherapy is only rarely seen in patients. In recent years, researchers discovered that another type of therapy could improve this effect of radiotherapy when added to it. For patients whose cancer has already spread, it is very important that the immune system can battle their cancer everywhere in the body. Therefore, it is important for these patients to study this combined therapy further because it could lead to new treatment options for them.
One bottleneck in developing this combination therapy further is that many factors, which are central to its successful delivery, remain poorly understood. This is because the laboratory models that researchers have been using, do not adequately mimic the complexity of the human body. Consequently, it is now necessary to improve these models and use new techniques to obtain more and better research data from them. Here, we will pilot new analysis workflows, which will allow us to apply for more funding to develop this therapy combination.
Characterisation of a senescence-associated immunopeptidomic signature for senolytic immunotherapy development
Main applicant: Faraz Mardakheh (Barts)
Co-applicants: Juan Pedro Martinez-Barbera (UCL)
The advent of immunotherapy has transformed the outlook of treatment in certain cancers, with a minority of late-stage patients even achieving complete cure. At the heart of immunotherapy lies the ability of our immune system to recognise and destroy cancer cells. This is mediated by tumour-
specific, as well as tumour-associated antigens, which get presented on the cell-surface to cytotoxic T-lymphocytes, in form of peptides associated with the Human Leukocyte Antigen-I (HLA-I). The majority of immunotherapy research has been focused on fully malignant tumours. However, some lines of evidence suggest that certain pre-malignant lesions can also become visible to and cleared by the immune system. Melanocytic naevi, benign pre-cancerous lesions formed of transformed melanocytes, are one such example. Several studies have shown that the immune system can actively detect and remove some naevi, but the molecular mechanisms as well as the antigens involved in this process remain unclear. Our preliminary results have revealed that oncogenic transformation triggers mis-presentation of diverse HLA-I-associated antigens on the surface of melanocytes, raising the possibility that this mis-presentation could be contributing towards the immunogenicity of naevi. Importantly, our findings indicate that this mis-presentation maybe linked to oncogene-induced senescence, a conserved tumour suppressive process which acts to arrest transformed cells and prevent their progression to full malignancy. In this project, we propose to further study the link between senescence and antigen mis-presentation, assessing whether mis-presentation is a general feature of all senescent cells. If true, our findings can lead to further studies aimed at harnessing the observed antigen mis-presentation for immunotherapeutic targeting of diverse types of pre-malignant cells.
Transcriptomic analysis of cell competition
Main applicant: Paulo Baptista-Ribeiro (Barts)
Co-applicants: Nicolas Tapon (FCI)
Cell competition was initially discovered in studies performed in the fruit fly Drosophila, but is now recognised as crucial for tissue homeostasis and in cancer. Cell competition arises when neighboring cells display different relative fitness and frequently results in the elimination of the less fit cells, in a process resembling Darwinian evolution at the cellular scale. Similar events occur in cancer, whose development is associated with the selection of genetic chances that confer a survival advantage to cells. The precise mechanisms of cell competition regulation remain incompletely understood. Our project exploits a genetic system that allows generation of cell populations with distinct fitness to characterise the mechanisms of cell competition, with a particular focus on the genes differentially expressed in cells with different fates following the competitive process. We aim to reveal new mechanisms controlling cell fate during cancer development/progression.
Identification of the metabolic determinants of the antileukemic effects of stearoyl-coA desaturase (SCD) inhibition
Main applicant: Paolo Gallipoli (Barts)
Co-applicants: Mariia Yuneva and Dr Richard Burt (FCI)
Specific metabolic vulnerabilities, which can be leveraged therapeutically, have been identified in many malignancies. Our work has highlighted lipid biosynthesis, particularly the stearoyl-coA desaturase (SCD) enzyme, as a promising therapeutic target in acute myeloid leukemia (AML). However it remains unclear which patients would mostly benefit from targeting this pathway. This work aims to identify metabolic determinants of sensitivity to SCD inhibition (SCDi) in AML preclinical models thus allowing a more personalized use of SCDi in AML patients.
2021 Development Fund Projects
Characterization of Pol Epsilon as a therapeutic target and marker of sensitivity to ATR and PARP inhibitors
Main applicant: Roberto Bellelli (Barts)
Co-applicants: Nnenna Kanu (UCL), Peter Cherepanov (Crick), Svend Kjae (Crick)
Genetic instability is a major hallmark of cancer and understanding its nature has provided avenues for patient-tailored therapies such as PARP inhibitors in BRCA1-2 mutated breast and ovarian cancer. In this project we will investigate the interplay between DNA Polymerase Epsilon levels/activity and PARP/ATR inhibitors. Results of this project will allow a deeper understanding of the mechanisms of action of these inhibitors and the potential exploitation of DNA Polymerase Epsilon as a novel marker of sensitivity and target in combination therapies.
Simultaneous quantification and localization of mRNA and proteins at (sub)cellular resolution in cancer samples treated with immunotherapy
Main applicant: Francesca Ciccarelli (KCL/Crick)
Co-applicants: Shahram Kordasti (KCL), Jo Spencer (KCL)
Combined innate and adaptive immune cell therapy for childhood cancer neuroblastoma
Main applicant: Karin Straathof (UCL)
Co-applicants: John Marshall (Barts)
Neuroblastoma is the most common extra-cranial solid tumour in childhood. About 50% of patients present with high-risk disease at time of diagnosis. Despite multi-modal, intensive treatment the 5-year survival for these children remains less than 50% indicating the urgent need for new treatments. Immunotherapy using T cells redirected to tumour specificity using a chimeric antigen receptor (CAR) provides an attractive approach to achieve selective deletion of tumour cells while avoiding unwanted effects on healthy tissues.
We have demonstrated anti-tumour activity of GD2 CAR-T cells in bone marrow and soft tissue sites of disease in patients with relapsed or refractory neuroblastoma (Straathof et al, Science Transl Med 2020). While this provides an important proof-of-principle for the use of CAR-T cell as treatment for childhood solid tumours like neuroblastoma, responses were short-lived. This is likely due to inhibition of CAR-T cell as well as recruited innate immune cell function within the tumour microenvironment (TME). Here, we will investigate the expression of immune-inhibitory molecules within the TME of neuroblastoma upon treatment with CAR-T cells and develop an advanced T cell engineering approach to support persistent CAR-T cell function and engage macrophage activity to achieve durable tumour responses.
Investigating the origins and evolutionary history of metastasis through single-cell DNA sequencing
Main applicant: Simone Zaccaria (UCL)
Co-applicants: Charles Swanton (Crick), Mariam Jamal-Hanjani (UCL)
Metastasis results from the migration of cancer cells from a primary tumour to other anatomical sites and, despite being the most common cause of cancer-related mortality, the origins and clonal evolution of such process still remain poorly understood. In fact, metastasis results from a complex and highly selective evolutionary process in which different subpopulations of cells accumulate distinct complements of somatic mutations, providing disseminating potential. However, our understanding of this process has been substantially limited by the use of standard bulk tumour sequencing, which uses unknown mixtures of millions of different cells. As such, the identification of relatively small subpopulations of cells has been unfeasible so far, as well as the unambiguous reconstruction of their evolution.
In this pilot project, we will explore the use of cutting-edge whole-genome single-cell DNA sequencing and sophisticated computational methods to investigate the origins and evolutionary history of subpopulations of metastatic cells. Specifically, we will use the recent Direct Library Preparation (DLP+) technology to sequence the whole genome of thousands (4,000-10,000) of single cells from primary tumour and matched-metastasis samples of 3-4 non-small-cell lung cancer patients from the TRACERx study and the PEACE national autopsy program. The resulting single-cell sequencing data will be then analysed using recent computational methods (e.g., the CHISEL algorithm) to identify distinct subpopulations of cells present in the primary tumour and metastasis. Therefore, the identified subpopulations of cells will be analysed to reconstruct the evolutionary history of metastasis.
Improving delivery and survival of T cell living drugs to neuroblastoma tumours by engineering an adaptation to low oxygen conditions
Main applicant: John Anderson (UCL)
Co-applicants: James Arnold (KCL), John Maher (KCL)
In this study we will use CAR-T cells in the solid tumour setting to test the hypothesis that fine tuning of gamma delta CAR-T cells to low oxygen conditions by upregulating CAR expression in low oxygen conditions, will lead to improved effector in the tumour microenvironment. We aim to show that modifications to the CAR design to be responsive to low oxygen concentration will decease CAR expression in T cells during manufacture leading to decreased tonic signaling and exhaustion. Secondly we will show that in the tumour environment, CAR-T will be expressed leading to greater effector function. Finally in normal tissues expressing a target antigen but with normal oxygen concentration, toxicity will be avoided since the CAR will not be induced.
Anticancer immunity and the microbiological tumour microenvironment during radiotherapy for head and neck cancer
Main applicant: Miguel Reis Ferreira (KCL)
Co-applicants: Tony Ng (KCL), David Moyes (KCL), Martin Forster (UCL), Sergio Quezada (UCL), David Eaton (KCL), Sarah Gulliford (UCL), Cynthia Sears (Johns Hopkins University, USA), Rebecca Carter (UCL)
Radiotherapy is a cornerstone in the treatment of head and neck cancer. However, interactions between radiotherapy, immunity and bacteria, and how they relate to treatment outcomes, are poorly understood. In this project, we will develop laboratorial models allowing us to study these relationships and we will also study how bacteria locate in cancers of the head and neck. Our work will set the foundations for developing novel treatment strategies focused on optimising radiotherapy using immunity and the microbiota.
Guided gamma-deltas for osteosarcoma immunotherapy
Main applicant: Jonathan Fisher (UCL)
Co-applicants: Jane Sosabowski (Barts), John Anderson (UCL)
gdT cells show potent antibody-dependent cytotoxicity against osteosarcoma (OS) in-vitro, but in the clinical context, too few may home to the tumour to have meaningful impact. We will enhance homing of gdT cells to OS by engineering homing receptors based on analysis of tumour and bone transcriptomes. We hypothesise that this will enhance accumulation of cytotoxic gdT cells in the tumour, which we will first test in vitro then track using SPECT-CT imaging in an in vivo model.
Targeted theragnostic liposomal probes for imaging and treatment of Acute Myleloid Leukaemia (AML)
Main applicant: Alethea Tabor (UCL)
Co-applicants: Dominique Bonnet (Crick), Ana Gomes (Crick), Kirsten Hawkins (UCL), Helen Hailes (UCL), Vijay Chudasama (UCL)
A current challenge in the treatment of AML is whether to target therapeutic intervention at endothelial cells within bone marrow or in leukaemia cells themselves. To resolve this, we will develop a series of targeted liposomal probes that can be used for imaging and delivery of small molecule or biological therapeutics, and use these to image the location where treatment is most effective.
Cellular immune therapy of acute myeloid leukaemia (AML): characterising the immune synapse generated with chimeric antigen receptors (CARs) targeting multiple AML antigens
Main applicant: Sara Ghorashian (UCL)
Co-applicants: John Gribben (Barts)
Patients with acute myeloid leukaemia (AML) face low survival and high relapse rates. The latter is attributed to AML cancer stem cells which cause relapse. Targeting AML stem cells is challenging as they are rare and their cell surface has markers which may be different from the bulk of cancer cells. As such, targeting a single AML marker may be insufficient to eradicate all AML cancer cells.
We have developed a therapy which targets multiple AML markers by generating a synthetic recognition molecule (receptor) which sits on the surface of immune cells and enables them to recognise multiple AML markers through complexed recognition areas. As such, the patient’s own immune system cells are engineered to fight AML cells by targeting 3 markers called CD33, CD123, and CLL1. To date, our receptor (TanCAR) is able to kill AML cells tby recognising each of the cancer markers, equally as well as receptors (CARs) that only recognise one cancer marker. Whilst promising, we would like to understand better whether the TanCAR forms similar areas of surface contact when recognising target cells compared to single CARs and natural immune cells in order to identify alternative, optimal immune cell receptors for targeting AML.
2020 Development Fund Projects
Understanding the impact of systemic immune tolerance caused by melanoma interacting with the liver microenvironment
Main applicants: Erik Sahai (Crick), Mala Maini (UCL)
Co-applicants: Rebecca Lee (Crick), Laura Pallett (UCL), Mariana Diniz (UCL)
Patients with liver metastases respond very poorly to checkpoint inhibitors (CPI) with both metastases within the liver and those at extra-hepatic sites progressing on therapy. We will study how liver metastases induce both local and systemic immune tolerance resulting in decreased response to CPI. Understanding of these processes will enable development of strategies to improve outcomes to CPI for patients with melanoma with liver metastases.
Tracing and timing pre-cancerous clonal dynamics in normal tissues
Main applicant: Marnix Jansen (UCL)
Co-applicants: Kit Curtius (Barts), David Graham (UCL), Matthew Banks (UCL)
Cancer starts many years before (pre-)malignant lesions become visible. The accumulation of mutations drives progressive clonal diversification in normal tissues, which may ultimately lead to selection of premalignant outgrowths that are the target of early detection programs. This clonal diversification process can be accelerated by exposure to carcinogens such as cigarette smoke (lung), acid-biliary reflux (oesophagus), or chronic Helicobacter infection (stomach). Understanding the rate of clonal diversification is essential to make accurate predictions about future risk, but current random biopsy programs are not sufficiently sensitive to derive such measures.
We have developed a novel method to visualise the clonal mosaic in the chronically inflamed, Helicobacter-infected stomach. In this way we can interrogate genetic and epigenetic diversity between individual precursor clones in at-risk patients. In previous work we have established that methylation marks, in particular differential drift, can be used as a molecular clock to estimate lesion age. Here we combine physical clone size measurements, mutation burden, and epigenetic clock ages to derive accurate estimates of clonal expansion rate in relation to mutation burden. This work is more broadly applicable and may lead to risk prediction tests through target biopsy strategies.
The differential contribution of tumour infiltrating and circulating neutrophils to chemotherapy resistance in early breast cancers
Main applicant: Sheeba Irshad (KCL)
Co-applicants: Ilaria Malanchi (Crick), Shahram Kordasti (KCL)
Many patients with early breast cancers are treated with neoadjuvant chemotherapy (NACT). Women with residual disease following NACT often suffer a poorer outcome, with early elapsed disease; and difficult to treat metastatic disease. The immune cell populations and their functions within chemotherapy resistant residual disease are much less well understood.
Neutrophils constitute a significant part of the tumour microenvironment (TME). Traditionally, few studies have focussed on their role in tumour progression considering them to be hallmarks of acute inflammation with short survival time (3-24hr). My co-investigator for this study, Dr Ilaria Malanchi has demonstrated that neutrophils specifically support metastatic initiation in the pre-metastatic niches of in vivo models. In the context of the tumour microenvironment, neutrophilic recruitment and activation have been shown to have broad effects on tumour cells and the microenvironment, which include direct cellular injury from release of oxidants and granular constituents, remodelling of the extracellular matrix, release of pro-angiogenic products, and cross-signalling to other inflammatory cells and tumour stromal constituents.
We now seek to investigate the role and interaction of tumour associated and circulating neutrophils in chemotherapy resistant cancers across the different breast cancer subtypes.
Evolution and ecology of oesophageal adenocarcinoma under neoadjuvant treatment
Main applicant: Trevor Graham (Barts)
Co-applicants: Melissa Schmidt (Barts), Marnix Jansen (UCL), Benny Chain (UCL)
Oesophageal adenocarcinoma (OAC) is the 8th most frequent cancer in Europe and remains challenging to treat with 40-55% of patients progressing on chemotherapy and 5-year survival of 12.6%.
In this pilot project we will make multi-omic genomic, transcriptomic, t-cell repotoire, and multi-marker immune profiling measurements of OACs at multiple time points (prior, during, and after therapy) in tumour tissue from OAC patients who are enrolled in a neoadjuvant therapy trial in Germany. We will then perform a detailed evolutionary analysis of these data, centred around tracking the size and emergence/disappearance of cancer clones over time, and the relationship of these evolutionary dynamics to tumour cell phenotypes and immune cell activity. We will use our data to parameterise mathematical models of tumour evolution to enable forecasting of individual tumour response to treatment.
The work is a collaboration between Dr Schmidt and Prof Graham at the Barts Cancer Institute (cancer genomics), Dr Jansen at UCL (pathology of OAC) and Prof Chain at UCL (immunogenomics).
Developing organotypic models of human osteosarcoma
Main applicant: Sibylle Mittnacht (UCL)
Co-applicants: Wenhui Song (UCL), Ilaria Malanchi (Crick)
Osteosarcoma (OS), despite rare, is a key cause of cancer death in children and young adults. Progress in rare cancers critically relies on tools and disease models that appropriately reflect their clinical presentation for conceptual studies and therapeutics testing. Ex vivo complex organotypic models that reflect the genetic and tissue heterogeneity of disease have been developed in many epithelial cancers but this has not been successful in OS thus far.
The proposed work seeks to combine front-line tissue engineering expertise in 3D scaffold-guided growth of human bone by the Song laboratory at the UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, translational therapeutic and cancer cell biology expertise by the Mittnacht laboratory at the UCL Cancer Institute and expertise in the study of tumour microenvironmental interactions by the Malanchi laboratory at the Francis Crick Institute, to build an organotypic platform for the propagation of patient-near orthotopic models of human OS.
The proposed work fills a recognized technology gap in OS research that is limiting therapeutics discovery and conceptual studies in this disease.
Targeted reversal of epigenetic silencing at specific tumour suppressor genes in lymphoma
Main applicant: Richard Jenner (UCL)
Co-applicants: Jude Fitzgibbon (Barts)
In 10% of diffuse large B-cell lymphoma and 25% of follicular lymphoma cases, gain-of-function mutation of the repressive chromatin modifier EZH2 drives tumourigenesis by silencing tumour suppressor genes. EZH2 inhibitors are in clinical trials but these activate repressed genes nonspecifically. We have developed the means to specifically inhibit EZH2 at individual genes. We will test whether this allows selective reactivation of tumour suppressors without affecting other genes.
2019 Development Fund Projects
Deep Learning of High Dimensional Genetic, Immune and Clinical Parameters to Predict Patient Response to Immune Checkpoint Blockade
Main applicant: Francesca Ciccarelli (Crick/KCL)
Co-applicants: Jo Spencer (KCL), Daniel Hochhauser (UCL), Manuel Rodriguez-Justo (UCL) and Kai-Keen Shiu (UCL)
Connecting Single-Cell Ligands, Receptors, and Signals in Tumour Microenvironment Organoids
Main applicant: Chris Tape (UCL)
Co-applicants: Vivian Li (Crick)
Tumours are heterogeneous mixtures of different cell-types. In addition to mutated cancer cells themselves, the tumour microenvironment contains multiple stromal and immune cells that each contribute to a patient’s cancer. While we now understand the cellular composition of tumours relatively well, how different cell-types collectively integrate to drive cancer is poorly defined.
Our ignorance of cell-cell communication in the tumour microenvironment largely stems from our inability to simultaneously measure ligands (cues), receptors (transducers), and signals (effectors) across all cells in a tumour. Without such data it is incredibly challenging to ‘connect’ mutations in cancer cells with deregulated phenotypes in stromal and immune cells.
To address this, the UCL Cell Communication Laboratory (www.tape-lab.com) have developed a novel mass-cytometry (CyTOF) technology to measure single-cell post-translational modification (PTM) signalling in organoid models of the colorectal cancer (CRC) tumour microenvironment. While incredibly powerful for understanding PTM signalling, CyTOF data cannot describe the 1,000s of putative cell-type specific ligands or receptors responsible for transducing each signal. As a result, we cannot connect signals between cancer, stromal, and immune cells in the tumour microenvironment.
The aim of this CRUK City of London Development Fund project is to integrate our single-cell PTM technology (CyTOF) with single-cell ligand and receptor transcriptomics (10x Genomics). By simultaneously measuring cell-type specific ligand / receptor expression and PTM signalling in organoid models of the CRC tumour microenvironment (in collaboration with Vivian Li Lab, Francis Crick Institute), this will allow us to ‘connect’ cell-cell signalling across the tumour microenvironment.
Targeting the Tumour Microenvironment to Enhance Immunotherapy: A Cross-Disciplinary Approach to Assessing Treatment Efficacy
Main applicant: Kairbaan Hodivala-Dilke (Barts)
Co-applicants: Ralph Sinkus (KCL)
Enhancing drug efficacy by manipulating the tumour microenvironment is a primary goal of our laboratory research. We have published that intravenous administration of the integrin-targetting agent, low dose Cilengitide (ldCil), increases tumor angiogenesis and drug delivery whilst reducing hypoxia and desmoplasia in gold standard preclinical models of lung and pancreatic (KrasLSL-G12D/+;p53R172H/+;PDXCre, KPC) cancers. Together this approach reduces tumour growth and metastasis, whilst extending survival (Reynolds et al., Nature Medicine, 2009; Wong et al., Cancer Cell 2015). We have also collaborated with medicinal chemists who have developed a second generation orally available agent, Agent X, currently under patent application. Our new data indicate that combination treatment including Agent X also reduces desmoplasia.
Magnetic resonance elastography (MRE) is an innovative non-invasive imaging technique that not only determines the presence of a tumour but also identifies the desmoplastic pathophysiological status of cancers and can be used to assess the anti-desmoplastic efficacy of cancer therapies. Our partner in this application, Ralph Sinkus’s has developed methods of improved MRE technologies across multiple cancer types has provided the opportunity to utilize MRE as a tool for therapy efficacy (Fovargue et al., NMR Biomed. 2018; Jamin et al., Cancer Res 2015).
Through this City of London Development Fund we now have the opportunity to join forces from Barts and Kings to examine the efficacy our new anti-cancer strategy using state of the art imaging thus bringing added-value to this cross institutional collaboration.
CAESAR: Comprehensive Analysis of Epigenetic Heterogeneity in SARcoma
Main applicant: Iben Lyskjaer (UCL)
Co-applicants: Adrienne Flanagan (UCL), Stephan Beck (UCL) and Peter Van Loo (Crick)
Despite progress in the histological classification of the different subtypes of sarcoma, the clinical outcome of patients with the majority of these subtypes has not improved over the last 40 years. To change this, there is a need to understand the molecular basis of sarcoma in the context of clinical presentation, outcome and response to therapies.
Deep sequencing of cancer genomes has revealed complex patterns of inter- and intra-tumour heterogeneity, providing insight into a tumour’s evolutionary trajectory and is starting to inform on patient prognosis and therapeutic decisions. The main clinical consequence of tumour heterogeneity and clonal evolution is the emergence of resistance to systemic drug therapy. Epigenetics has been shown to contribute to intra-tumour heterogeneity and evolution, as first reported in haematological malignancies, by measuring DNA methylation at single-nucleotide level using Reduced-Representation Bisulfite Sequencing (RRBS).
This study aims to generate a comprehensive profile at base pair resolution of the DNA methylation heterogeneity in osteosarcoma tumours and for the first time determine if locally disordered methylation exists in osteosarcoma. Building on the samples already collected and submitted to the 100,000 Genomes project, which includes whole genome sequencing of up to 8 samples per osteosarcoma, we will interrogate DNA methylation heterogeneity at a single nucleotide level using enhanced RRBS targeting over 4 million CpG dinucleotides in CpG-rich regions of the genome. Further, we will characterise the epigenetic tumour evolution in osteosarcoma tumours by looking at multiple samples from each tumour lesion, and determine associations between heterogeneity and the presence of particular driver mutations by using WGS data from the 100,000 Genomes Project.
Intra Tumour Heterogeneity at the Level of Ploidy: A Need to Re-Evaluate Copy Number Inference from Bulk DNA Profiling
Main applicant: Maxime Tarabichi (Crick)
Co-applicants: Nischalan Pillay (UCL), Peter Van Loo (Crick), Kevin Bryson (UCL), Andrew Feber (UCL) and Marnix Jansen (UCL)
Most cancer evolution studies, because they rely on bulk DNA sequencing data, are inevitably compromised by ambiguous estimates of tumour ploidy.
Aberrations in ploidy and in particular whole genome doubling are macro-evolutionary events that are associated with increased fitness of cancer cells and poor prognosis. The largest pan-cancer bulk DNA sequencing studies to date have relied on ploidy estimates derived in silico, which are ambiguous and often incorrect. The problem arises from the fact that, in theory, multiples of 2 times the ploidy are mathematically equivalent solutions to fit the data, and although hints in the data can help select between the various potential solutions, this exercise remains hand-wavy. In addition, tumours can show heterogeneity at the level of ploidy, containing multiple populations with very different ploidy values, which is not modelled by current copy number inference methods.
Hence, our current pan-cancer picture of heterogeneity at the level of copy number and ploidy is challenged, and, although previous and recent results strongly support the use of systematic experimental ploidy validation to inform sequencing-based copy number callers, this still has to become good practice in the field. This is especially relevant and timely for large whole genome sequencing programs such as the 100,000 genomes project, but also for all DNA-profiling-based studies of cancer evolution and intra tumour heterogeneity.
This is why we aim to develop standards for the field by benchmarking ploidy estimated from bulk sequencing against experimental ploidy using FACS, single cell sequencing and digital imaging; and study the extent and spatial mapping of intra-tumour heterogeneity at the level of ploidy. This will be done across multiple cancer types, with a particular focus on undifferentiated sarcomas, which were recently shown to display high amounts of inter- and intra-tumour heterogeneity at the level of ploidy.
A Novel Approach for Identifying Neoantigens from Cancer Cell-lines and Organoids
Main applicant: Faraz Mardakheh (Barts)
Co-applicants: Chris Tape (UCL)
Immunotherapy has revolutionised the outlook on treatment of various cancers in recent years. Several strategies have been developed for immunotherapy, majority of which ultimately depend on presence of neoantigens, tumour-specific antigens which arise from coding mutations that get translated and presented on the surface of the cells in form of peptides associated with Human Leukocyte Antigen-I (HLA-I). The ability to detect and monitor these neoantigens is critical, not only for better understanding the process of cancer cell detection by the immune system, but also for devising novel immunotherapies against cancer such as personalised vaccines. Despite years of research, however, neoantigen discovery and validation remains a daunting problem in the cancer biotherapeutics field.
The most common method for neoantigen discovery is in silico prediction of neoantigens from bulk tumour sequencing data. Although relatively easy to implement, the actual success rate of in silico methods for predicting neoantigens that can elicit an immune response remains very low. Direct identification of neoantigens by mass spectrometry (MS) represents an alternative to in silico based prediction. However, current available methods either suffer from lack of specificity, or are labour-intensive and require large quantities of input material, thus rendering their widespread use challenging. In this project, we propose to develop a novel approach that overcomes these major limitations, enabling rapid MS based identification of HLA-I-bound neoantigens, with high specificity, from a variety of live cancer models. As a proof-of-concept, we will then apply our method to analysis of neoantigens a panel of patient-derived colorectal cancer organoids grown in 3D culture.
Exploring How Rho Regulated Kinases Modulate the Immune Landscape in Colorectal Tumours
Main applicant: Angus Cameron (Barts)
Co-applicants: Shahram Kordasti (KCL)
Immunotherapy has provided new hope for many cancer patients, with the potential to treat or cure even advanced metastatic disease. Although considered a huge breakthrough, immunotherapy only currently works in a subset of patients. Identifying ways to predict which patients will respond and approaches to sensitise non-responders, are critical next steps to extend impact. In colon cancer, immunotherapy ‘checkpoint inhibitors’ have already been approved for use in a subset of cancer patients who show high mutation rates (MSI+ tumours). Immunoscore – a quantitative assessment of the immune infiltrate in tumours – is also emerging as a powerful indicator of response to immunotherapy in colon cancer. As a consequence, interventions which modulate the immune infiltrate are of huge interest as they could be used to expand the group of patients who could benefit.
Our multidimensional and in vivo data indicate that Rho effector kinases may suppress tumour growth and promote an anti-tumour immune landscape. In this project, we wish to assess the immune cell repertoire in colorectal tumours induced in a Rho effector knockout model, to assess a novel mechanism to predict or modulate immunotherapy responses. We will use state-of-the-art Mass Cytometry (CyTOF) and tumour phenotyping to examine a broad range of immune cell types in colon tumours from our novel in vivo models. Our preliminary data suggest that specific Rho effectors may promote infiltration of tumours with CD8+ T-cells; intervention by activating or inhibiting this pathway would be expected to modulate both the immune infiltrate and response to immune checkpoint inhibition. This study will lay the ground work for the development of novel therapies to use in conjunction with existing immunotherapy drugs.
Exploring Order in Chaotic Cancer Genomes
Main applicant: Nicholas McGranahan (UCL)
Co-applicants: Sarah McClelland (Barts)
Cancer genomes contain a plethora of genomic alterations, affecting single base pairs up to whole chromosomes. Recurrently altered genomic regions likely contain important cancer genes that could represent novel targets for cancer therapy. However, teasing out which of these regions represent important drivers from those that are more prone to alterations has remained a challenge. We aim to use single-cell data to investigate which copy number alterations are important in cancer.
Non-invasive Imaging of Immune-mediated Tumour Ferroptosis
Main applicant: Timothy Witney (KCL)
Co-applicants: Crispin Hiley (UCL)
Ferroptosis is a morphologically and biochemically distinct form of regulated cell death that results from the excessive peroxidation of polyunsaturated fatty acids. Ferroptotic cell death is catalysed by iron and if left unregulated results in a chain reaction of lipid-derived reaction oxygen species (ROS) and eventual membrane destruction. Glutathione metabolism and antioxidant capacity mediate the sensitivity of tumours to ferroptosis through the combined activity of glutathione peroxidase and the cystine/glutamate transporter, xCT. Recently it has been shown that that immunotherapy-activated CD8+ T-cells induce ferroptosis-specific lipid peroxidation in tumour cells. T-cell immunity was enhanced by immune checkpoint blockade through a mechanism of interferon gamma release and subsequent xCT downregulation.
We are currently evaluating a novel PET imaging agent, [18F]FSPG, as a non-invasive marker of the tumour redox microenvironment. [18F]FSPG is taken up by tumour cells via xCT, providing a non-invasive measure of its activity. In this City of London Centre Development Fund project, we will monitor the efficacy of T-cell immunotherapy with [18F]FSPG in in vivo models of lung cancer. In genetically-modified animals and in patient-derived xenografts, we will image tumour-induced ferroptosis with [18F]FSPG following checkpoint blockade. Tumour-associated T-cell infiltration, activation and dysfunction will be assessed ex vivo along side lipid peroxidation as a marker of ferroptosis. Together, this will provide a rapid, whole-body assessment of the treatment efficacy for these novel immunotherapies.
Identification of Novel Mechanisms of Cancer Immunoevasion
Main applicant: Paola Scaffidi (Crick)
Co-applicants: Francesca Ciccarelli (KCL), Gabriella Ficz (Barts), Julian Downward (Crick)
Immuno-surveillance is a critical tumour-suppressive mechanism that transformed cells need to evade to establish a full-blown cancer. Many immunoevasive strategies employed by cancer cells rely on aberrant transcriptional regulation of immunomodulatory molecules, implicating chromatin and DNA methylation in these processes.
Despite the recent success of immune checkpoint inhibitors, a significant fraction of patients do not respond to the therapy, suggesting that cancer cells likely exploit yet unidentified immunoevasive strategies. Using a unique experimental model, we have identified chromatin regulators whose inactivation favours the transition from an immunogenic to an immunoevasive phenotype.
We now propose to dissect the processes underpinning this transition, assess their prevalence in various cancer types, and provide a proof of principle that interfering with the identified mechanisms synergizes with other therapies.