NIHRDataInsights/HRCSData huggingface dataset:
Title: Systems biology of cell polarity networks
Funder: The Francis Crick Institute

Abstract: One of the current grand challenges in biology is bridging the gap between detailed gene and interaction lists and the phenotypic, systems-level behaviour of biological networks. Fortunately, we have an unprecedented ability to image and perturb cellular systems in a quantitative manner. This surge of quantitative information has spurred resurgence in the application of physics and mathematics to integrate these quantitative data within appropriate theoretical frameworks to facilitate our understanding of network design principles. My lab seeks to apply this approach to understanding generation of spatial information in the context of cell polarity, symmetry-breaking and cell fate specification. Cell polarity, defined as the generation of a geometric and functional axis within the cell, is essential for cells’ sense of direction. Our lab focuses on the conserved metazoan PAR (par-titioning defective) pathway, which drives polarity in contexts as diverse as cell migration, directional growth, asymmetric cell divisions and tissue architecture. This pathway is essential for animal development and function and is often mis-regulated in cancer, leading to active efforts to develop novel therapeutics. Polarisation of cells by the PAR pathway requires the opposed activity of two classes of PAR protein, which define complementary membrane domains. These domains define the polarity axis and spatially regulate numerous downstream pathways. Genetic analysis has uncovered most, if not all, key players and many physical interactions are known, providing a baseline of foundational knowledge. However, understanding how patterns at the scale of the cell emerge from these nanometer scale molecular interactions will require: (1) quantitative insight into the dynamic behaviour of these molecules, (2) an understanding of how these behaviours are modified in space and time, (3) identification of the core feedback and regulatory pathways that define the phase space of patterns available to the system, and (4) development of theoretical frameworks to integrate all this information and provide testable predictions to inspire new lines of investigation. To tackle these issues, our lab uses the C. elegans embryo as a model due to the unparalleled ability to image and manipulate the PAR pathway in cells in real time as they undergo polarization. We are developing and applying a variety of genetic, pharmacological and imaging techniques to tackle the above questions in the hope of defining the core organizing principles of this polarity network.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Transcription and the repair of DNA damage
Funder: The Francis Crick Institute

Abstract: Our laboratory is interested in understanding the interface between RNA polymerase II transcription and the maintenance of genome stability. Despite decades of study, the cellular response to UV-irradiation remains poorly understood. The effect of UV-induced DNA damage on transcription is particularly complex. At the local level, a UV-induced DNA lesion causes stalling of RNAPII, blocks transcript elongation and triggers transcription-coupled nucleotide excision repair, the process whereby DNA damage in the transcribed strand of active genes is preferentially removed. This process remains a conundrum. However, UV-irradiation also affects transcription genome-wide, so that even genes that are not themselves damaged temporarily cease to be expressed. Alternative mRNA splicing also changes dramatically. The mechanisms and factors that underlie the global, DNA damaged-induced changes in gene expression, and its eventual normalization, are poorly understood as well. Conversely, while transcription is greatly affected by DNA damage, it also itself has the potential to cause genome instability. Indeed, transcribed regions are more prone to mutation and other genome instability. A number of molecular pathways have therefore evolved to minimize the negative impact of transcriptional activity, but, again, our knowledge of the mechanisms and factors underlying them remains minimal. Our laboratory aims to identify and characterize new factors and mechanisms involved at the interface between transcription and the maintenance of genome stability. For this purpose, we use proteomic and genomic screening in parallel, combined with genome-wide mapping techniques. In any individual proteomic or genomic screen it is often impossible to distinguish ‘real’ candidates from the scores of false-positives, and false-negative results are extremely frequent as well. Our multi-omic approach explores the same processes from different angles and the integration of multiple screen results has thus resulted in the identification of several new factors and unexplored molecular processes, which we now further pursue. To this end, we use biochemical and cell biological approaches, as well as proteomics and genomics, to further functionally characterize the interface between transcription and the maintenance of genome stability in great mechanistic detail.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Cell polarity and tissue morphogenesis
Funder: The Francis Crick Institute

Abstract: The laboratory uses both Drosophila and mice as model organisms to explore how cells construct epithelial tissues during development and how epithelial tumours can arise. We focus on the question of how cell signalling and cell polarity organise the behaviour of cells within an epithelium. We take three main approaches: genetic analysis of gene functions in vivo; live-imaging of epithelial tissue development; computational modelling of cell polarity and cell behaviour. We aim to combine these approaches to identify molecular mechanisms responsible for organising cell polarity and cell behaviour during tissue growth and morphogenesis in epithelia. Our recent work has examined two different types of cell polarity in epithelia, apico-basal polarity and planar polarity.


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: Molecular cell biology of autophagy
Funder: The Francis Crick Institute

Abstract: The focus of my laboratory’s research is mammalian macroautophagy, an intracellular degradative pathway mediated by lysosomes. Macroautophagy, which is called autophagy, is fundamentally a sequestration process during which cytosolic solutes, proteins, and organelles are engulfed and sequestered into autophagosomes, followed by fusion of the autophagosomes with lysosomes and degradation of the sequestered material. The function of autophagy is to maintain intracellular homeostasis (through removal of damaged cytosolic components) under normal conditions, and to enable survival under stress (through replenishment of amino acids and metabolites). Many of the proteins required for autophagy, first identified in yeast and called Atg (autophagy related) proteins, have now been identified in mammals. However, their molecular function remains largely unknown and it is their molecular function we aim to understand. Importantly, autophagy has been shown to play a role in human diseases including cancer. My laboratory aims to understand the process of autophagosome formation and maturation at a molecular level building upon our identification of three essential mammalian Atg proteins, ULK1, Atg9 and WIPI2, and new regulatory or accessory molecules that my lab has recently identified. Specifically, our studies involve a molecular dissection of 1) the earliest event, autophagosome formation and 2) regulatory mechanisms controlling expansion, and maturation of autophagosomes. ULK1 is the kinase contained within a multi-subunit complex which initiates autophagy, and it controls the multi-spanning membrane protein Atg9 which is required for autophagy. WIPI2 is the main effector of the lipid Phosphatidylinositol 3-Phosphate produced by the class III PtdIns 3-kinase. We are studying the subcellular localization, and interdependence of these Atg proteins. We are also seeking to identify post-translational modifications that activate and allow recruitment of these proteins upon induction of autophagy, including phosphorylation, fatty acid modification, and ubiquitination. These experiments provide a platform for our second aim, to identify and understand regulatory, or accessory, proteins required for autophagy. We speculate that these regulatory molecules control or fine-tune autophagic flux, the process from formation to degradation of content. Regulatory proteins and candidates have been obtained through our proteomic analysis of proteins interacting with ULK1, Atg9 and WIPI1 and 2, and other candidates have been obtained from a siGenome screen, and a screen targeting Rab proteins (small GTPases involved in vesicle formation and targeting). Understanding both the essential machinery and how it is regulated will direct future research towards understanding key functional nodes or individual proteins that can be targeted to manipulate autophagic flux.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Cell fate and gene regulation
Funder: The Francis Crick Institute

Abstract: How cells make the decision to differentiate is important to the understanding of development of multi-cellular organisms and treatment of diseases including cancer. Cell differentiation or cell fate is controlled by signals that regulate gene expression networks consisting of canonical protein-coding transcripts and non-canonical transcripts such as mRNA isoforms, long noncoding, antisense and intragenic RNAs. In eukaryotes including human cells a significant fraction of the genome is transcribed into non-canonical RNA transcripts. The function of the majority of these transcripts is yet to be determined. The goal of my lab is to illuminate how non-canonical transcription regulates cell fate and gene expression using budding yeast gametogenesis as a model. Gametogenesis or sporulation in yeast is a highly conserved differentiation program during which a diploid progenitor cell gives rise to four haploid gametes. During gametogenesis at least three waves of gene transcription regulate the different phases of this cell differentiation program. Given that there is substantial mRNA isoform, intragenic and noncoding transcription during yeast gametogenesis, we hypothesize that non-canonical transcription is important for this cell differentiation programme. We would like to address several questions. (1) How do long noncoding and mRNA isoforms control gene expression and cell fate? (2) What are the mechanisms by which long noncoding RNAs and mRNA isoforms regulate gene expression? We have identified examples of genes at which noncoding transcription can lead to gene repression, but also to gene activation using mechanisms that reminiscent to those identified in mammalian cells. Recently, we have identified a novel mechanism by which an essential gene is temporally repressed during a cell-fate stage by expression of a 5’ extended mRNA isoform. We found that transcription of a 5’ extended isoform causes the establishment of repressive chromatin in the down-stream coding promoter. We are currently using genome-wide approaches to determine how wide-spread this mechanism is. In general, we use yeast genetics, single cell techniques such RNA fluorescence in situ hybridization and live-cell imaging, but also genome-wide techniques such RNA and ChIP sequencing to tackle the questions of my lab. It is our hope that the results from these studies will shed light on how non-canonical transcription regulates gene expression and cell fate in higher eukaryotes including mammalian cells.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Single molecule imaging of DNA replication
Funder: The Francis Crick Institute

Abstract: Before a cell divides it has to duplicate its genome so that two identical copies of its DNA content can be partitioned into daughter cells. In eukaryotic cells, replication is initiated at thousands of origins on the DNA, each resulting in the assembly of two replisomes that travel away from the initiation site in opposite directions. Complete and high-fidelity duplication of the genome is essential for faithful transmission of genetic information. When DNA replication goes awry, the result could be cells with mutations, missing or extra genetic material a hallmark of the genomic instability seen in most cancers. Our laboratory aims to investigate processes involved in eukaryotic replication using a combination of conventional biochemistry and single-molecule imaging tools. To copy their DNA in preparation for cell division, cells must separate the two strands of the double helix. All cells contain a ring-shaped hexameric DNA helicase, which performs this task. In eukaryotes, an 11-subunit complex known as CMG (Cdc45, MCM2-7, GINS) that acts as the helicase at the replication fork. We aim to investigate the molecular mechanism by which CMG acts on DNA using a combination of ensemble biochemistry and single molecule imaging tools. To study eukaryotic replication at the single molecule level we use a number of model systems including Xenopus egg extracts, SV40 replication system, and extracts derived from budding yeast. Using novel methodologies that combine single-molecule imaging and DNA nanomanipulation in extract-based systems and conventional bulk assays, we aim to gain a comprehensive understanding of the overall architecture and dynamics of the eukaryotic replisome by fluorescently labelling individual component proteins of the replisome and visualizing these proteins in real-time during replication. One of our main goals is to understand how the eukaryotic replisome deals with replication barriers such as nucleosomes, DNA-protein crosslinks and DNA interstand-crosslinks. Microscopic analysis of DNA replication products has been carried out by electron microscopy as well as fluorescence microscopy for many years. While electron microscopy offers high spatial resolution, differential labelling of nascent strands is not possible. An alternative method to observe DNA replication intermediates has been DNA fiber analysis that allows specific visualization of replication products through fluorescence labelling of nascent strands. However, due to low spatial resolution of fluorescence microscopy it has not been possible to detect both daughter strands on replicated DNA products using this technique. To overcome these limitations, we are developing super resolution fluorescence techniques that will allow us to obtain high-resolution fluorescence images of replication intermediates.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Title: Hypoxia biology
Funder: The Francis Crick Institute

Abstract: The overall aim of the programme is to define mechanisms by which cells detect and respond to hypoxic and metabolic stresses that are commonly encountered in human diseases, including ischaemic vascular diseases and cancer. The work builds on the laboratory’s discovery of pathways that deploy ‘dioxygen splitting’ Fe (II) and 2-oxoglutarate dependent oxygenases (2-OG oxygenases) to regulate the stability and activity of hypoxia inducible transcription factors (HIFs) by post-translational hydroxylation and hence signal to a broad range of cellular and systemic processes that defend oxygen homeostasis. Specific aims are to define: (i) The existence and extent of biological oxidations catalysed by 2-OG oxygenases, focusing on those enzymes that are most closely related to the HIF hydroxylases and which are known or predicted to catalyse protein oxidations. (ii) The physiological action of these oxidations on cellular processes, particular extending beyond the known role of HIFs in transcriptional regulation (iii) The implications of high levels of connectivity in these pathways, particularly for attempts at therapeutic modulation and for theories of disease pathogenesis such as cancer The work will be pursued though a series of interdisciplinary approaches encompassing biochemical and biophysical characterization of protein oxidation (e.g. by mass spectrometry), cell biological assays (e.g. of transcriptional and post-transcriptional effects) and disease-based analyses (e.g. in cancer model systems). The aim is to provide sufficient biological and disease-linked insights into specific signalling enzyme/substrate couples to enable assessment of the potential for therapeutic manipulation (e.g. by inhibition of the relevant 2-OG oxygenase by ‘drug-like’ 2-OG analogues). Data obtained (and associated IP) would potentially provide starting points for drug development programmes in partnership with the pharmaceutical industry.


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: p53 and metabolism
Funder: The Francis Crick Institute

Abstract: Perturbations in the p53 pathway play an important role in development and progression of most human cancers. Our goal is to increase our understanding of p53 function to allow the development of improved cancer therapy. There is a growing appreciation of the complexity of the p53 family (including p63, p73 and various isoforms of each protein), their regulation and function. p53 can control broad and complex patterns of gene and miRNA expression, while transcriptionally independent activities of p53 have also been described. How p53 controls tumour development and the contribution of p53 to other aspects of normal development and disease remain open questions. Our research programme is divided into three main projects that focus on functions of wild-type p53, functions of mutant p53 and the regulation of p53 activity. In our studies of wild-type p53 activity, we are interested in understanding which functions of p53 are important for tumour suppression, how the p53-inducible protein TIGAR impacts tumour development and why some tumours retain wild-type p53. Our analysis of mutant p53 function is focused on the activities of mutant p53 that contribute to tumour progression, whether expression of mutant p53 provides cancer cells with advantages or vulnerabilities that might be used for new therapeutic approaches and whether different cancer derived p53 mutants behave in the same way. Much of our work is focused on how p53 can regulate metabolism and whether this information could reveal new approaches to cancer therapy. Studies of the regulation of p53 activity address the mechanism of function of MDM2, the major regulator of p53 stability, and how MDM2 might be targeted for cancer therapy. We are also looking more generally into how metabolic adaptations help to support tumour development and progression, and whether these changes introduce any tumour specific vulnerabilities that might be exploited for treatment. Taken together, our work constitutes a contribution to the global research effort to understand and exploit p53 and metabolism for cancer patient benefit.


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: Cancer Systems Biology
Funder: The Francis Crick Institute

Abstract: We are studying the faulty genetic networks inside cancer cells that drive tumour growth and evolution, so that we can develop more effective treatments. Genes are the instructions that tell cells what to do, when to multiply, and when to die. Faults in certain genes lead to cells multiplying out of control and failing to die when they should, leading to cancer. Over recent years, researchers have discovered many gene faults that are linked to cancer, but they have usually only been studied in isolation. We are investigating how multiple genes are controlled and work together in cancer cells, creating large aberrant networks that drive cells to grow out of control. We are using large data-sets to find out more about these faulty genetic networks and find new ‘cancer genes’ in tumour samples taken from cancer patients, focusing on bowel and oesophageal cancers in particular. We are also investigating how these genetic networks evolve and change over time as a cancer responds to chemotherapy or becomes resistant and grows back after treatment. Our work is revealing a deeper understanding of how the interconnected abnormal genetic networks in cancer cells fuel tumour growth and evolution, pointing us towards potential targets for the development of new, more effective cancer therapies in the future.


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: Molecular mechanisms of Wnt signal transduction
Funder: Medical Research Council

Abstract: The Wnt/beta-catenin signalling pathway is ancient and controls normal development and tissue homeostasis in all 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 mechanisms underlying the relay 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. Current questions include how Dishevelled assembles Wnt signalosomes to inactivate the Axin-APC complex and how it pivots from beta-catenin to non-canonical Wnt signalling branches. We are also engaged in collaborations with plant groups to explore whether the ‘Dishevelled paradigm’ (i.e. the cross-linking of dynamic polymers) underlies plant polarity and heritable gene expression. Our approach is to combine biochemical, biophysical and structural analysis of Wnt signalling components with functional assays in mammalian cell lines and in whole-organism models such as Drosophila and Arabidopsis (the latter by collaboration) to gain insights into the assembly of dynamic signalosome-like biomolecular condensates. We have also been awarded a CRUK programme grant to develop the potential of various Wnt signalling components as drug targets.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE