NIHRDataInsights/HRCSData huggingface dataset:
Title: Investigating mRNA methyl cap regulation, function and therapeutic potential
Funder: Medical Research Council

Abstract: We investigate the regulation and function of the mRNA methyl cap with the ultimate aim of developing new families of compounds to inhibit the growth and proliferation of tumour cells and parasites. The methyl cap is a structure added to mRNA during synthesis, marking transcripts for processing and translation initiation. We have made major contributions to the current understanding of the methyl cap. We discovered the first example of methyl cap regulation; c-Myc oncogene upregulates mRNA cap methylation and this is necessary for c-Myc-dependent gene expression and cell proliferation. We discovered an essential activator of the mRNA cap methyltransferase enzyme, RAM. Fundamental questions remain about how the methyl cap is synthesized, regulated and functions. Answering these questions will have significant impact for our understanding of regulated gene expression, and provide new therapeutic opportunities. Our objectives: 1 To determine the mechanism by which the methyl cap is synthesised in mammalian cells 2 To determine how cellular signaling pathways regulate the methyl cap, including c-Myc oncogene and CDK-cyclins 3 To determine the function of regulated cap methylation 4 To develop small molecule inhibitors of mRNA cap methylation for use as tools compounds and to investigate their therapeutic potential in both cancer and trypanosome parasites We will use biochemistry and mass spectrometry to characterize methyl cap synthesis, biophysical techniques including X-ray crystallography to investigate cap methyltransferase structure, transcriptome sequencing and bioinformatics to investigate the function of regulated cap methylation, and the latest screening techniques in collaboration with the Dundee Drug Discovery Unit to identify cap methyltransferase inhibitors. During this fellowship we aim to initiate drug discovery programmes to target tumour cells and trypanosome parasites


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Novel statistical approaches for the characterization of genomic structural rearrangements in cancers from high-throughput genome sequencing data
Funder: Medical Research Council

Abstract: The objective of this project is to develop advanced statistical algorithms to address limitations in existing methods for analysing cancer genome sequencing data. The aim is to build a set of related robust statistical tools for genomic copy number profiling of cancer that can operate using a variety of data platforms (array, whole genome or targeted sequencing) and in a range of experimental scenarios (single or multiple specimens, cohort or obtained from the same patient, single cell, etc). This tool will use multi-scale techniques to decompose genomic profiles into different scales of interpretation and data augmentation techniques to integrate the use of data from previous cancer studies through a series of cancer karyotype libraries that will be constructed as part of this project. These reference libraries will contain genomic copy number profiles and clinical information for patients that have previously been examined and will be act as ``prior information" in the classification of new patient specimens. The algorithms will attempt to relate copy number changes in the unclassified patient to previously observed events in the reference libraries allowing patients to be clustered and common clinicopathological and other genomic features to be investigated. These investigations may lead to plausible patient stratification groups that could be the basis of targeted therapies and clinical management strategies.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: Treating Multiple Myeloma by Targeting the NF-Kappa-B Pathway with Gadd45-Beta/MKK7 Inhibitors
Funder: Medical Research Council

Abstract: The NF-kB pathway is aberrantly upregulated in many cancers, where it promotes survival. A paradigm of these cancers is Multiple Myeloma (MM), an incurable plasma cell malignancy. Existing MM treatments fail to induce lasting remissions, leading to relapse and/or refractory disease. NF-kB is a promising therapeutic target in MM. Despite the industry's long-standing pursuit of NF-kB inhibitors, however, no such inhibitor has been clinically approved to this day. Likewise, proteasome inhibitors with MM indication, such as bortezomib, inhibit NF-kB and other cellular functions, and do not specifically target cancer cells, resulting in low therapeutic indices and dose-limiting toxicities. We reasoned that an attractive alternative to globally targeting NF-kB would be to block the non-redundant, cancer-specific effectors of NF-kB-dependent survival. Recently, we identified the interaction between the NF-kB-regulated gene product, Gadd45b, and the JNK kinase, MKK7, as a novel therapeutic target in MM. Gadd45b is elevated in MM cells relative to healthy tissue and promotes survival therein by suppressing MKK7/JNK-induced apoptosis. Further, with MRC support, we developed a novel D-tripeptide, DTP3, which specifically disrupts the Gadd45b/MKK7 interaction, kills MM cells at low-nM concentrations and, importantly, completely lacks toxicity to normal cells. Due to this cancer-selective target specificity, DTP3 has similar anti-MM activity to bortezomib, but more than 100-fold higher therapeutic index in vitro. DTP3 also has excellent tolerability and far greater therapeutic index than bortezomib in vivo. Consequently, it virtually eradicates MM xenografts in mice without apparent side effects. We currently aim to progress DTP3 to a Phase 1 trial to deliver clinical PoC for a cancer-selective NF-kB-targeting strategy and an effective therapy with no preclusive toxicity, alongside a diagnostic test, for MM and potentially other cancers where NF-kB promotes survival via Gadd45b.


Research activity codes: 5.1 PHARMACEUTICALS;6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Clinical Translation of Gene Modified T-cell Therapy for Solid Tumours
Funder: Medical Research Council

Abstract: Aim: The aim of this fellowship is to develop immunotherapy for prostate cancer for the purpose of clinical translation. Methodology: A chimeric antigen receptor (CAR) P28z, which selectively recognises the prostate cancer antigen prostate specific membrane antigen (PSMA) co-expressed in one retroviral open reading frame with a chimeric cytokine receptor 4ab and the human sodium iodide symporter (hNIS) (collectively known as PiN4) has been generated. The expansion, survival and homing of PiN4 T-cells requires optimisation. To this end two novel immunocytokines will be compared with interleukin-2 (IL-2) and IL-4 for their ability to support PiN4 cytotoxicity via the 4ab. PiN4 function will be evaluated by production of pro-inflammatory cytokines and destruction of tumour monolayers after co-culture. Cytotoxicity will be quantified by MTT assays. Homing, and persistence of PiN4 cells in vivo will be studied by SPECT and PET imaging of the adoptively transferred T-cells capitalising on expression of the hNIS. The optimal combination of PiN4, immunocytokine/cytokine support and treatment schedule will be determined in vivo by studies of tumour xenograft destruction quantified by bioluminescence imaging of established xenografts engineered to express luciferase. Scientific and medical opportunities of the research: The scientific opportunities of this work focus on overcoming hurdles to translation of CAR therapy in solid tumours. Specifically to improving T-cell homing and persistence in the tumour micro-environment, whilst reducing the risk of PiN4 T-cells damaging normal tissues in which low levels of PSMA can be found. If successful these techniques can be used to enhance the function and safety of CARs targeting different tumour associated antigens. Medically the generation of a protocol and regulatory documents for a first in man study is the ultimate goal of this fellowship.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Programming the Notch Response
Funder: Medical Research Council

Abstract: Notch signalling is critical for many aspects of development, from stem cell maintenance to epithelial growth control, and its dysregulation underlies many diseases, especially cancers. These conditions of pathological Notch signalling reveal that there must exist mechanisms that normally keep the Notch pathway in check, which are defective in these diseases. Furthermore, although Notch activity promotes tumourigenesis in many contexts, including T-cell acute lymphoblastic leukaemia and breast cancers, in others Notch acts to suppress tumours, making it problematic to rely on general Notch inhibitors for therapeutic intervention. It is important therefore to discover how different subsets of genes are selected for Notch regulation to account for the disparate outcomes of Notch activity. Our goal is to use a combination of genomic, genetic and biochemical approaches in Drosophila and in human cells to discover the fundamental mechanisms that programme different Notch responses. As Notch acts directly to change gene expression, our primary focus is on the network of genes that are Notch-regulated in different contexts, including tissue hyperplasia. We have two major aims: (1) to discover the mechanisms that normally attenuate Notch signalling in different tissues and how this machinery is disrupted in disease models (2) to elucidate how genes are selected to be Notch-responsive, yielding tissue-specific differences in the outcome of Notch signalling. Our results will uncover general principles that explain how these diverse effects of Notch activation arise in tissue development and in different types of cancers, especially breast cancers. In doing so they will identify mechanisms of attenuation and of gene selection that are indicative of particular disease outcomes, permitting better diagnosis, and suggest strategies for targeted therapies to avoid the serious side effects from more general Notch inhibitors.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Clinical Investigation of a Humanized Anti-CD47 Antibody in Targeting Cancer Stem Cells in Acute Myelodi Leukaemia (and Solid Tumours).
Funder: Medical Research Council

Abstract: Many cancers are organized as a cellular hierarchy initiated and maintained by cancer stem cells (CSC). CSC comprise a subset of tumor cells that are relatively resistant to current therapy, which often shrink tumors, but do not lead to long-term cures. Such cures require strategies to target all the CSC. CD47 is a immunomodulatory protein expressed on the surface of CSC and cancer cells from nearly all human tumors. CD47 binds SIRP-alpha on phagocytes, which delivers an inhibitory signal to block phagocytosis. CSC and cancer cells upregulate CD47 expression, presumably to suppress phagocytic attack. This proposal outlines a clinical development plan to evaluate the safety, tolerability, and efficacy of our therapeutic, the humanized anti-CD47 antibody Hu5F9-G4. Hu5F9-G4 is a blocking anti-human CD47 antibody that prevents the binding of CD47 to SIRP-alpha, disrupting its inhibitory signal, and enabling the phagocytic removal of CSC and cancer cells. In xenograft models, we have demonstrated that Hu5F9-G4 has potent efficacy against AML. In non-human primate toxicokinetic studies, Hu5F9-G4 was well-tolerated at doses able to achieve sustained serum levels in a potentially therapeutic range. Simultaneously, we generated a cGMP-qualified master cell bank, and have initiated GLP/GMP manufacturing of Hu5F9-G4. We have had positive initial regulatory interactions with the FDAand MHRA in the UK, and and are on track to file two separate IND/IMPDs, one for AML, and one for solid tumors by early 2014. Here, we propose parallel first-in-human Phase 1 clinical trials in the US and UK of Hu-5F9-G4 in patients with either AML or separately a diversity of solid tumors for whom there are no further standard therapies. The primary objective will be to assess the safety and tolerability of Hu5F9-G4, to identify the maximum tolerated dose (MTD) or optimal biologically effective dose (OBED), and to get a preliminary assessment of tumor reduction for further efficacy studies.


Research activity codes: 5.1 PHARMACEUTICALS;6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Defects in replicative DNA polymerases linked to cancer predisposition and tumour development
Funder: Medical Research Council

Abstract: Germline mutations in the exonuclease domain of replicative DNA polymerases delta and epsilon have been recently shown to be associated with a predisposition to colorectal cancer. In addition a wider range of exonuclease domain mutations have been found as somatically variants in colorectal and endometrial cancer, suggesting that changes in polymerases may more widespread as a step leading to genome instability in tumourigenesis. The exonuclease domain contains the active site for a 3'-5' exonuclease activity required for proofreading, capable of removing misincorporated nucleotides that are not correctly base paired to the template. In this grant we will characterize the polymerase variants associated with colorectal cancer predisposition and endometrial tumours by constructing equivalent mutations in a model organism, fission yeast, and by purifying human polymerases containing the relevant mutations. We will compare the phenotype of the strains constructed and the biochemical properties of the purified polymerases with exonuclease null version of the polymerases, where key catalytic residues in the exonuclease active site have been changed, to clarify the extent to which the phenotype is due to loss of exonuclease activity. We will grow strains expressing polymerases with exonuclease domain mutations for many generations and perform genomic sequencing to determine the mutational spectra and whether specific regions of the genome are prone to mutagenesis. We will establish why some exonuclease domain mutants require an intact checkpoint for survival in yeast, and whether this is relevant to the mechanism of mutagenesis. This will allow insight into the mechanism whereby polymerases with exonuclease domain defects promote tumour development in humans.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Circulating tumour DNA as a specific diagnostic biomarker for ovarian cancer.
Funder: Medical Research Council

Abstract: The overall objective of this project is to develop new non-invasive methods for diagnosis of ovarian cancer that can be utilised earlier in the diagnostic pathway to improve prognosis for women with ovarian cancer. Primary hypothesis 1.Can ctDNA be detected in plasma from women with OC at the time of diagnosis? Using a tagged-amplicon deep sequencing technique (TAm-Seq), a new method for non-invasive mutation analysis recently developed by the Rosenfeld and Brenton labs, we propose to sequence DNA from matched plasma and tissue samples from the time of diagnosis in women with ovarian cancer. A second phase of the study will look at symptomatic women with elevated CA125 and a pelvic mass on transvaginal ultrasound to explore the ability of TAm-Seq to discriminate between benign and malignant masses when clinical suspicion is equivocal. Exploratory Endpoints 2.Can mutations detected in plasma samples at diagnosis be detected in cervical smear samples? Using TAm-Seq we propose to compare sequencing of genomic DNA from cervical smear samples and cervical mucous aspirates to plasma and tissue in patients at the time of diagnosis of OC. If these results are promising, future work will explore the development of methods using a self-inserted tampon for collection of tumour DNA that might acceptable for use by patients. 3.Is molecular analysis of routine cervical smear samples a sensitive method for diagnosis of ovarian and endometrial cancer? In a population based study we propose to sequence all routine cervical smear samples classified as showing possible glandular abnormalities for a panel of mutations known to be associated with both OC and endometrial cancer to assess the utility of population based cervical smears in screening for OC.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Preclinical efficacy of an antibody of the IgE class against a melanoma-associated antigen
Funder: Medical Research Council

Abstract: The clinical landscape for the lethal skin cancer, melanoma, is transformed by novel agents including an antibody targeting T-cell regulatory pathways, which, despite moderate clinical responses and high toxicities, demonstrates promise for antibody therapies. Yet, there are presently no antibodies directly targeting melanoma cells. This strategy entails an antibody targeting melanoma antigens that is engineered with Fc regions of the IgE antibody class. Attributes of IgE such as natural tissue immune activatory functions and high affinity for cognate Fc receptors on frequently tumour-resident effector cells can translate into superior protection against solid tumours compared to conventionally-used IgGs. These advantages are demonstrated by efficacy and safety in three in vivo tumour models and remarkable progress through process development of our successful first IgE antibody targeting Folate Receptor alpha-expressing cancers, now approaching first-in-man clinical trials supported by the CRUK New Agents Committee. We engineered IgE and IgG1 antibodies recognising CSPG4, a cell surface tumour antigen over-expressed by 80% of melanomas; CSPG4 participates in melanoma pathogenesis and progression through activation of key signalling pathways. CSPG4 IgE demonstrated superior efficacy in targeting melanoma and direct and cell-mediated tumour-killing activities, suggesting a multifactorial mode of action. Background IP is owned by KCL through a PCT application filed in 2011. Here, we will evaluate efficacy and safety of this agent through functional assays on patient and healthy volunteer blood and in disease-relevant models, some of which will also serve to support future evaluations in the pre-clinical development and clinical study stages. Study design is based on expertise with our lead antibody, to directly progress CSPG4 IgE to process development and clinical trials.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Molecular and Cellular Mechanisms Underlying Pituitary Tumours
Funder: Medical Research Council

Abstract: We have generated and published mouse models of human adamantinomatous craniopharyngioma (ACP) and validated that these are relevant to understand the aetiology and pathogenesis of the human tumours. Using these mice, we have recently uncovered a paracrine model of tumorigenesis, whereby mutated Sox2+ pituitary stem cells secrete signalling factors that act on surrounding cells resulting in cell transformation and tumorigenesis in a non-cell autonomous manner. Our data suggest that cell senescence and low-grade senescence-induced inflammation are critical players in tumour initiation in both mouse and human ACP. Many questions remain unanswered about this novel mechanism of oncogenesis: (i) Which molecular pathways promote the abnormal expression of secreted factors by mutated Sox2+ stem cells? (ii) Which are the critical secreted signals that induce the tumours? (iii) Could inhibition of these signals result in the development of novel chemical treatments for the patients? (iv) Which is the cell-of-origin of the tumours? Answering these questions will provide mechanistic insights into the paracrine model of tumorigenesis to further understand the pathophysiology of pituitary tumours, and with broader implications for oncology and the role of somatic stem cells, senescence and inflammation in cancer (Aim 1). In addition, it will lead to a better understanding of the initial steps of tumour formation and the identification of the cell-of-origin of ACP (Aim 2), which will facilitate the development of new tools for early diagnosis and will allow validation of targeted treatments against oncogenic signalling pathways. To achieve this, I will use a multidisciplinary approach combining: (i) Mouse genetics (genetic tracing, gene deletion, preclinical studies using small-molecule inhibitors). (ii) Cell isolation by flow cytometry. (iii) Molecular biology (gene expression and mutational profiling by RNA-Seq). (iv) Developmental biology (generation of chimeras).


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Wnt signaling in senescence, nevogenesis and melanomagenesis
Funder: Medical Research Council

Abstract: Senescence is an irreversible proliferation arrest that is activated by various molecular triggers, including activation of proto-oncogenes, such as BRAF and N-Ras, in primary human cells. Like melanoma, virtually all benign human nevi harbor activating mutations in N-RAS or its downstream effector, BRAF. But, typically, benign nevi do not progress to melanoma. At least in part, this is because cellular senescence blocks proliferation of the nevus melanocytes. In the canonical Wnt signaling pathway, extracellular Wnt proteins bind to their cognate transmembrane receptors. Binding of Wnt to its receptor indirectly stabilizes beta-catenin, which then acts in the nucleus, in a complex with one of a family of heterodimeric binding partners, TCF family members, to drive expression of proliferative genes, such as c-myc and cyclin D1. Activated Wnt signalling promotes early stages of melanomagenesis by virtue of its ability to abrogate melanocyte senescence. In light of the above, we and others have been surprised to find that benign human nevi express activated beta-catenin and proliferation-promoting Wnt targets, such as cyclin D1, c-myc and MITF. This would be expected to antagonize stable senescence-associated proliferation arrest. To reconcile these observations, we have initiated a deeper analysis of the role of Wnt signaling in cell senescence, nevogenesis and melanomagenesis. We hypothesize that during nevogenesis, melanocyte proliferation and nevus formation depends on a sufficient level of Wnt signalling activity that is appropriately targeted to proliferation-promoting Wnt target genes. Since activated Wnt signalling in human nevi is expected to antagonize senescence-associated tumor suppression, we also predict that inhibition of Wnt signalling will suppress nevus to melanoma transformation. This application can lead to biomarkers for melanoma risk assessment in nevi and strategies for melanoma chemoprevention.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS