NIHRDataInsights/HRCSData huggingface dataset:
Title: Wnt signalling and cancer
Funder: Medical Research Council

Abstract: The Wnt/beta-catenin signalling pathway is ancient and plays a key role during the normal development and tissue homeostasis of animals. This pathway is often dysregulated in human cancer. In particular, most colorectal cancers are due to hyperactive beta-catenin signalling in the intestinal epithelium, caused by mutational inactivation of its negative regulator, the Adenomatous polyposis Coli (APC) tumour suppressor, or by mutational activation of beta-catenin itself. Our aim is to understand the molecular and cell-biological mechanisms underlying the transduction of the Wnt signal from the plasma membrane to the nucleus in normal and malignant cells. In focus are the molecular functions of positive regulators of the Wnt pathway that have potential as drug targets, including Dishevelled and the Pygo-BCL9 complex. Our main questions are how Dishevelled assembles Wnt signalosomes to inactivate the Axin-APC complex, and how the Pygo-BCL9 complex enables the Wnt enhanceosome to activate beta-catenin-mediated transcription. Our approach is to combine biochemical, biophysical and structural analysis of these proteins with cell-biological analysis and functional assays in mammalian cell lines (including colorectal cancer cells) and in whole-organism models such as Drosophila and mice. We have also been awarded a CRUK programme grant to develop the potential of these Wnt signalling components as drug targets and to examine their regulation by the ubiquitin system.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Quantitative Gene Expression
Funder: Medical Research Council

Abstract: Living cell must generate sufficient amounts of biomolecules to reach and maintain an optimal size. Cell size is related to function and can span orders of magnitudes from tiny lymphocytes to giant neurons. Accurate size control requires careful coordination of growth and division. While control of the progression through the cell-cycle has been extensively studied, much less attention has been devoted to mechanisms controlling cell growth and cell size. This is a very important problem because understanding how cells generate biomass is indispensable to decoding how cells function. It is also directly relevant to medical research because de-regulated growth is deleterious with pathologies such as cancer, or cardiac hypertrophy. Cell growth has universal and profound implication for the control of gene expression. The number of molecules a cell must produce and maintain depends on its size and on the rate at which it creates biomass. Therefore growth is a dynamic process that necessitates continuous adjustments of gene expression. Moreover, growth and division cycles generates fluctuations in molecules number that affect cellular physiology. Our goal is to understand how the complex interplay between growth and gene expression affects cell physiology and phenotypic diversity. Our programme integrates experimental and computational approaches to study how growth and size interact with gene expression and phenotypic variability. We approach this problem from two complementary angles in cells populations and single cells. We aim at identifying how global genome expression is adjusted to increased demand in RNA and protein numbers when cells grow. We identify factors that limit growth, and study cellular economics during normal and extreme growth. We also investigate the interplay of cellular metabolism with chromatin structure during growth. Together, this will help identifying how optimal growth is achieved. In the second half of our program, we use single cell approaches to investigate the crosstalk between cell growth, transcriptional noise and phenotypic heterogeneity. We analyse cells growing at different rates to identify cellular features that regulate phenotypic heterogeneity. We also analyse the transcriptomes of single cells growing at different rates and dividing at different size to understand how gene expression variability relates to phenotypic heterogeneity. Finally we investigate the influence of transcriptional and post-transcriptional layers of regulation on gene expression noise as growth and size vary. Together our programme will shed light on the complex interplay between growth cell size and gene expression.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Statistical Genomics; modern statistical approaches to the analysis and interpretation of high-throughput genomics data.
Funder: Medical Research Council

Abstract: Our aim is to develop and refine statistical approaches to the analysis and interpretation of high-throughput genomics data arising from mouse models of human disease. Recent developments in high-throughput genomics including sequencing technologies have lead to the routine generation of large complex data sets. Analysing and interpreting such data is complicated by the high-dimensionality and non-standard variation in the data. Our research programme is aimed at developing statistical methods and tools to enable scientists to understand dependencies within the data in an unbiased and optimal fashion. To do this we make use of statistical programming languages, such as R, to compose computer programs that can be used by the community for their data analyses needs. For instance, we have recently developed methods for the analysis of copy-number-variation in genome-wide data from SNP genotyping arrays and whole genome sequencing. The methods make use of decision theory and Bayesian statistics to define appropriate prior probabilities on the nature of copy-number-variation and loss functions to make calling of copy-number-events. We are extending our approaches in germline DNA to look at copy-number-variation in cancer cells. Analysis is complicated by the heterogenous nature of cancers, with possibly many distinct sub-types of cells within a tumour. This requires the use of deconvolution approaches to tease apart the individual sources of variation contained within the combined signal. Further tailored statistical methods are currently being developed for the analysis of data arising from the International Mouse Phenotyping Consortium (IMPC) project.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Understanding how genome stability is maintained in response to chromosomal breaks.
Funder: Medical Research Council

Abstract: Histone H3 lysine 36 (H3K36) methylation plays a central role in both orchestrating the DNA damage response (DDR) and in suppressing tumorigenesis. We have discovered key roles for H3K36 trimethylation (H3K36me3) in the DDR where it both promotes homologous recombination (HR) repair of DNA double-strand breaks (DSBs) (Pfister et al., Cell Reports 2014), and is also essential for DNA replication restart following replication stress resulting from checkpoint kinase inactivation (Pfister et al., Cancer Cell 2015). Accordingly SETD2-dependent H3K36me3 is frequently depleted in a number of cancer types, including high-grade pediatric gliomas (>50%), and metastatic renal carcinomas (~60%), for which prognosis is poor. We recently exploited a conserved synthetic lethal relationship we identified in fission yeast to target H3K36me3-deficient cancers, using the WEE1 inhibitor, AZD1775, which is already in Phase II clinical trials. As a result of these studies, together with the development of a biomarker to detect H3K36me3 loss in patient tissue, the use of AZD1775 to target H3K36me3-deficient cancers has now been adopted into the MRC-supported FOCUS4 clinical trial. Despite these advances, how H3K36me3 coordinates these distinct DDR functions is unknown. Moreover, the extent to which this synthetic lethal relationship can be expanded and translated into the clinic has not yet been explored. We therefore propose to determine how H3K36me3 maintains viability in response to replication stress, thereby better understanding this synthetic lethality (Aim 1); to delineate the role of the H3K36me3 pathway in homologous recombination repair (Aim 2); and to further translate these findings into the clinic through identifying other targetable disease sites, by determining the AZD1775 sensitivity of cancers with intermediate H3K36me3 levels, by improving cancer targeting through combining AZD1775 with other agents, including ionizing radiation, and by understanding the mechanisms and pathways leading to AZD1775 resistance (Aim 3). We will use a powerful combination of yeast and mammalian genetics, together with small molecular inhibitors to achieve these aims. We anticipate that the proposed research will provide mechanistic insights into how histone H3K36 trimethylation promotes DSB repair and maintains cell viability in response to such replication stress. Further, we predict that by expanding this synthetic lethal relationship through genetic triangulation we will broaden both the biological and clinical application of our findings.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Computational and Disease Genomics
Funder: Medical Research Council

Abstract: We seek to advance the molecular mechanistic understanding of genetic disease and transcriptional regulation. To do so we take advantage of our recent analytical and technological advances in understanding noncoding sequence functionality, sequencing the DNA and RNA of single cells, and identifying distantly related homologues. We have three main aims: • Determine the causal contribution made by variable transcription factor binding to an individual’s susceptibility to complex disease • Tracing the competing lineages of genomic/transcriptomic crisis from very early oncogenesis • Determine the function and evolutionary history of new protein domains. Our first hypothesis is that variation of trait susceptibility occurs via a causal effect on gene expression arising from genetically or environmentally altered transcription factor (TF) binding. We are using Mendelian randomization approaches that predict causal relationships and do so for genetic, rather than purely environmental, contributions to disease risk. We study a TF for which there is existing genetic (i.e. causal) evidence of contribution to complex disease and whose activity can be easily and safely modulated therapeutically. We seek to predict the benefit of this therapy for persons according to their polygenic risk for specific complex diseases that we will identify objectively. Our selected factor is the vitamin D receptor (VDR), a TF of the nuclear receptor family that functions as a heterodimer with retinoid X receptor (RXR), chosen because supplementation of vitamin D (cholecalciferol or ergocalciferol) at pharmacological doses is common and is safe. The approach that we are developing will, however, be applied later to other factors in additional cell types. Secondly, we will identify competing lineages of genomic/transcriptomic crisis from very early oncogenesis. At the origin of all cancers is a chance event occurring in a single cell. This somatic mutational event tips the balance in favour of the cell’s progeny becoming oncogenic. We will first identify such tipping point driver mutations lying near to the root of pre-neoplastic cell lineages by sequencing both the DNA and RNA from single cells. We then will determine whether the subsequent genotypic evolution of this cellular lineage is reproducible. By sequencing both the DNA and the RNA from the same cells we will trace the cells’ phenotypic trajectory as they acquire successive mutations down their lineage. Finally, we will assess competition among co-existing clones. Thirdly, we have predicted and are experimentally investigating novel domains found within the 30 subunits of human Mediator. The approaches that we have developed are also being applied to other large complexes of central importance to human disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Epithelial Cell Polarity & Tissue Maintenance
Funder: Medical Research Council

Abstract: Apical-basal polarity is essential for epithelial cell function, and in epithelial tissues its loss is a hallmark of cancer. The overall aim of our research group is to elucidate how polarity arises in epithelial cells and how it is maintained in mature tissues. To this end we combine work in Drosophila tissues and human cell lines, using optogenetic, biophysical methods and super resolution imaging approaches. With this three-year funding support, our goal is to address the following specific aims: (1) Explore the extent to which regulated nuclear export of polarity factors acts as a main mechanism of cell polarity in animal cells. We have obtained evidence that regulated RanGTP-dependent nucleocytoplasmic transport and in particular release of the polarity protein PAR4/LKB1 from the nuclear export machinery regulates epithelial polarity. We will determined how exactly this new polarity mechanism operates and how widespread it’s function is during polarized cell morphogenesis (2) Test whether the PAR complex acts as a receptor for the exocyst to translate polarity at the cell cortex into plasma membrane morphogenesis, including cell-cell contact maturation. We have recently discovered that in components of the conserved PAR complex binds to subunit of the exocyst. The exocyst is an octameric complex that is conserved across phyla and promotes membrane delivery, raising the possibility that the PAR complex regulates cargo delivery during polarized morphogenesis. Altogether, our two research aims to elucidate the mechanisms that generate epithelial polarity and maintain epithelial tissue integrity, a prerequisite for understanding epithelial cells function and how defects in polarity and tissue integrity impact on human diseases such as cancer.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Elucidating the birth of haematopoietic stem cells
Funder: Medical Research Council

Abstract: This programme aims to delineate the cellular and molecular events that regulate definitive hematopoietic stem cell (HSC) generation in the mammalian embryo. Obtaining a mechanistic understanding of this process as it occurs in vivo is challenging, but critical to the design of rational approaches to improve current HSC-based therapies and develop new ones. This programme also relates to broader fundamental questions in developmental biology, i.e. how genes are regulated, and how different types of adult stem cells are generated. The entry point for our studies of the hematopoietic system is the transcription factor Runx1, a master regulator of HSC emergence. There are three specific aims: 1) Comprehensive identification and characterization of Runx1 cis-regulatory elements and trans-acting factors in developmental haematopoiesis. 2) Characterization of the process of endothelial-to-haematopoietic transition (EHT). 3) Identification and characterization of Runx1 transcriptional target genes in developmental haematopoiesis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Ubiquitylation pathways controlling the end of chromosome replication
Funder: Medical Research Council

Abstract: My group studies the mechanisms and regulation of the eukaryotic replisome – the molecular machine that produces a single copy of the chromosomes in each cell cycle. Replisome biology is defective in many human tumours, providing opportunities for the development of new therapies. We discovered that disassembly of the eukaryotic replisome during DNA replication termination is a regulated process that is controlled by ubiquitylation of the DNA helicase known as CMG (Cdc45-MCM-GINS), around which the relisome is built. Ubiquitylation leads to disassembly of the CMG helicase, and thus of the replisome, dependent upon the Cdc48 ATPase that probably denatures the ubiquitylated subunit of CMG. Moreover, we found that metazoa have a second mechanism for replisome disassembly that acts during mitosis and is regulated by a factor mutated in a variety of human cancers, suggesting a potential future strategy for disease treatment. Our preliminary data indicates that there are yet more replisome disassembly pathways to define and characterize. We aim to study their mechanisms and regulation, and then investigate their links to human disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Dynamic mechanisms of FGFR activation in cancer by kinase mutations
Funder: Medical Research Council

Abstract: Fibroblast growth factor receptors (FGFRs) play essential roles in a wide range of biological processes including embryonic development, angiogenesis and wound healing. As they are also key actors in a number of developmental disorders and cancers, FGFRs are important drug targets. The core of the proposed programme is the implementation of an innovative, powerful combination of experiment and simulation to study protein kinase regulation in normal and disease biology. Using this approach, we will develop an understanding of the free energy landscapes that describe the conformational transitions accompanying rearrangements of the activation loop of wild-type and mutant FGFR1 kinases. Our combined NMR and computational approach will allow us to understand in unparalleled detail the molecular mechanism of a novel autoinhibitory mechanism for FGFR kinase activity, and of its subversion by disease-causing mutations. This understanding will improve our knowledge of how FGFRs regulate their catalytic activity in response to external stimuli under both normal and disease settings, as well as informing future strategies for development of conformationally-selective inhibitors as potential mutation-targeted therapeutics. Building on our previous published work in this area, we will address the following three main objectives: 1. To establish how the pathogenic N546K and/or N546S gain-of-function mutants of FGFR1 alter the conformational dynamics of the kinase. 2. To establish how another pathogenic FGFR1 gain-of-function mutation, R675G, alters FGFR conformational dynamics and compare with the N546 mutation. 3. To develop a comprehensive understanding of the mechanism of important structural transitions in activation and inhibition of FGFR1 in the presence and absence of disease-associated mutations, by using in silico metadynamics simulations guided by NMR-derived experimental restraints.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: MICA: Developing Micro-Community Analytics for Histology Landscapes (MiCAHiL)
Funder: Medical Research Council

Abstract: The recent arrival of digital slide scanners into diagnostic pathology laboratories in the UK marks a new revolution in pathology practice in the NHS trusts. Tissue microenvironment in a high-resolution image scanned from a tissue slide presents itself as a 'histology landscape' containing rich information about tens of thousands of cells, communities of cells, and their spatial relationships with each other. In this project, we will develop multi-scale community analytics methods for histology landscapes in order to reveal intuitive, biologically meaningful, and clinically relevant spatial trends and patterns involving various types of cells and communities of cells. We will use colorectal cancer as a case study, while creating methods with wider applicability to other diseases. Novel analytics methods developed in this project offer several advantages: First, accurate, large-scale quantification of the cell types and their spatial distribution including recognition of concept-driven or empirically derived diagnostic motifs at both cellular and community levels will allow more precise prognostic and therapeutic stratification than is currently possible by conventional analysis relying on the human eye. Second, recognition and quantification of social interactions between various different cell populations is likely to lead to novel prognostic data with relevance to personalised medicine. And finally, for diseases with heavy genetic influence such as cancer, a combination of results of image analytics and molecular level changes in the DNA of tumour cells can enable us to understand the downstream effects of genomic alterations on spatial tumour microenvironment, i.e. how such alterations manifest themselves in terms of tumour morphology, micro-architecture, and social networks of cell communities.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.4 POPULATION SCREENING;4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE