NIHRDataInsights/HRCSData huggingface dataset:
Title: From kinase molecular mechanisms towards new cancer therapeutics
Funder: Cancer Research UK

Abstract: Background The protein kinase field has made remarkable progress towards understanding the regulation of catalytic activity in normal cellular processes, and how mutations confer constitutive activity in cancer cell survival and proliferation. These insights have contributed to the development of protein kinase inhibitors as effective cancer therapeutics. In almost all cases, clinical kinase inhibitors act through competition for the ATP binding pocket, which is highly conserved and therefore these inhibitors have off-target effects. The majority of mutations that confer drug resistance do so by affecting the binding of ATP and/or inhibitors to this site. Up-regulation of kinase activity and scaffolding interactions, however are underpinned by mechanisms outside the ATP binding site. Our research aims to characterize the structural mechanisms that underpin kinase activation and scaffolding functions relevant to cancer signaling, and to develop allosteric inhibitors to target these mechanisms. Aims To understand how oncogenic kinase fusions such as EML4-ALK drive signalling and confer targetable dependencies. To understand the how Aurora-A kinase regulates Myc stability and function through both catalytic and scaffolding activities. To develop and validate approaches to targeting cancer-mutated kinases at allosteric sites, outside the ATP binding pocket. Methods We will decipher molecular mechanisms using established biochemical, biophysical and structural biological approaches such as protein crystallography and NMR spectroscopy. Molecular tools, such as proteins with site-specific mutations and small molecules will be generated to probe these mechanisms and dissect signaling pathways. In addition, innovative strategies such as stapled helix peptides, nanobodies and adhirons will be used to block the sites of protein-protein interactions and to lock kinases into inactive conformations. These resources and know-how will enable us to dissect signaling mechanisms and probe allosteric targeting approaches in cells. This research will be supported by collaborators in cancer cell and clinical biology, who will assist us to validate our work in relevant models. How the results will be used Our studies into will inform the development of optimal treatment strategies for patients who harbor kinase mutations. This may require the inhibition of more than one kinase due to genetic heterogeneity and drug resistance. We believe that highly specific allosteric kinase inhibitors will be a valuable component of combination therapies. Although these may be discovered serendipitously, targeted approaches based on mechanistic insights will accelerate their discovery. We collaborate closely with clinicians and CRUK-funded drug discovery groups and results from this programme of work will be taken forward into therapeutic development. (Cancer sites: Lung, Neuroblastoma, All Sites)


Research activity codes: 5.1 PHARMACEUTICALS;1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Cellular and molecular characterisation of epithelial tumour initiation
Funder: Cancer Research UK

Abstract: Background My research focus is driven by the fact that we still have little understanding of how hundreds of identified genetic aberrations impact tissue homeostasis leading to tumour development. While hugely significant, work to date on large-scale sequencing efforts and a handful of well-characterised mutations has barely scratched the surface and the early stages of precancer tumour development remains poorly understood. Yet, it has a huge potential to improve success rates of early detection, prevention and treatment of cancer. Recent sequencing studies of normal tissue suggest that acquiring putative oncogenic drivers is not sufficient to initiate tumour development. This points towards elements, such as the cell of origin, differentiation state and the microenvironment, all playing a key role in mediating tumour initiation. My laboratory works on defining the early cellular and molecular events that drive tumour initiation and development. In particular, we focus on how the cell of origin affects the differentiation trajectory of nascent tumour cells and dictates changes in the microenvironment thus enabling tumour growth and immune evasion. Since the establishment of my laboratory five years ago, and with generous funding support from CRUK (CEA) we have made several important contributions to the understanding of how aggressive subtypes of breast and lung cancer develop1–4. In particular, we have identified the transcription factor BCL11A as an oncogene in triple negative breast cancer (TNBC)1,4 and lung squamous carcinoma (LUSC)3. Aims Going forward I would like to build on our successes to date by initiating a programme of research with two major aims: 1) characterising the role of BCL11A in epithelial tissue homeostasis and tumour development and; 2) comprehensive identification of cellular and molecular changes associated with the initiation of breast tumours. Methods The proposed programme of research is comprised of two major work packages which will combine the use genetically engineered mouse models, RIME proteomics and single cell genomics to deliver on the two aims of the proposal. How results will be used? I am proposing an ambitious multidisciplinary programme of research for the next six years. By the end of the PFA I expect to have a more comprehensive understanding of the cellular and molecular changes that take place in the lead up to epithelial tumour formation. I anticipate this study will lead to the development of novel approaches for early detection, prevention and treatment of epithelial tumours.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Role of autophagy in glioblastoma progression and survival
Funder: Cancer Research UK

Abstract: Background. The main purpose of this proposal is to study autophagy as a prosurvival pathway in glioblastoma, the most common and aggressive type of brain tumour. During autophagy, cytoplasmic material is targeted for lysosomal degradation maintaining cellular homeostasis and recycling of biological building blocks and energy in the cell. In tumour cells, autophagy is activated as a stress response implicating tumour progression and response to therapy in a context-dependent manner. Understanding the role of autophagy in cancer is particularly important in treating aggressive cancers with unmet clinical need such as glioblastoma. Aims. My current data strongly indicate that autophagy is essential to enable continuous, unconstrained growth of glioblastoma cells. In order to further investigate the potential therapeutic targeting of autophagy in glioblastoma, this proposal aims to: (1) Dissect the impact of autophagy inhibition on the growth of glioblastoma subtypes associated with specific oncogenic mutations. (2) Model the role of autophagy inhibition during glioblastoma development using a novel mouse model. (3) Identify molecular events underpinning the impact of autophagy inhibition in GBM. (4) Characterise the effects of newly identified chemical inhibitors of autophagy on the growth and survival of glioblastoma cells. Methods. To achieve these goals, I will use a number of established and unique approaches including: glioblastoma mouse models (induced by somatic gene transfer or xenograft of patient-derived cancer cells), temporally regulated gene expression systems, molecular profiling of cellular pathways (proteomics) and cell transformation and survival assays. A combination of these approaches will enable detailed understanding of the role of autophagy in glioblastoma as well as the discovery and verification of novel drug targets. How the results of this research will be used. Success of this study will not only lead to the identification of pathways required for glioblastoma survival, but will also provide insights into the development of novel therapeutic approaches that target autophagy. The novel mouse model and chemical inhibitors of autophagy will be useful for a number of disease models and in pre-clinical studies. Overall, the findings are likely to enhance the translational outcomes of the currently utilised anti-cancer treatment and their applications can be extended to multiple types of cancers.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Exploiting the innate and adaptive immune interface for effective cancer therapy
Funder: Cancer Research UK

Abstract: Background The success of immunomodulatory monoclonal antibodies (mAbs) provides proof-of-principle that host immunity can be manipulated to treat cancer. However, much current research is focussed on the effect of these reagents on T-cells, with minimal investigation of innate immunity. The significance of this oversight is exemplified by my recent observations showing that stimulation of T cells by agonist anti-CD27 mAb indirectly activates innate effectors, such as myeloid cells, to mediate previously unheralded levels of killing by tumour-targeting mAbs. These observations have translated into a clinical trial combining varlilumab (anti-CD27) and rituximab (anti-CD20) in B-cell lymphoma (RiVa). These findings demonstrate the need to better understand the innate and adaptive immune interface, and highlight a novel means of combining mAbs to promote effective cancer immunotherapy. Aims • To understand and optimise T-cell stimulation of innate immune effectors in haematological and solid tumours. • Define the optimal format of agonistic mAbs, using CD27 reagents as an example. • Select the best combinations of agonistic and tumour-targeting mAbs to control haematological and solid tumours. Methods A panel of immunostimulatory mAbs will be tested in immunocompetent mouse tumour models (lymphoma, melanoma, colon and breast cancer). Changes in innate and adaptive immune systems will be analysed using multicolour flow cytometry, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and immunohistochemistry. Functional immunological assays (macrophage phagocytosis and cytokine release) will be used to scrutinise the immunological consequences. The appropriate transgenic mice (e.g. CD27-/- mice) will be employed to dissect the contribution of individual cell types in adoptive transfer experiments. In parallel, in vitro assays using human PBMC cultures will be performed to assess T-cell stimulation, monocyte activation and cytokine release after mAb treatment. RNA sequencing will also be performed on pre- and post-treatment samples stored from RiVa. To define the optimal format of agonistic mAbs, using anti-CD27 as an example, different mAb and isotype/Fc variants will be produced. These mAb, differing in agonistic potential, will be assessed by epitope analysis using truncation and alanine scanning mutants to determine associations between agonism, epitope and isotype. The optimal agonistic mAbs in relevant combinations will then be tested in humanised cancer models (lymphoma and breast). How the results of this research will be used These results will provide an in-depth understanding of how innate and adaptive immunity can co-operate to transform therapeutically sub-optimal tumour-targeting and immunomodulatory mAbs into efficacious combination therapies for cancer, including solid tumours.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Structure and molecular function of the DREAM complex in gene expression programs of cellular quiescence.
Funder: Wellcome Trust

Abstract: The cell cycle is the fundamental biological process where the cell coordinates chromosome replication and segregation with cell growth and division. In response to internal/external cues individual metazoan cells exit from the cell cycle. Cell cycle exit is reversible during cellular quiescence, a process crucial for tissue regeneration and cancer cell resistance to therapy. Progression through the cell cycle is promoted by the cyclins, which activate the cyclin-dependent kinases. During quiescence, cyclin gene expression is repressed by the DREAM complex, which assembles at cyclin gene promoters, thereby repressing their transcription. To understand the DREAM complex molecular function in quiescence, I propose to reconstitute and determine the cryo-electron microscopy structures of the ~450 kDa 8-subunit human DREAM protein complex, the complex of DREAM with its target DNA sequences and the nucleosome, and to perform structure-based functional studies in biochemical assays and cancer cell lines. The DREAM complex pathway is misregulated in ovarian carcinoma, where it promotes the formation of quiescent tumour cells resistant to therapy. Understanding the molecular mechanism of DREAM-mediated cell cycle regulation will allow to (i) understand the molecular biology of quiescence and to (ii) design novel anticancer drugs to be used in more effective therapies against ovarian cancer.

Lay abstract: My research plan focuses on the fundamental cellular process of quiescence where cells stop proliferating by exiting from the cell cycle to guarantee the maintenance of reservoirs of stem cells, which are crucial for tissue regeneration. Quiescence is also a strategy used by the cancer cells to survive anti-cancer drugs in both primary and metastatic tumours. I plan to perform a molecular characterization of a key promoter of quiescence named the DREAM complex. I will determine the DREAM structure by cryo-electron microscopy in the context of its functional environment, including chromatin of target genes, which this complex represses, and use this information to further characterize DREAM function in human cancer cells. The findings of my research will expand our knowledge of cellular mechanisms regulating the cell cycle and will give foundations to structure-based drug development aiming to target the quiescent state and to prevent cancer resistance and spread.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: CRUK/14/022: SCOPE2 - A randomised Phase II/III trial to study radiotherapy dose escalation in patients with oesophageal cancer treated with definitive chemo-radiation with an embedded Phase II trial for patients with a poor early response using positron emission tomography (PET)
Funder: Cancer Research UK

Abstract: Background: In the UK, oesophageal cancer is the sixth most common cause of cancer death and accounts for around 5% of all cancer deaths. Definitive chemo-radiotherapy (dCRT) is usually offered to those patients who are unsuitable for surgery. Increasingly, dCRT is considered a standard of care in patients with oesophageal squamous cell carcinoma (SCC) and adenocarcinoma (ACA). In the recently reported SCOPE1 trial, the outcome in the standard dCRT arm was unprecedented with a mOS of 25.4 mo and 2-yr OS of 56% thus providing an excellent platform on which to design future studies to test new treatment regimen. The majority of patients who succumb to the disease, do so due to progressive/recurrent loco-regional disease. There is evidence for a radiotherapy dose response effect in oesophageal cancer. Based on low rates of toxicity seen with the SCOPE 1 regimen, tumour control modelling and the use of newer radiotherapy techniques, it should be possible to safely intensify treatment using a higher dose of radiation to a highly conformal target volume within the context of a high quality RTTQA program. The lack of an early metabolic response to neo-adjuvant chemotherapy defined by FDG –PET predicts for a poor outcome in patients with operable oesophageal cancer. We hypothesize that dCRT can be improved by switching to an alternative chemotherapy backbone in PET non-responders and/or increasing the radiotherapy dose. Study Questions: • Does high dose RT (60Gy/25f) improve overall survival compared to standard dose RT (50Gy/25)? • In PET non-responders, does switching chemotherapy and/or RT dose escalation improve treatment response? Methods: SCOPE2 is an umbrella study which incorporates two parallel trials in SCC and ACA patients. Each trial being a randomised, open label study (SCC:phase II/III and ACA:phase II) comparing high vs standard dose RT. Within the trials is an embedded Phase II study comparing cisplatin+capecitabine vs carboplatin+paclitaxel (carbo/taxol) chemotherapy in PET non-responders. A total of 580 patients with oesophageal cancer (440 SCC and 140 ACA) will be randomised to 50Gy or 60Gy radiotherapy, given concurrently with chemotherapy. Those patients identified as 14 day PET non-responders will be randomised to either continue cisplatin+capecitabine chemotherapy or switch to carbo/taxol chemotherapy. How the results of this research will be used: The Phase III trial in SCC will define optimum clinical practice for this group of patients. The Phase II trials (PET/chemo & ACA) will determine whether or not to continue to a Phase III study.


Research activity codes: 6.1 PHARMACEUTICALS;6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: The role of the Spindle Assembly Checkpoint in Genomic Stability
Funder: Cancer Research UK

Abstract: Title: How is genomic stability ensured in mitosis? Background: The Spindle Assembly Checkpoint (SAC) is essential to prevent aneuploidy and is itself a chemotherapeutic target. The SAC responds to unattached kinetochores, which catalyse the production of the Mitotic Checkpoint Complex (MCC) to inhibit the Anaphase Promoting Complex/Cyclosome (APC/C) and prevent it from ubiquitylating Cyclin B1 and securin. This ensures that the separase protease remains inactive – thereby ensuring sister chromatid cohesion is maintained – and that cells cannot exit mitosis. The SAC has the notable properties of being very potent - just one unattached kinetochore can delay anaphase - but highly responsive: the APC/C turns on within one minute of the SAC turning off. The ratios of the different SAC components has been shown to be crucial to proper SAC function and although mutations in SAC components are relatively rare in cancer, an imbalance in their levels is common and indeed predisposes to cancer: exactly why is unclear. Aims: The overall aim of my research is to determine how cells ensure that the two daughter cells receive an equal and identical set of chromosomes and the crucial role played by the mutual regulaction between the SAC and the APC/C is the key to this . I have three specific aims for the next 5 years: 1) Is there a SAC-independent mechanism that contributes to genomic stability? 2) How is the SAC made potent but responsive? 3) How does perturbing the SAC machinery contribute to aneuploidy? Methods: We will use a combination of CRISPR/Cas9 gene editing, live cell assays, in vitro human cell extracts and mass spectrometry analysis to elucidate the molecular mechanisms regulating Cdc20, the APC/C and the MCC in both normal diploid and aneuploid human cells. How the results of this research will be used: A greater knowledge of how the SAC is activated and inactivated could lead to the identification of new drug targets that are as effective but better tolerated than the taxanes and vinca alkaloids. Our research on the ABBA motif-dependent interaction between the MCC and the APC/C could also lead to the development of small molecule inhibitors of the SAC that could have therapeutic value.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Investigating resistance to PI3K pathway inhibitors to combat castration-resistant prostate cancer
Funder: Cancer Research UK

Abstract: Prostate cancer claims the lives of over 300,000 men globally each year. The primary cause of death is castrate-resistant prostate cancer (CRPC), which develops when androgen-deprivation therapy fails. To improve survival rates, new treatments that prevent or overcome CRPC are urgently needed. The phosphoinositide-3-kinase (PI3K) pathway is activated in nearly all CRPC tumours, thus presenting an attractive therapeutic target. However, PI3K pathway inhibitors have shown limited efficacy in clinical trials, predominantly reflecting incomplete target suppression owing to resistant signalling events. Dr Pearson's research addresses the key question of resistance to PI3K-directed therapies in CRPC and the role of PI3K signalling in the surrounding tumour microenvironment, with a view to discovering new therapeutic approaches and biomarkers for prostate cancer that improve patient care and outcome.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: BRCA1 pathways in cancer predisposition and treatment
Funder: Cancer Research UK

Abstract: • Background Inheritance of a mutation in the Breast Cancer 1 gene, BRCA1, confers a high risk of breast and ovarian cancer while de novo or somatic mutations are found in 3-7% of young breast and ovarian cancer patients. BRCA1 controls several pathways that contribute to genome stability. For several years we have understood that the BRCA1 protein functions in the homologous recombination (HR) DNA repair pathway. HR-directed therapies such as Poly (ADP-ribose) Polymerase 1 inhibitors (PARPi) act, in part, by targeting the poor repair of BRCA1-deficient cancer cells. However these agents do not target all carrier tumours successfully and cancers develop resistance. There is a lack of understanding of how particular BRCA1 functions relate to cancer predisposition. Moreover the degree to which different pathways influence treatment responses and disease resistance or whether they could be targeted to improve treatments for familial and sporadic cancer patients is not clear. • Aims The proposed programme aims to elucidate the molecular details of several emerging roles of BRCA1 in distinct DNA repair pathways. This is in order to ask which are responsible for cancer development and to identify new vulnerabilities exposed by loss, or an altered balance, of particular functions. • Methods Our approach is based on separation of function mutations in the BRCA1-BARD1 system in human and mouse cells able to differentiate activities and regulatory events. • How the results of this research will be used. The data generated will build a view of whether different functions of BRCA1 are associated with tumour development, helping to classify patient substitution variants and improve our understanding of cancer development. The data will demonstrate what pathways remain open to targeting in PARP-resistant BRCA1 deficient tumours. The data may also show how some sporadic tumours, due to changes in the BRCA1 system are vulnerable to specific targeting.


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