NIHRDataInsights/HRCSData huggingface dataset:
Title: The Cancer Research-UK Nucleic Acid Structure Research Group : Nucleic acid structure and interactions with proteins
Funder: Cancer Research UK

Abstract: DNA and RNA are the cell's genetic molecules. Cancer is fundamentally a genetic disease, resulting from abnormal connections between DNA molecules, or failure to repair damaged DNA. Our goal is to understand branchpoints in DNA, central to DNA repair and rearrangement. We employ advanced biophysical methods for this. Helical junctions play important roles in both DNA and RNA. Four-way DNA (Holliday) are the central intermediates of DNA repair and recombination, and both three and four-way junctions can be created in DNA by stalled replication forks. Junctions are key elements in the architecture of functional RNA molecules, important in structure and folding and the biogenesis of RNA-based assemblies such as the ribosome. The processing of DNA junctions by proteins is critically important in DNA recombination, replication and repair. These enzymes are highly selective for the structure of branched DNA, and our goal is to understand the mechanism by which these structure-selective DNA-protein interactions are mediated. 1. We will define the general principles behind these interactions using the well-defined prokaryotic enzymes. These studies will build on our detailed biophysical studies of the enzymes, and our crystallographic analysis of a complex between the junction-resolving enzyme endonuclease I and a four-way DNA junction. 2. We have recently begun to study a series of nucleases of human origin that selectively cleave four- and three-way junctions. They will be subject to an analysis of their enzymatic and binding activities using rigorous kinetic and thermodynamic approaches as worked out in this laboratory for the analysis of phage enzymes. These are :a. The human GEN1 and C. elegans Gen1 enzymes, that exhibit specificity for cleavage of four-way DNA junctions. b. The human SLX1-SLX4 complex, that also cleaves four-way DNA junctions.c. The human SLX4-MIS81 complex, that cleaves three-way junctions.d. The human MTMR15 protein, that induces a precise site-selective cleavage into nicked three-way junctions (analogous to a replication fork) and related 3' flap structures. There has been very little investigation of DNA-protein interactions in such structures.We shall continue to extend our structural studies of RNA folding elements, as well as larger RNA species. We shall also continue our studies of the mechanisms and chemical origin of RNA catalysis. An exciting new area is sequential RNA folding. In the cell, RNA folds co-transcriptionally, as it is synthesized from 5' to 3'. This has been broadly neglected; we intend to use two parallel approaches :a. FRET, SAXS and HO. probing analysis of a series of truncated molecules, representing incompletely-synthesized species at various stages. b. Single-molecule FRET analysis of sequential RNA displaced using a novel approach currently being developed in this laboratory.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Mechanistic and preclinical relevance of IGF1R activation in paediatric glioblastoma
Funder: Cancer Research UK

Abstract: Background We have identified IGF1R to be a potential therapeutic target in paediatric glioblastoma due to (a) high levels of IGF2 expression and (b) IGF1R amplification in tumour samples, as well as (c) receptor activation and (d) efficacy of IGF1R inhibitors in paediatric glioblastoma cell lines. Cancer relevance The clinical outcome for children with glioblastoma is dismal, with a current two-year survival rate of just 10-15%. In order to make progress in the treatment of paediatric glioblastoma, we need a better understanding both of the molecular biology underpinning the disease, as well as the mechanisms by which tumour cells escape from both chemotherapeutic and targeted therapies. Aims The aim of this proposal is to follow up these observations with a detailed molecular pathological characterisation of the IGF system in paediatric glioblastoma coupled with in vitro and in vivo preclinical work aimed at unraveling the differential mechanisms of action and resistance of two inhibitors (PPP and AEW541). Plan of Research It is our intention to screen the following molecules for protein expression by immunohistochemistry on the paediatric (n=181) and adult (n=400) TMAs: IGF1R, phospho-IGF1R, IGF2R, IRS1, phospho-IRS1, IRS2, phospho-IRS2, INSR, phospho-INSR, IGF1, and IGF2. We will also investigate copy number by FISH for IGF1R and IRS2. Data will be correlated with tumour histology, age at diagnosis and clinical outcome as well as existing genomic data on these cases. We have previously identified differential effects of treating paediatric glioblastoma cells in vitro with the IGF1R inhibitors PPP and NVP-AEW541. We will now test the hypothesis that AEW541 exerts its cell cycle effects via CDK2, rather than PPP which acts via CDK1, by a combination of Western blots, FACS and electron microscopy to assess autophagy. We will also explore the differential mechanisms of action of the two compounds by an unbiased approach using expression profiling and phosphoproteomics. We will further extend our in vitro work to in vivo models, specifically testing the efficacy of anti-IGF1R strategies in subcutaneous and orthotopic intracranial models we have developed. We will also examine the chemosensitisation effects of IGF1R inhibitors in combination studies with temozolomide, both in vitro and in vivo. Finally we will undertake to derive resistant lines in vitro such that we can explore, by measurement of relevant signalling proteins as well as unbiased approaches, the mechanisms of resistance to IGF1R inhibitors, and potential strategies for overcoming this.


Research activity codes: 5.1 PHARMACEUTICALS;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Iterative Design, Randomisation, Selection, Truncation and Characterisation to Generate Small High Affinity Antagonists of the Activator Protein-1 Motif
Funder: Cancer Research UK

Abstract: Activator Protein 1 (AP-1) is a key DNA binding protein controlling cell growth and division. In certain cancers this process becomes deregulated. We have established a novel library screening system to generate small highly specific peptide inhibitors that target correct AP-1 components and will elucidate their mechanism of action. We will advance knowledge and contribute to improved health by screening small length peptide libraries derived using two techniques that I have already demonstrated to be highly effective with this system; æ'Protein-fragment Complementation Assays' (PCA) in which I have considerable expertise to select tight binding peptides, and a 'Competitive And Negative Design Initiative' (CANDI) which I have explicitly developed to increase the specificity of PCA derived antagonists in binding and sequestering key homologues of AP-1.The specific aims are to:i) Use PCA to screen reduced length large-scale peptide libraries based on our tightest-binding antagonists. This will be iterative in that each winner will serve as the template for the next truncated design round.ii) Use CANDI-PCA to improve peptide specificity, and therefore efficacy, at each design round.iii) Characterise our truncated peptides using biophysical in vitro methods as well as in vivo techniques to demonstrate peptide-target stability and functionality, and efficacy.iv) Undertake a detailed study of the folding pathway of PCA and CANDI-PCA selected antagonists with their target and tailor rate constants based on these findings in later design rounds. The ultimate aim is to generate highly effective peptide antagonists de novo, which will contribute to translational science by accelerating the peptide drug design process with a pre-defined screen for efficacy. Elucidation of kinetic design rules therefore has the potential to accelerate the design of stable and specific pairs by using rules that lead to further design iterations and specific sequestration of key AP-1 homologues without binding to AP-1 proteins that are functioning normally. Once stable and specific peptides are generated, collaboration and further funding will be sough to pursue peptidomimetic drugs of most effective molecules to improve human health.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Analysis of MRN-dependent and -independent topoisomerase removal mechanisms: implications for resistance against Camptothecin and Etoposide derivatives
Funder: Cancer Research UK

Abstract: To identify and characterise proteins which provide resistance to topoisomerase poisons, a group of clinically important cancer drugs. I will study the contribution of these proteins to topoisomerase removal in molecular detail and establish their suitability as targets for drugs that increase the sensitivity of cancer cells to existing treatments. Last updated / / Camptothecin (CPT) and etoposide derivatives are clinically important cancer drugs that kill proliferating cells by locking Top1 and Top2, respectively, covalently onto the DNA, interfering with transcription and DNA replication. For a cancer cell to survive treatment with these drugs, the covalently bound topoisomerase must be removed. The Mre11/Rad50/Nbs1-Ctp1 (MRN-Ctp1) protein complex is involved in a wide range of early responses to DNA damage. I have recently demonstrated that the nuclease activity of Mre11 (Rad32 in S. pombe) contributes to removal of both Top1 and Top2, and that the MRN-Ctp1 complex thus provides a major contribution to cellular resistance against CPT and etoposide derivatives. In the long term, I want to establish the suitability of the MRN-Ctp1 protein complex and other proteins involved in topoisomerase removal as targets for drugs that increase the sensitivity of cancer cells to CPT and etoposide derivatives. My data show that the topoisomerase removal activity of the MRN complex is separable from its role in DNA repair downstream of removal, which is essential for the maintenance of genome stability and prevention of carcinogenesis. These unique characteristics make the MRN complex a particularly promising target for drugs that specifically raise the sensitivity of cancer cells against CPT and etoposide derivatives, without negatively affecting other genome stability maintenance mechanisms Apart from MRN-Ctp1, other proteins have previously been implicated in topoisomerase removal. The specific aims of this proposal are to analyse the mechanism of MRN-Ctp1 dependent topoisomerase removal in molecular detail and to establish the relative contribution of MRN-Ctp1 dependent and independent mechanisms to topoisomerase removal and resistance to CPT and etoposide derivatives. I therefore propose to 1) purify the MRN-Ctp1 complex and associated proteins and analyse the mechanism of topoisomerase removal in vitro, 2) identify and analyse in molecular detail protein domains and post-translational modifications in MRN-Ctp1 and associated proteins which are specifically involved in topoisomerase removal and 3) identify and characterise MRN-independent topoisomerase removal pathways and establish their relative contribution to removal in different phases of the cell cycle and in the context of replication and transcription. Last updated / /


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Control of gene expression through small regulatory RNA
Funder: Cancer Research UK

Abstract: My laboratory is investigating how cells decide to divide or to differentiate. If cells get these decisions wrong, cancer may be the consequence. Our particular focus is a class of small regulatory genes (microRNAs) that act like molecular switches in cells and are directly involved in human cancer. Background: One of the major advances in biology over the last ten years has been the discovery of short RNAs (sRNAs) as key regulators of gene regulation in eukaryotes. sRNAs include microRNAs (miRNAs), piRNAs and endo-siRNAs. miRNAs are essential for animal development, physiology and homeostasis. piRNAs and endo-siRNAs are required for silencing of transposable elements, genome stability and fertility. Artificial sRNAs have revolutionized molecular genetic experiments through the technique of RNA interference (RNAi). RNAi is currently being developed as a next generation therapeutic. Despite much progress, however, many basic questions about sRNA biology and mechanisms remain unanswered.Relevance to cancer: sRNA research is in the process of changing many areas of cancer research. Firstly, miRNA expression data are proving highly informative, technically easy to obtain and are currently being developed into human cancer diagnostics and prognostics in clinical trials. Secondly, many miRNAs are directly regulating or are directly regulated by oncogenes or tumour suppressor genes (TSGs). Thirdly, a number of miRNAs and miRNA biogenesis genes have recently been demonstrated to act as oncogenes or TSGs. Fourthly, interfering with miRNAs through RNAi is a new anti-cancer strategy currently being tested in a number of clinical trials. Finally, a deeper understanding of the biology of sRNAs will be essential to develop effective RNAi based anti-cancer strategies targeting miRNAs or other genes.Specific aims of research: We aim to discover miRNA regulatory networks in vivo; to identify new genes required for miRNA biogenesis, mechanism and degradation; to reveal the biogenesis and mechanism of piRNAs and other sRNAs; to identify sRNAs deregulated in cancer and to link new sRNAs to cancer networks. It is our hope that this work and the work of others in the field will lead to new targets for anti-cancer therapy, new markers for diagnostics and prognostics and new anti-cancer strategies.Outline of research plan: We will use molecular genetics, molecular biology, systems biology and chemical genomics approaches to investigate the biology of miRNA and other small RNA pathways using the nematode Caenorhabditis elegans. This animal offers unique and powerful genetic tools, is the simplest common laboratory animal in which miRNAs have been described, and most importantly many pathways relevant for human cancer are conserved in C. elegans. We will translate this work to mammalian systems by utilizing mammalian cancer cell lines and mouse models and analyze miRNA expression in human tumours. Last updated / /


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Growth control by the actin cytoskeleton: transcriptional targets of MRL/SRF signalling and their role in hyperplastic growth
Funder: Cancer Research UK

Abstract: (1) a brief background to the proposal; Signalling by growth factor receptors such as the epidermal growth factor receptor (EGFR) stimulates cell proliferation and promotes tumour formation. These functional characteristics are broadly shared by the Mig10/RIAM/Lpd (MRL) family of adapter proteins, which transduce signals derived from growth factors, via interactions with Ras GTPases and/or phospholipids, to changes in the actin cytoskeleton. (2) the relevance to cancer; There is mounting evidence that increased cell growth, proliferation and motility resulting from aberrant MRL function may contribute to cancer development or progression. Understanding how changes in actin dynamics are linked to altered cell behaviours may help to improve our knowledge of the molecular pathogenesis underlying EGFR-mediated cancers and identify novel molecular targets for therapeutic intervention. As deregulated EGFR signalling is associated with a variety of aggressive tumours, which are frequently resistant to conventional treatment, a better understanding of the underlying molecular pathology is of major clinical and scientific importance. (3) the specific aims of the research; We recently showed that MRL proteins drive hyperplastic growth via changes in actin dynamics and Serum Response Factor (SRF) activation. Here, we will identify the transcriptional targets of MRL-SRF signalling and determine how MRL-mediated changes in the actin cytoskeleton specifically promote hyperplastic growth. (4) an outline plan of research. I propose to address these issues in drosophila, which offers many advantages for the study of conserved signalling networks that go awry during tumour formation and cancer progression. We will use molecular cell biology, employing advanced cell imaging techniques, to determine the organisation and regulation of MRL-SRF signalling in cells. Recent technological advances in digital transcriptomics will be combined with bioinformatic modelling and classical genetics to identify transcriptional targets of MRL-SRF signalling and their contribution to MRL-mediated tissue overgrowth.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: CRUK/10/039: EuroNet PHL-LP1
Funder: Cancer Research UK

Abstract: Background_x000D_ Published literature suggests that very little or no treatment is sufficient for long-term survival in children with early stage [ES] nodular lymphocyte predominant lymphoma [nLPHL]._x000D_ Specific aims_x000D_ To clarify whether surgical resection alone is sufficient for a select group of children with fully resected disease and whether a non-intensive chemotherapy regimen comprising CVP*could replace standard chemotherapy without compromising efficacy in children with unrescectable ES nLPHL._x000D_ _x000D_ Summary of study_x000D_ Non-randomized two arm study. All eligible children with ES nLPHL in the participating centres will be enrolled on to the study which requires_x000D_ a] Real time confirmation of nLPHL histology by UK pathology panel_x000D_ b] Central review of imaging in Germany_x000D_ _x000D_ Treatment arms:_x000D_ Surgery alone - "Watch and Wait"_x000D_ All disease completely resected at initial diagnostic biopsy_x000D_ If second look surgery removed all residual disease_x000D_ _x000D_ Stage IA or II A disease - CVP chemotherapy_x000D_ Second look surgery not feasible_x000D_ Unsuccessful_x000D_ Unacceptable to patient_x000D_ CVP* - Cyclophosphamide 500mg/m2 iv d1, vinblastine 6mg/m2iv d1&8 & prednisolone 40mg/m2 orally d1to8._x000D_ Children who achieve a complete response will enter regular clinical follow up. Patients who relapse after surgery alone with ES disease are eligible to be treated with CVP.


Research activity codes: 6.4 SURGERY;6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: CRUK/07/024: ESPAC 4T: European Study Group for Pancreatic Cancer Trial 4 prospective sample collection
Funder: Cancer Research UK

Abstract: Our hypothesis is that markers in resected tumour or blood, and/or urine taken before adjuvant (post-surgery) chemotherapy for pancreatic cancer will predict which patients will respond best. We will make samples from a large trial available for empirical or theory based studies to identify or test these markers. Last updated 21/08/2009 Background: The ESPAC-1 trial demonstrated that adjuvant treatment with 5-fluorouracil offers significant survival benefit to patients with pancreatic cancer. ESPAC-3v2 demonstrated no significant survival difference between adjuvant 5-FU/FA versus gemcitabine. CR-UK funded retrospective collection of samples from ESPAC-1/3v2 is ongoing (samples from over 600 patients). ESPAC-4 is an adjuvant trial addressing the question of whether combining capecitabine with gemcitabine offers any benefit over gemcitabine alone in pancreatic cancer. The proposed study (ESPAC-4T) will produce one of the most extensive collections of pancreatic cancer tissue from clinical trials. Aims: To collect samples from 1080 patients in the ESPAC-4 trial to ensure a greater variety of samples and better standardisation of collection. This will facilitate identification of markers in primary tumours and other samples taken before chemotherapy which predict improved survival for either treatment regimen; providing a basis for future studies in pancreatic cancer. Summary: Samples will be collected before and after chemotherapy in the largest clinical trial on adjuvant treatment of pancreatic cancer. Manufacture of tissue-microarrays and baseline analysis of the samples will be carried out and a database produced linking samples to clinical outcome. An independent committee will allocate samples to high quality projects to identify or to test markers. Last updated 21/08/2009


Research activity codes: 4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: CANCER AND NEOPLASMS
Title: CRUK/10/008: ANZMTG-WBRT: Whole brain radiotherapy following local treatment on intracranial metastases of melanoma - a randomised phase III trial.
Funder: Cancer Research UK

Abstract: To determine whether whole brain radiotherapy reduces the risk of melanoma brain metastases developing, after initial treatment (with surgery or targeted radiotherapy) for these; and to determine if this improves survival after initial treatment Last updated 21/08/2009 Background Brain metastases are a common cause of death in patients with melanoma. The use of whole brain radiotherapy (WBRT) after excision and/or stereotactic irradiation for melanoma brain metastases is variable and controversial because there is no high quality evidence to guide practice. Aims To determine the effect of adding WBRT to local treatment on distant intracranial control, quality of life, performance status, neurocognitive function, progression-free and overall survival. The primary end point is the proportion of patients with distant intracranial failure after 12 months, defined as new disease appearing over 1cm from an index metastasis. Summary Multi-centre 2-arm phase III trial involving 200 patients with melanoma who have had 1-3 brain metastases excised and/or stereotactically irradiated. Patients must have an ECOG performance status of two or better. Patients with leptomeningeal disease, or previous WBRT or localised treatment for cerebral melanoma will not be eligible. Patients are randomly allocated, within 6 weeks of local treatment, to receive either: - immediate WBRT (start within 8 weeks of local treatment) - observation (with WBRT permitted at recurrence of brain metastases) WBRT treatment is administered as 30 Gy in 10 fractions via parallel opposed lateral beams dosed to the midpoint. Last updated 21/08/2009


Research activity codes: 6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS