NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular characterization of the human DNA repair factor CtIP and its interactions with DNA and partner proteins
Funder: Wellcome Trust

Abstract: Double-stranded DNA, the genetic material in most organisms, carries all the information required for fundamental life processes. Damages to DNA molecules in the form of breaks occur due to factors like irradiation, mechanical stress and reactive oxygen species. Cells have evolved mechanisms to repair breaks in their DNA which are otherwise lethal. The first step of the repair pathway involves recognition and resection of the DNA end. Resection inhibits error-prone repair by classical end joining and is mediated by nucleases and helicases (MRN, Exo1, Dna2). CtIP, a DNA binding protein and cofactor for the MRN complex, is critical for DNA end resection which promotes DNA break repair by homologous recombination (HR). Here we are seeking to understand how cells repair breaks and the role of CtIP using biochemical and biophysical approaches including HDX-MS and X-ray crystallography. CtIP interacts with other protein partners and we will also aim to elucidate the roles of these interactions in the repair pathway. Mutations in CtIP are associated with cancer and neurological diseases like Seckel and Jawad syndromes. This work will provide new insights into the repair mechanisms and the possible role of CtIP in these disease states.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: The calibration of decision-analytic models.
Funder: Wellcome Trust

Abstract: Background: Mathematical models are often used to inform decisions on how best to spend finite public health resources. These models combine relevant information (in the form of model parameters) about disease processes and relevant interventions to estimate the long-term consequences of the interventions. Unfortunately, some disease processes can not be directly observed but could be estimated through calibration. Model calibration identifies the values of input parameters for which the resulting model outputs are consistent with the observed data. Calibration methods are either Bayesian or non-Bayesian. While Bayesian methods identify the posterior distribution of the parameters, it is easier and quicker to perform non-Bayesian methods. Nonetheless, these methods agree on some occasions. The questions posed by this study are, first, what is the error associated with using non-Bayesian calibration approaches, when are such methods suitable, and what is the value of employing Bayesian methods? Second, what is the error in the net benefits associated with employing imperfect calibration target data, and what is the value of collecting better data? Approach: We will survey relevant literature to identify calibration methods, develop (adopt) methods to answer posed questions, utilise simulations to test developed methods and apply developed methods in a real case study.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Integrative pathology modelling of epithelial-to-mesenchymal transformation in cancer
Funder: Wellcome Trust

Abstract: The epithelial to mesenchymal transition (EMT) is a key process in cancer that leads to tumours spreading from their original site and resisting various treatments. Tumours can be classified into three states within this process based on their genetic data. Identifying these states in tumour tissue that is routinely collected during surgery would enable us to predict whether a cancer patient is at high risk for developing metastases and responses to therapies. While artificial intelligence approaches have revolutionised our ability to detect patterns of interest in cancer tissue images in recent years, it has not yet been shown whether EMT states can be identified in tumour images. Furthermore, how cells in different EMT states organise spatially and interact with other non-cancer cells in their environment is not known. We will predict EMT states from pathology images by developing deep learning based methods. We will also analyse the spatial arrangement of the tissue in these different states from the tumour images. This will be carried out using graph-based methods and will enable us to further characterise EMT. Overall, this project will provide a greater understanding of how cancer cells transform and progress towards more advanced stages by interacting with their environment.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Targeting protein-protein interactions of transcriptional regulators in leukaemia
Funder: Wellcome Trust

Abstract: Translocations of the MLL gene lead to acute leukaemias with poor prognosis. Recently, small molecule compounds that disrupt the protein-protein interaction (PPI) between MLL and its binding partner Menin (MEN1) have shown efficacy against a subset of leukaemias. However, beyond changes in the expression of a few genes regulated by MLL, the consequences of inhibiting Menin’s protein-protein interactions on leukaemia cells remain poorly understood. We will use proximity labelling followed by quantitative mass spectrometry to identify proteins interacting with Menin in leukaemia cells, and identify changes in interactions after treatment with the Menin PPI inhibitor. In addition, we will characterise Menin's role in transcriptional regulation through its activity at enhancers by integrating multiple methods for profiling chromatin, including ChIP-seq, ATAC-seq and Capture-C. Understanding Menin's role in transcriptional regulation and its proximal protein environment can reveal vulnerabilities in cancers that depend on pathways regulated by Menin PPIs. This can offer insights into which patients are most likely to benefit from emerging treatments targeting Menin PPIs.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Active Learning and Optimisation of Drug Combinations
Funder: Wellcome Trust

Abstract: The combination of different drugs for treatment of illnesses such as cancers holds great potential for advances in healthcare due to its ability to achieve more effect with less toxicity. However, the interaction between drugs is highly complex due to combinatorial explosion in possible associations, diverse drug-to-drug interactions and differences in drug metabolism that impinges on the drug dose regime. In this project, we aim to leverage advances in statistical learning and data science to optimise drug-to-drug interactions and learn from a large and complex data space of novel and potentially synergistic drug interactions. To achieve this with high accuracy, we will use both monotherapy and drug combination data to design and model the effect of drug interactions. We aim to combine the approach with active learning strategies to provide information about the most informative drug combinations given the landscape of interaction. Furthermore, this statistical model will enable us to optimise the dose-response problem, providing novel insights on tasks such as how to minimise dose while retaining effective outcome.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: The role of RNA modifications in myeloid leukaemogenesis
Funder: Wellcome Trust

Abstract: Acute myeloid leukaemia (AML) is a devastating cancer with a long-term survival below 30% for which mainstream treatments remain unchanged for several decades. Advances in genomics have highlighted the importance of epigenetic corruption in both initiating and maintaining the disease, making the epigenome an important therapeutic focus. Recently, using CRISPR-Cas9 recessive genetic screens, we identified several RNA-binding/modifying proteins as essential for AML cell survival. We have since confirmed that the RNA methyltransferase METTL3 is required for AML maintenance through its role in co-transcriptional N6 adenosine methylation of target RNAs, but is dispensable for normal haematopoiesis proposing it as a novel “druggable” therapeutic target in AML (Barbieri, Tzelepis et al, Nature 2017). Here, I propose to extend the investigation of the epitranscriptome as a new therapeutic focus in AML by studying promising AML-essential RNA-binding/modifying proteins, including METTL1 and METTL16, using unique reagents and expertise as well as access to clinically relevant bespoke models and human samples.

Lay abstract: Acute myeloid leukaemia (AML) is a devastating disease whose long-term survival remains poor at less than 30%. Despite scientific progress in understanding how this cancer develops, the mainstream therapies for AML remain unchanged for decades. To help address this unmet medical need, we recently established a powerful genetic screening method for identifying weaknesses in AML cells which can be used as therapeutic targets. Through this we identified a new set of leukaemia-essential genes which appear to function by modifying the AML cells’ RNA. Our initial studies with one such gene, METTL3, showed that it is essential for AML, but not for normal blood formation making it a good treatment target. In this application, I propose to extend my studies to related genes, including METTL1 and METTL16, in order to improve our understanding of how such genes sustain leukaemia cells and in so doing help develop new effective treatments against AML.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Genetic approaches to gain new insights into cellular iron metabolism and oxygen sensing
Funder: Wellcome Trust

Abstract: Maintaining appropriate levels of iron in the body is indispensable for human survival. Low iron levels can lead to anaemia and are an important feature of cancer. Too much iron can result in the death of cells and contribute to chronic diseases affecting the lungs, liver and brain. Therefore, most organisms have developed mechanisms to adapt to the abundance of iron in their environment, but our understanding of how iron is regulated within cells remains poorly understood. Here, I propose to use forward genetic approaches in human cells to uncover new pathways for iron regulation. We have developed a dynamic iron fluorescent reporter, based on the sensitivity of Iron Regulatory Protein 2 (IRP-2) to iron availability, and will use this reporter in genome wide mutagenesis screens to find genes that are required to regulate iron. Ultimately this work will identify new elements of the iron pathway and potentially uncover novel targets for drugs to treat a range of diseases which are worsened by dysregulation of iron levels.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Understanding the gene expression dynamics that regulate glioma stem cell transitions
Funder: Wellcome Trust

Abstract: It is believed that glioblastoma multiforme (GBM), the most aggressive form of adult primary brain cancer, arises from abnormal cells of origin (stem cells) in the brain known as glioma stem cells (GSCs). There is no cure for GBM. Importantly, GSCs can assume either an "active" or "dormant" state. Research suggests that GSCs in the "dormant" state are especially resistant to treatment and when made "active" again, result in deadly regrowth of cancer. Findings from my host laboratory suggest that such cell-state transitions are controlled by unique patterns of gene expression ('expression' being the process by which a gene is converted to its relevant protein) as opposed to genes simply being turned on or off. My research will use cutting edge tools to label genes of interest with markers that give off a fluorescent glow. This will allow us to identify patterns of gene expression that causes changes in GSC states. If this research is successful, future treatments could be developed to give doctors control over these cell states. For example, we might be able to prevent "dormant" cells from becoming re-activated. By doing so, we can hopefully change what is currently a deadly disease into a chronic manageable condition.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Multi-spectral in vivo optical imaging system
Funder: Wellcome Trust

Abstract: The use of bioluminescence reporting has revolutionized the imaging of small animals. Bioluminescence imaging (BLI) provides a robust technique, enabling researchers to gain essential insights into complex biological systems. BLI is used for the tracking of events in vivo, including the longitudinal monitoring of gene expression, tumour growth, enzyme activity, response to experimental drug therapies, and protein-protein interactions. The IVIS Spectrum is a state-of-the-art preclinical optical imaging system that allows for the sensitive detection of bioluminescence and fluorescence, providing a high-throughput platform for the functional whole-body molecular imaging across all organs in rodents. The equipment is simple to use, and the data obtained straightforward to analyse, making it ideal for multiple and non-expert users. The equipment has a vast range of applications across all biomedical disciplines, including the quantification of regenerative stem-cell and therapeutic immune-cell homing; monitoring bacterial infection; and following the development and treatment of tumours. Multispectral BLI can report on the location of multiple cells type or biological events. In vivo fluorescence imaging is capable of detecting targeted and activatable fluorescent probes and reporters against specific molecular processes, allowing in vivo assessment of angiogenesis, apoptosis and matrix remodelling. Cherenkov imaging of radioactive isotopes provides opportunities for radiotracer development.

Lay abstract: Recent research has made it possible to genetically modify cells and tissues so that they generate light. Using genes from fluorescent jellyfish and bioluminescent fireflies we can make regenerative stem cells or metastatic tumour cells glow. Once these cells are injected into animals the location of stem cells, or the progression and treatment response of tumours can be seen inside living mice. However, the amount of light generated by these glowing cells is low, meaning a specialised imaging system is required. In this application we request a highly sensitive camera housed within a light tight chamber, into which live mice can be placed. This equipment will allow us to follow the location and number of regenerative stem cells use to treat heart attacks or strokes, or will quantify the amount of tumour cells and their response to cancer treatments, thus providing invaluable data on the efficacy of new therapies.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Spineless in the gut - intestinal function of the aryl hydrocarbon receptor from flies to mammals
Funder: Wellcome Trust

Abstract: The aryl hydrocarbon receptor (AHR) has essential functions in the intestine, protecting mice from infection and cancer. However, the underlying mechanisms are still unclear as research has been hindered by the complex regulation and multiple feedback loops governing mammalian AHR. I will therefore use a simpler model system. Spineless, the homolog of AHR in Drosophila, binds the same DNA motif as AHR, but is regulated only on the gene expression level. My preliminary data suggest that Spineless may have similar functions to AHR, influencing epithelial regeneration and survival during infection. I will take advantage of this simpler pathway and the genetic tools and ease of manipulation in the fly in order to rapidly dissect how AHR/Spineless expression is regulated and to systematically analyse its target genes. I will first generate the necessary tools and then answer three main questions: what are the target genes of Spineless, how is Spineless gene expression regulated, and how does Spineless function in the context of intestinal infection. Results obtained from these experiments will be compared with existing data from the Stockinger group on AHR in mice to advance our understanding of intestinal physiology and the critical functions of AHR/Spineless that are conserved across species.

Lay abstract: The aryl hydrocarbon receptor (AHR) has essential functions in the gut, protecting mice from infection and cancer. However, the underlying mechanisms are still unclear as research has been hindered by the complex regulation of AHR. I will therefore use a simpler model system. I found that the equivalent of AHR in fruit flies, Spineless, also seems to be important during infection in the gut, but its regulation is less complicated. I will take advantage of the ease and speed of genetic manipulation in fruit flies to answer three main questions: what are the target genes of Spineless, how is Spineless regulated, and what is the function of Spineless in the context of intestinal infection. Results obtained from these experiments will be compared with existing data from the Stockinger lab on AHR to advance our understanding of intestinal physiology and critical, evolutionary conserved functions of AHR/Spineless in this context.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Exploiting transcription of repetitive DNA to study early events in colorectal cancer
Funder: Wellcome Trust

Abstract: Molecular changes occurring before cancer can be detected by commonly used methods provide potential biomarkers for early detection if routine screening were in place. To date, research has focused mainly on unique DNA largely disregarding the 55% composed of repetitive sequences like LINE-1s. LINE-1s are usually silenced in normal tissues but active in cancer and are best known for their ability to move to other locations in the genome with obvious deleterious implications. Mobilisation first requires activation of LINE-1’s promoters, but, intriguingly, those of both mobile and immobile LINE-1s become active in cancer. To fully understand the functional consequences of this transcriptional activity requires overcoming the challenges of studying individual LINE-1s. Using innovative approaches, we identified a LINE-1 whose activation is linked to silencing of a tumour suppressor gene and whose product can be detected in the blood of colorectal cancer patients. I will build on this knowledge to determine to determine why and which LINE-1’s promoters are active in colorectal cancer and what are the effects of this activation on neighbouring genes. I will examine in liquid biopsies the biomarker potential of the novel, aberrantly expressed genes so identified, with a long-term aim to help refine current tests.

Lay abstract: Despite many advances, cancer remains a leading cause of death worldwide, partly due to limited knowledge of the changes occurring in early stages of the disease. Research into early changes has focused mainly on unique DNA (e.g. protein coding sequences) and overlooked 55% of our DNA made up of repetitive sequences (e.g. LINE-1s) that are inactive in normal cells but active in cancer. Although difficult to distinguish and study individual elements, using new strategies we have identified a LINE-1 whose activation is linked to silencing of a tumour suppressor gene and whose product can be detected in the blood of colon cancer patients, highlighting LINE-1s’ potential as therapeutic targets and as tools for screening. I will build on this knowledge to investigate: why and which LINE-1s become active in colorectal cancer; what are the effects of their activation; and the potential of using their products as tests for early detection.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Biocontainment Level 2 high-parameter FACS: applications for the Cambridge biological sciences community
Funder: Wellcome Trust

Abstract: Provision of cutting edge cell-sorter, with class II biocontainment to allow flexible workflows as applied to a broad range of studies within the Cambridge biomedical research community. The acquisition of a CL2 high-parameter cell-sorter will provide critical ability to purify live-cell populations. This capability is desperately needed to match the explosive growth in high-parameter single-cell analysis in the Cambridge biomedical community (high-parameter flow-cytometry, CyTOF mass-spec, single-cell (sc)-RNA-seq). Parallel cell-sorting capacity of mouse and human live-cells is crucial for validation of findings, and in-depth exploration of the biology of highly purified cell populations. Currently, there is no capacity in Cambridge for high-parameter CL2-designated cell-sorting. This Wellcome Trust multi-user equipment grant application will provide a critical resource to the Cancer Research UK, Cambridge Institute (CRUK-CI), and wider Cambridge biomedical community.

Lay abstract: Our bodies are composed of trillions of individual cells, all of which work in concert to achieve our form and function. Using new technologies, we can now more reliably classify individual cells, which has revealed a profound diversity within previously-believed uniform populations. Studying how these diverse cell-types interact within their environment is central to our understanding of how our bodies function, or malfunction in disease. To investigate the roles of these diverse cell-types, we propose to use a technology called fluorescence activated cell-sorting (FACS), which is highly adaptable for multiple uses. We will use our expertise in FACS, as well as other leading technologies, to purify live cells from complex, rare human (and other) samples to ask questions about their individual roles in health and disease. Thus, the proposed FACS machine will help both clinicians and basic scientists in Cambridge focus important research on very specific cell-types in our bodies.

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