NIHRDataInsights/HRCSData huggingface dataset:
Title: Algorithms in a functional genomics study of cichlid fish evolution
Funder: Wellcome Trust

Abstract: Epigenetics, or “on top of” genetics, refers to biochemical modifications to the DNA that do not alter the underlying sequence. Such modifications influence the likelihood that individual genes are expressed, allowing many degrees of freedom for the overall gene expression network in an organism. This is believed to underpin how certain organisms exhibit the ability to diversify into a large number of species in short evolutionary time. A famous example is the cichlid adaptive radiation of the East African Great Lakes, which comprises over 2,000 phenotypically diverse species, in terms of their microhabitat, size, morphology, feeding behaviour and colouration. My PhD project will be a collaboration between myself and Audrey Putman, an experimentalist student from Eric Miska’s lab. Our plan is to explore, characterise and quantify how epigenetic differences can manifest in the cichlid system. I will develop computational and statistical methodologies to analyse epigenomic data, under the guidance of a computational supervisor, Martin Hemberg. The impact of the work include developing efficient algorithms to process large scale datasets, and effectively integrate information from various sequencing technologies, with the ultimate goal of addressing the fundamental biological question of speciation.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Interpreting the microtubule code
Funder: Wellcome Trust

Abstract: All our cells contain mesh-like networks that are formed from tube-shaped protein structures called microtubules. These microtubules help to maintain cell shape, allow cell movement and facilitate cell division. Additionally, they also act as railway tracks in which motors can travel down to transport their cargo to specific areas of the cell. Proteins can bind to microtubules to control their function and determine what is transported along them. Many of these proteins have been identified however the list is still not complete. Identifying and exploring further this collection of proteins using a technique called mass spectrometry may help us discover new functions for microtubule networks. To create even more specific functions, individual railway tracks can be decorated with a variety of different removable groups which distinguishes them from each other. This is known as the tubulin code and allows individual tracks to be recognised by different proteins and alter whether they bind or not. As this tubulin code is not well understood, we will modulate these modifications to identify and explore proteins that bind to specifically decorated railway tracks. This research will help us understand the importance of these removable decorations and how they control the functions of microtubules.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Regulation of the Translocase of Outer mitochondrial Membrane (TOM) complex by reversible ubiquitylation.
Funder: Wellcome Trust

Abstract: Mitochondria are tiny power plants that produce energy for cells in our body. To work properly, mitochondria need to continuously import new parts, mostly proteins, through specialised gates and channels, we call TOM complexes. When mitochondria are damaged and/or proteins get stuck in the gate, TOM complexes are tagged with a protein named ubiquitin. This tag is recognised by the waste disposal machinery in the cell. Diseased mitochondria are wrapped up and safely destroyed through a process we call mitophagy. In people with Parkinson’s disease, mitophagy does not work properly, leading to problems in the brain. We are interested in proteins that remove ubiquitin and can act as a brake on mitophagy. In particular, one of these, USP30, removes ubiquitin from TOM complexes. Interfering with USP30 allows cells to clear away damaged mitochondria more efficiently. On the mitochondria, a very small amount of USP30 has to survey a large number of TOMs. We want to understand more about the relationship between ubiquitin, USP30 and TOM complexes. In particular, we would like to know what distinguishes those TOM complexes that USP30 works on and how the addition and removal of ubiquitin from these gates affects their function.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: How are nutrient signalling and membrane trafficking coupled at the lysosome by the Folliculin-FNIP complex?
Funder: Wellcome Trust

Abstract: BACKGROUND Folliculin (FLCN) is a tumour-suppressor protein implicated in control of lysosome-associated nutrient signalling pathways. Loss of FLCN function causes Birt-Hogg-Dubé (BHD) syndrome, a rare genetic disorder associated with an increased risk of kidney cancer. In complex with its interaction partners FNIP1/2, a role is emerging for FLCN as a co-ordinator of small GTPases at the lysosome. FLCN-FNIP can act as a GTPase activating protein for RagC to control lysosomal mTORC1 activity, and regulates lysosome dynamics by acting through several Rab GTPases and their effector protein RILP. Thus, the FLCN-FNIP complex sits at a pivotal position where it couples nutrient signalling and trafficking/transport events at the lysosome. APPROACH A clear mechanistic understanding of how these complex activities are carried out is currently lacking. I will integrate structural, biochemical and cellular approaches to study the intact human FLCN-FNIP complex, with the aim of describing its activities in molecular detail. I will particularly focus on its potential role as a co-ordinator of GTPases in relation to nutrient signalling and intracellular transport of the lysosome. IMPACT By tying together two branches of lysosome biology we will uncover the normal function of the FLCN-FNIP complex and establish the underlying pathology of BHD syndrome.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Must the relatives be told? Legal and ethical issues in relation to the non-disclosure of genetic information by healthcare professionals to relatives
Funder: Wellcome Trust

Abstract: Genetic information is becoming increasingly utilised by healthcare professionals in order to provide patients with more precise diagnosis and treatments. An individual's genetic information may show their risk of inheriting a genetic disorder, and although most individuals would consent to healthcare professionals sharing their genetic information with relatives who may also be at risk, some individuals refuse. It can be argued that a failure to disclose the risks of inheriting genetic disorders to relatives is ethically wrong, because it restricts the autonomy of individuals to make life choices. Alternatively, it can be contended that it is legally wrong for a healthcare professional to not adhere to the duty of confidentiality that they owe to patients. This debate demonstrates the conflict of duties that healthcare professionals face as the use of genetic information in medicine develops, and highlights the need to develop a new legal framework which takes into account the needs of patients, relatives, and healthcare professionals. In order to create an appropriate legal framework, I aim to assess academic commentary, examine case law, and conduct qualitative interviews with healthcare professionals in order to assess scientific opinion, and potentially inform new policy guidance.


Research activity codes: 8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE
Title: Hydrodynamic interactions in molecular simulations at the biological mesoscale
Funder: Wellcome Trust

Abstract: Macromolecules under flow at the biological mesoscale (10 nm < L < 1 &mu;m, 1 &mu;s < t < 1 ms) can influence the dynamics of each other via hydrodynamic interactions (HIs), however, there is a dearth of mesoscale simulation tools that consider them. Most simulations that include HIs occupy continuum scales (L > 1 &mu;m, t > 1 &mu;s) whereas atomistic scales (L < 50 nm, t < 1 &mu;s) are too small to model long range effects. Using a test-driven development methodology, I aim to address this capability gap by implementing HIs in the Fluctuating Finite Element Analysis (FFEA) software, which represents biological macromolecules as 3D viscoelastic continuum objects that thermally fluctuate. I will validate FFEA simulations of fibrinogen and ribosome macromolecules by exposing them to large viscous forces in extensional flow device (EFD) experiments. This work will improve our simulation capability at the biological mesoscale, which will complement the burgeoning range of experimental imaging techniques such as cryo-electron microscopy (cryoEM) and x-ray crystallography. Furthering our understanding of HIs is crucial in biomedical topics such as fibrin network formation in blood clots, as well as improving the industrial production of biopharmaceuticals and biomimetic fibres.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Rational engineering of antibody binding kinetics
Funder: Wellcome Trust

Abstract: Therapeutic antibodies – drugs made from defence molecules produced by the body – are becoming increasingly important in treatment of diseases ranging from cancer to hepatitis. These drugs work by binding to the molecules they target called antigens. In order to be effective, an antibody must bind its antigen tightly and this depends in part on how fast it binds the antigen. For example, it has been shown in a set of antibodies against malaria that the ability of antibodies to neutralise the pathogen is highly dependent on the binding rate. Our research will use a multidisciplinary approach to engineer antibodies with the aim of achieving faster binding. Using both computational tools and experiments that characterise the physical properties of antibodies, we aim to identify factors that contribute to the rate of binding. Next, we would like to use this knowledge to generate software to predict changes that can be introduced to an antibody to increase its binding rate. As a way to validate our conclusions, we plan to improve antibodies against malaria. These studies will provide us with insight into the factors that make good therapeutic antibodies and also provide a tool for use by the wider scientific community.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE
Title: A Multifunctional Genetic Probe for Networking Lysosomal Calcium Biology
Funder: Wellcome Trust

Abstract: The lysosome, once thought to be a cellular ‘trash-can’, is now found to be the key to understanding the signalling controlling human ageing, neurodegeneration, and a range of diseases from diabetes to cancer. Developing tools to understand how the lysosome works will be key to future biological studies. In this project, we will develop and analyse a new imaging probe which will allow us to examine calcium signalling in functional lysosomes in live-imaging, proteomic and lipidomic modalities to develop a fine-grained understanding of how lysosomes function in health and disease. The genetic probe we are developing makes it easy to isolate, image, and manipulate lysosomes in living cells and in cellular extracts using one transfectable tool, offering many avenues of application to basic and industry-focused research. One key regulator of lysosomal calcium storage is the messenger NAADP, which we will examine in detail. We will produce coordinated maps of the behaviour of calcium levels inside the lysosome under conditions known to alter NAADP signalling, coupled with the metabolic and proteomic profiles of lysosomes in the same conditions and in mutants of the muscular dystrophy gene INPP5K: giving a comprehensive map of the regulation of this key signalling axis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Dissecting causal relationships and molecular mechanisms in disease using genetic risk profiles
Funder: Wellcome Trust

Abstract: Many common diseases such as obesity, diabetes and hypertension are caused by a combination of genetic, environmental and lifestyle factors. Better understandings of the causal factors of complex diseases may aid disease prevention and health research. Conventionally, studies on disease causal factors rely on health intervention experiments which cost enormous time and labour. The recent availability of large-scale databases, which contains genetic, lifestyle and disease information on tens of thousands of individuals, allows researchers to construct polygenic risk scores (PRS) to represent individuals’ genetic liability to develop a trait or disease. This score could be used to investigate disease causal factors in Mendelian randomisation (MR) analyses, a genetics-based approach analogous to a randomized controlled trial. My PhD will involve constructing and analysing the PRS for complex diseases and generating a large resource of PRS and MR results which we plan to share with the scientific community. I will improve the method of PRS constructions and develop analytical pipelines to identify causal modifiable risk factors for diseases, key genes and pathways underlying disease mechanisms. Furthermore, I will also assess the capability of PRS to predict causal risk factors during childhood which may therefore have important implications for preventing later life disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Structural and biochemical studies on mRNA 3’-end processing and transcription termination in fission yeast
Funder: Wellcome Trust

Abstract: In the cell, genetic information from the DNA is copied into RNA molecules in the nucleus of the cell before being exported to the cytoplasm, where the information they carry is used to make proteins. In eukaryotes, these messenger RNA molecules (mRNA) are modified before they are exported out of the nucleus. An enzyme called the Cleavage and Polyadenylation Factor (CPF) cleaves the mRNA at the end and adds a string of adenosines to create a polyA tail. This polyA tail is important for the stability of the mRNA, and the cleavage process ensures that the enzyme that makes the mRNA, RNA Polymerase II, stops at the end of the gene and goes back to the beginning to repeat the process of making mRNA. The aim of my project is to study how the CPF modifies mRNA and interacts with RNA Polymerase II to ensure functional mRNA are properly produced. I will use techniques such as electron microscopy and x-ray crystallography, as well as biochemical techniques, to look at the structure of CPF to understand how it works. Through this work, we expect to gain a more detailed understanding of this fundamental biological process.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Development and Evolution of Cichlid Pigmentation
Funder: Wellcome Trust

Abstract: The cichlid fish in the African Great Lakes are incredibly diverse despite being genetically very similar to each other. We will study the development of colour pattern in Astatotilapia calliptera, which consist of arrangements of specialised colour-bearing cells, chromatophores. We will focus on the variable circular markings on the fin known as egg-spots, as these play a role in reproductive behaviour and therefore have direct consequences for species evolution. Four genes have been identified as associated with variation in egg-spots number and colour in A. calliptera. We will use CRISPR-Cas9 to knock-out these genes to identify their effect on egg-spot development. We will also check whether the same genes are associated with egg-spot variation between different cichlid species. We will then model the interactions between chromatophores - these interactions affect the movement, differentiation, and death of chromatophores during development, affecting the resulting colouration. We will use this model to test which mechanisms the genes act through. Understanding how the slight genetic changes between cichlids affect embryo development and lead to such different appearances can help us understand the huge diversity of species we see today, and how the porcesses of embryo development and evolution affect each other.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: An Investigation into the Fundamentals of Mitochondrial ‘Stop-Transfer’ Import and Processing
Funder: Wellcome Trust

Abstract: Background Mitochondria are membrane-bound organelles implicated in cellular energy generation and an increasing number of cellular processes. Critically, these processes rely on proteins being imported into the mitochondria via the mitochondrial protein import apparatus. ‘Stop-transfer’ import (Figure 1) is a means to achieve delivery of proteins to a mitochondrial sub-compartment termed the inter-membrane space (IMS). PTEN-induced kinase 1 (PINK1), a mammalian mitochondrial protein kinase and Mgm1, a mitochondrial protein in yeast, are both implicated in mitochondrial ‘health’ and are critical substrates of this pathway. Approach Thorough mechanistic characterization of stop-transfer protein import and the role of processing of these proteins is required to better understand delivery to the IMS in native and damage contexts. I will apply biochemical and biophysical (spectroscopic) approaches to report on import into the IMS using purified PINK1 and Mgm1 in mammalian and yeast cell-based import assays respectively, while also focusing on the role of interacting proteins during the import process, markedly TOM/TIM proteins and PGAM5. Impact Design of a probe to report on mitochondrial import into the IMS will reveal new details of the molecular control of stop-transfer import and its regulation, markedly for critical substrates such as PINK1 implicated in human disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Development of pathway-based predictive models and their use in multi-omics clinical studies
Funder: Wellcome Trust

Abstract: As the field of systems biology continues to develop, huge volumes of molecular data are being generated, including 'omics' data which aims to characterise activity at various levels of the biological system, such as genomics, transcriptomics, and metabolomics. A key challenge is the integration of multiple omics datasets to obtain a more holistic understanding of how the layers of the biological system work together. Pathway analysis is a method for assigning molecular entities to their respective biological pathways, to better facilitate biological interpretation of omics data. Current tools for the integration of multi-omics data focus on integrating the data at the level of individual molecules. However, the integration of omics data at the level of biological pathways has not yet been investigated. As biological entities are known to interact within pathways, I propose the development of a novel method for combining multi-omics data by integrating the layers at the pathway level using statistical/machine learning approaches. This work will result in novel methods researchers can use for integrating omics data at the pathway level, with a focus on improving interpretability, sensitivity (the ability to detect biological signals), and predictive ability (using the model to predict e.g. disease status) of current methods.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: The role of Xist binding partners in Xist localization
Funder: Wellcome Trust

Abstract: X chromosome inactivation (XCI) is the mechanism that equalises X-linked gene expression in mammalian XX females relative to XY males. It is triggered by the expression of the 17Kb long non- coding RNA Xist. Upon transcription, Xist spreads in cis ‘coating’ the elected inactive X (Xi) and recruits factors acting in concert to modify the underlying chromatin and repress gene activity. A crucial step for XCI is the limited in cis localization of Xist, ensuring its action is restricted to the Xi elect only. Previous studies revealed Xist to be tightly anchored to the Xi territory through interaction with nuclear matrix proteins, however the mechanisms governing this process remain poorly understood. I will investigate the nature and the single-cell dynamics of Xist interactions with its anchoring factors through the genetic dissection of their functional domains in mouse model systems, using a combination of molecular biology and advanced microscopy approaches, such as live imaging and super resolution microscopy. Our research will elucidate the single-cell interplay between Xist and its localisation factors and their potential role in influencing Xist behaviour, providing insights into the mechanisms governing Xist spreading and retention within the Xi territory.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating ancestral structure in the founding populations of modern humans in Africa
Funder: Wellcome Trust

Abstract: Current research suggests that homo sapiens originated in numerous subdivided populations, opposing the traditional view that we evolved from a single region/population. Existing methods for detecting the size of ancestral populations are limited by their assumption that populations develop in isolation (without mixing with other populations), therefore necessitating new methods that can detect ancient population mixing.My approach is to simulate different population ancestries – generally speaking, mixing vs non mixing – and see if any of the current methods for population size estimation hold any information in their model parameters that change in the presence of population mixture. Using these results, I will aim to analyse the extent of mixing in ancestral African populations by examining real genome data of extant peoples, such as the San and Yoruba. The impact of my research will be to shed more light upon the origin of homo-sapiens as we developed in Africa, 150,000 to 400,000 years ago.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Exploring the interdependence between cell cycle dynamics and cellular differentiation at the single-cell level
Funder: Wellcome Trust

Abstract: The cell cycle and cellular differentiation, two of the most fundamental biological processes, have been shown to be interdependent in embryonic stem cells, and during the development of blood cells and neurons. I aim to understand whether cell cycle alterations are associated with cellular differentiation in other developmental contexts as well, and how both processes jointly shape the cell’s epigenome and higher-order chromatin structures. To this end, I will establish a murine embryonic stem cell line stably expressing fluorescent cell cycle reporters, which will allow me to jointly quantify cell cycle progression and perform single-cell RNA sequencing and single-cell ATAC-sequencing during cell cycling and cellular differentiation. I will also use a low input chromosome conformation capture technique to study the regulatory genome interactions around cell cycle genes and master transcription factors in the same cells, which will allow me to characterise the regulatory elements governing the expression of these genes. These studies will help us better understand the interdependence between the cell cycle and cellular differentiation, which might have important implications for stem cell research, regenerative medicine, and for our understanding of the fundamental processes governing organismal development.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE