Research Opportunities

The brain is a site of relative immune privilege, long considered isolated from the peripheral immune system. We recently identified a population of resident T cells in the healthy mouse and human brain, important for the maturation of microglia (Pasciuto et al, Cell 2020). By analysing the kinetics of migration between the blood and brain, we found that the key bottleneck controlling the number of anti-inflammatory regulatory T cells in the brain was the high rate of cell death the cells exhibit when housed within the brain. Through developing a unique tool, with potential therapeutic application, we were able to deliver a biologic directly to the brain and enhance the size of the regulatory T cell population. The approach protects mice from brain damage following traumatic brain injury, stroke and multiple sclerosis. In this project we wish to explore the immunological processes that drive damage during neuroinflammation, and to harness immune-modulating biologics to prevent damage to the brain. 

Despite recent improvements in population health and prevention, heart failure prevalence and mortality are stagnant overall, with a disproportionate burden in Black, Hispanic and South Asian populations.

Single centre studies provide highly phenotyped populations covering genomics, metabolomics, advanced imaging and longitudinal health trends. In contrast large centralized healthcare data covers decades of hospital admissions and mortality for millions of people, with this data growing in depth, richness and complexity. Collaborations that leverage both approaches have the unique potential of providing needed new insights in the poorly understood heart failure syndrome.

Using advanced cardiac magnetic resonance imaging capabilities and novel biomarkers (NIH), we will conduct deep phenotyping in a diverse cohort of patients with heart failure to elucidate disease phenotypes and differences between races. At a national level (University of Cambridge) we will look at equitability of access to advanced imaging (such as MRI) and interventions (implantable defibrillators) and the impact of these on health outcomes.

Accumulation of vascular smooth muscle cells (VSMCs) is a hallmark of cardiovascular diseases such as atherosclerosis, which cause heart attack and stroke. In healthy vessels, VSMC contraction regulate blood flow and blood pressure but loose their contractile function and undergo extensive transformation upon vasuclar insult. This process results in the generation of a wide spectrum of phenotypically changed cells within atherosclerotic lesions, which are predicted to impact differently on disease progression. Using clonal lineage tracing in mouse models of atherosclerosis, we demonstrated that disease-associated cell accumulation result from extensive proliferation of a small subset of VSMC that can generate the full range of distinct cells. By combining lineage tracing with single cell RNA sequencing (sc-RNAseq) in mouse models, we have identified signatures of VSMC-derived cells subpopulations. Interestingly, cells displaying mesenchymal stem cell character are rare in healthy vessels and their numbers increase in disease models. The aim of this project is to understand how specific VSMC-derived cell populations in human disease arise, using a combination of genomics and functional assays, in order to allow efficient cell targeting in atherosclerotic lesions.

The human placenta is the first organ of the embryo and it is functional immediately after implantation. Before fetal organogenesis, the placenta holds a multi-functional and unique role as a physical, chemical, and cellular barrier. It alone orchestrates the chemical communication between mother and fetus. Most of this communication is mediated by the secretion of specific placental peptide hormones (hCG, hPL, etc.) into the maternal bloodstream. Despite these hormones having developmental and irreplaceable functions, little is known about their intracellular life: synthesis, intracellular traffic, secretion, and degradation. More importantly, many pregnancy disorders are associated with lower expression and levels of these hormones in circulation, such as fetal growth restriction and preterm birth. The cell biology of these diseases is not well understood.

With the recent advance in human placenta organoid development and novel culture techniques of trophoblasts derived from stem cells, we can now finally interrogate the fundamental questions about placental hormones' intra and extra-cellular fate. In combination with the diverse set of advanced imagining methods available between the co-mentors of this project (advanced fluorescence and cryo-electron microscopy), innovative multi-omics techniques, and advanced biochemistry and cell biology approaches, we propose to 1) discover the diversity of secretory granules (SGs) expressed in and secreted from the human placenta; 2) implement a novel in vitro secretomics approach to determine the molecular machinery that regulates the secretion of the SGs and their content; 3) validate the mechanisms using human placenta and isolated trophoblasts from donated tissue and new placenta organoids culture.

The successful candidate will have the opportunity to train on several modern imaging techniques and learn about the fundamentals of placenta development and physiology while using a multi-disciplinary approach in a team of expert cell biologists from both institutions and generating impactful basic and applied research.

Adolescence and early adulthood are important developmental periods when young people develop health-related habits that are likely to persist through their adult life. This is also a period when health inequalities emerge, as young people finish their education and enter the labour market, developing their individual socioeconomic position. Improving our understanding of the factors that contribute to the development of diet, related health behaviours, and health inequalities over this life stage will help to identify targets for public health policy and intervention.

We currently know little about the factors which influence changes in health behaviours over the transition from secondary education into further education and employment. This PhD project will focus on this question through analysis of data from the US-based NEXT Generation Health Study and from the UK-based DEBEAT study, applying epidemiological methods to assess changes in health behaviours (diet, physical activity and sleep) through adolescence and early adulthood, analyse dynamic relationships between different behaviours, and investigate how differences in these patterns of development between different groups of the population contribute to health inequalities.

Maternal over-nutrition and obesity during pregnancy is known to have long-term effects on the health of the offspring, including increased risk of obesity. Weight gain in offspring exposed to maternal over-nutrition is at least in part caused by hyperphagia- implicating altered function of hypothalamic energy homeostatic pathways as an underlying cause- but the precise mechanisms by which the in utero environment impacts on hypothalamic development is unclear. Key metabolic hormones such as insulin, leptin and ghrelin have a dual role during brain development as growth factors. These metabolic hormones are altered in an obese pregnancy, providing a direct route by which the maternal nutritional state can impact on offspring hypothalamic development. We will use a combination of in vivo manipulation of hormone levels (e.g. fetal brain injection) and ex vivo neuro-developmental techniques (e.g. neurospheres) to examine the consequences of altered metabolic hormone levels for early hypothalamic development. We will also use immunofluorescence and viral tracing to study hypothalamic architecture in the offspring of obese mothers once they reach adulthood, and correlate the anatomy with functional readouts of complex feeding behaviours using operant and metabolic chambers.

During pregnancy, nutrients must be supplied to the fetus for growth but also to the mother to maintain the pregnancy. This nutrient balance depends on the placenta, an organ that develops during pregnancy to transfer nutrients to the fetus and that secretes hormones into the mother with metabolic effects. Impaired placental function disrupts the materno-fetal nutrient balance and results in major pregnancy complications, including abnormal birthweight with both immediate and long-lasting effects on offspring health. However, our understanding of the importance of placental endocrine function in the control of fetal growth and long-term health of the offspring is unknown. To address this knowledge gap, we have developed new and robust models of genetically-induced placental endocrine malfunction in mice. Using these models, we have found that placental endocrine malfunction is associated with programmed changes in insulin and glucose handling of both the female and male offspring in adult life.

This PhD will extend these important findings by:
1. Identifying which tissues in the offspring are affected by placental endocrine malfunction and responsible for the altered glucose and insulin handling of offspring in later life.
2. Exploring the intrauterine mechanisms by which metabolic organs of the developing offspring are programmed by placental endocrine malfunction.

This will be achieved by studying the function of key metabolic organs in female and male offspring that were supported by placentas with endocrine malfunction. Particularly, it will use genetic manipulation and a range of in vivo physiological (metabolic testing, NMR scanning), and in vitro molecular (respirometry, RNAseq, western blotting, qPCR, epigenetic analysis), histological and biochemical assays.

Antiviral restriction factors (ARF) are a critical element of cellular innate immunity, representing the first barrier to viral infection that can determine outcome. We aim to identify and characterise novel ARF and their viral antagonists, since therapeutic interruption of viral antagonism can enable restoration of endogenous antiviral activity.

We employ a number of human pathogens, in particular Human Cytomegalovirus (HCMV), Monkeypox virus (MPXV) and its vaccine, Modified Vaccinia Ankara (MVA). Our systematic proteomic analyses determine which cellular factors each pathogen targets for destruction, since we have shown these to be enriched in novel ARFs. For example, we recently developed a multiplexed proteomic technique that identified proteins degraded in the proteasome or lysosome very early during HCMV infection (Nightingale et al, Cell Host & Microbe 2018). A shortlist of 35 proteins were degraded with high confidence, and we have since shown that several are novel ARF, with characterisation of these factors forming ongoing projects. Application to MVA infection indicated further candidates, and identified novel mechanisms of vaccine action (Albarnaz et al, in review, https://www.researchsquare.com/article/rs-1850393/v1). Furthermore, interactome screens can identify the viral factor(s) responsible for targeting each ARF, and indicate mechanism (Nobre et al eLife 2019).

This project will now identify and characterise critical pan-viral ARF, which can restrict diverse viruses. For the most potent, we will determine both the mechanism of restriction and the mechanism of virally mediated protein degradation. In order to prioritise the most important factors, there will also be the opportunity to use novel multiplexed proteomic screens.

Mitochondrial diseases are caused by defects in genes required for energy production and oxidative phosphorylation (OxPhos). We find it intriguing that some patients with mitochondrial disease present late in life, with very tissue-specific phenotypes. It seems that not all cells and tissues are equally susceptible to mitochondrial disease.

We mainly study how mitochondrial dysfunction and mutations in the mitochondrial genome affect neural stem cell behaviour in Drosophila and mouse. The questions we address are:
(1) how mitochondrial dysfunction affects normal and pathological cell fate decisions in the developing brain. We previously showed that neural stem cells in the brain rely heavily on mitochondrial energy production and now study how they interact with the glial cells that make up their stem cell niche.
(2) how transcription of the nuclear genome is regulated when a cell is confronted with mitochondrial dysfunction. We employ and develop innovative DamID-based in vivo chromatin profiling technology to study metabolism of chromatin modification.
(3) how mutations in the mitochondrial genome evolve over time, during brain development and aging. We use in situ hybridisation-based methods and single-cell CRISPR screening to identify novel regulators of mitochondrial genome maintenance.

In order to study these questions in an in vivo context, in (stem) cells surrounded by their appropriate tissue environment, our primary model system is the fruit fly, Drosophila melanogaster. In addition, we actively translate our findings and the technology we develop into mammalian model systems, in particular the mouse embryonic cortex.

Relevant references
- van den Ameele J, Krautz R, Cheetham SW, et al., Reduced chromatin accessibility correlates with resistance to Notch activation. Nat Commun. 2022;13(1):2210.
- van den Ameele J, Li AYZ, Ma H, Chinnery PF. Mitochondrial heteroplasmy beyond the oocyte bottleneck. Semin Cell Dev Biol. 2020 Jan. 97:156-66.
- van den Ameele J, Brand AH. Neural stem cell temporal patterning and brain tumour growth rely on oxidative phosphorylation. eLife. 2019;8:e47887.
- Tiberi L*, van den Ameele J*, Dimidschstein J, Piccirilli J, Gall D, Herpoel A, Bilheu A, Bonnefont J, Iacovino M, Kyba M, Bouschet T, Vanderhaeghen P. Bcl6 induces neurogenesis through Sirt1-dependent epigenetic repression of selective Notch targets. Nat Neurosci. 2012 Dec;15(12):1627-35.
- Gaspard N, Bouschet T, Hourez R, Dimidschstein J, Naeije G, van den Ameele J, Espuny-Camacho I, Herpoel A, Passante L, Schiffmann SN, Gaillard A, Vanderhaeghen P. An intrinsic mechanism of corticogenesis from embryonic stem cells. Nature. 2008 Sep 18;455(7211):351-7.

The presence and role of neural stem cells (NSCs) in the adult human brain is a long-debated issue in neuroscience. Recent work has demonstrated that stem-like cells exist in the embryonic, foetal, and human adult brain where they persist well into adulthood and can even contribute to neurogenesis. However, their role in neurodegenerative disease is unknown. Ongoing work in the lab has led to the hypothesis that NSCs may become dysfunctional in neurodegenerative disease resulting in senescence chronic inflammation, and thereby acting as pacemaker cells driving neuronal demise. This ambitious project aims to identify disease-associated NSCs and their phenotype in the context of human neurodegeneration using spatial biology approaches, including imaging mass cytometry, RNA scope and single nuclear RNA sequencing. Relying on post-mortem brain tissue of different stages of Alzheimer’s disease, traumatic brain injury, vascular dementia and chronic stroke, this project will study NSCs in a range of human diseases characterised by neurodegeneration and neuronal injury. Ongoing work in the lab identifies NSC-specific markers based on transcriptomics and protein profiling experiments in brains with progressive multiple sclerosis, enabling to investigate the distribution of NSCs in a wide range of diseases. Spatial transcriptomics and proteomic approaches will allow to study their phenotype and dysfunction in relation to other cell types and local pathology. This project will shed light on the role of NSCs in neurodegeneration and has the potential to identify an entirely novel mechanism of neurodegeneration in human disease.

This project will be co-supervised by Prof. A. Quaegebeur.

Immunity and immune-tolerance at mucosal and other barrier surfaces is vital for host survival and homeostasis with antibodies or immunoglobulins (Ig) playing a key role. However, the specific roles of B cell sub-types, particularly, the innate-like B-1 cell subset is poorly understood. The surgeon James Rutherford Morrison (1906) called the omentum in the peritoneal cavity the "abdominal policeman" and it promotes gut IgA production by peritoneal B-1 cells. IgA is the most abundantly produced antibody isotype and is known to be important for mucosal immunity. It is estimated that ~50% of IgA is derived from B-1 cells. In addition, B-1 cells are thought to be important because they make T cell-independent “natural” IgM circulating in our blood, and they can rapidly respond to mucosal perturbations such as an infection. By contrast, it will take conventional B-2 cells weeks to mount a germinal center (GC) reaction and generate antibodies that have undergone T cell-dependent affinity maturation and isotype switching. Textbooks currently do not entertain the possibility that B-1 cells can also participate in GC reactions. This project aims to challenge such an assumption. After all, B-1 cells in the gut mucosa and probably other mucosal tissues can undergo class switch recombination to IgA. However, the differentiation program that leads to this distinct pathway of IgA production is not well understood: for example, it is unknown if this process occurs outside or within GCs in mucosa-associated lymphoid tissues (MALT). Expertise on B-1 cells in the Muljo lab and the GC reaction in the Turner lab will be combined to explore this potentially paradigm-shifting research. Both wet-bench and bioinformatic research opportunities are available.

Students will learn about the fundamentals of transcriptional; epigenetic and post-transcriptional regulation; immunometabolism; in vivo CRISPR screening; CRISPR editing in primary B cells; and systems immunology. The combination of classical immunological techniques and cutting-edge, multi-disciplinary approaches will enable important discoveries to define the in vivo biology of B-1 cells. Ultimately, we seek novel insights that can be translated to inform vaccine design targeted to activate B-1 cells and/or therapeutics to inhibit their activity when necessary.
 

Recent publications:

Turner, D. J., Saveliev, A., Salerno, F., Matheson, L. S., Screen, M., Lawson, H., Wotherspoon, D., Kranc, K. R., and Turner, M. (2022). A functional screen of RNA binding proteins identifies genes that promote or limit the accumulation of CD138+ plasma cells. eLife, 11, e72313. PMID: 35451955; DOI: 10.7554/eLife.72313.

Osma-Garcia, I.C., Capitan-Sobrino, D., Mouysset, M., Bell, S.E., Lebeurrier, M., Turner, M. and Diaz-Muñoz, M.D. (2021). The RNA-binding protein HuR is required for maintenance of the germinal centre response. Nature Communications, 12(1):6556. PMID: 34772950; DOI: 10.1038/s41467-021-26908-2.

Wang, S., Chim, B., Su, Y., Khil, P., Wong, M., Wang, X., Foroushani, A., Smith, P. T., Liu, X., Li, R., Ganesan, S., Kanellopoulou, C., Hafner, M. and S. A. Muljo. (2109). Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3. Genes & Development, 33: 1048-1068. PMID: 31221665; DOI: 10.1101/gad.325100.119.

The Rayon’s lab (www.rayonlab.org) overall aim at the Babraham Institute in Cambridge is to investigate the molecular and metabolic pathways that control biological timing and lifespan. To answer these questions, we work with mouse and human stem cells and embryos and employ a variety of quantitative and genomic techniques. We are looking for applicants that are curious about evolution, developmental biology and embryonic stem cells.

We are interested in the following topics:
1.    Understanding the regulation of enhancer timing. We want to test the existence of species-specific enhancers and their dynamics.
2.    Exploiting genetic variation to investigate dynamics of regulatory networks in stem cell models.  
3.    To develop a high-content imaging assay to screen for modulators of timing. Develop a screen to explore if epigenetic, metabolic, and turnover factors impact the pace of differentiation.

A background on cell culture or molecular biology, as well as skills in bioinformatics or computational approaches would be useful, but ample opportunities for training will be provided.

Dengue viruses continue to circulate endemically through large parts of the globe. Dengue virus is an antigenically variable pathogen, with individuals able to get reinfected numerous times. The risk of severe disease or death is increased in individuals with pre-existing antibodies generated from prior infections. This antibody-dependent phenomenon has complicated efforts to generate vaccines. The proposed research program aims to tackle this complexity through the combination of computational and experimental work in a joint project between the laboratories of Dr. Henrik Salje, a Professor at the University of Cambridge and the head of the Pathogen Dynamics Group and Dr. Leah Katzelnick, who is Chief of the Viral Epidemiology and Immunity Unit at the NIH. These two labs have a long track of working together, especially focusing research on well characterised settings where we have been able to characterise antigenic, genetic and epidemiologic features of dengue within the same communities. We have previously shown that there are long term trends in the antigenic properties of viruses circulating in the same location, suggesting of evolutionary pressures from local immunity. However, the exact immune and genetic mechanisms remain unknown.

In this PhD project, we will use computational approaches to identify candidate amino acid sites that are linked with shifts in antigenic space and to track these changes over a 30 year period. We will then experimentally test the antigenic movement of viruses mutated at the candidate locations. Finally, we will evaluate how antigenic shifts relate to dengue epidemic dynamics and disease. This project will provide much needed insight into how pathogens change to escape immunity, and will help guide vaccine efforts.

Virus infection of brain stem cells represents a major global health concern, but also offers treatment possibilities in neurodegenerative diseases and in malignant brain tumours. For example, Zika Virus targets SOX2+ neural progenitors in the developing brain to cause microcephaly in babies born to mothers infected during pregnancy; likewise, it targets SOX2+ glioma stem cells in the most common and lethal malignant brain tumour, glioblastoma (GBM) (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4135719). Stem cells have been shown to exploit a distinct set of antiviral mechanisms compared to somatic cells (https://doi.org/10.1016/j.cell.2017.11.018), and viral permissivity varies widely between example developing brain and glioblastoma stem cell populations. Understanding and manipulating the cell-intrinsic mechanisms underpinning antiviral resistance in brain stem cells will inform approaches to protect and exploit neural stem cell function and to ablate cancer stem cells in GBM.

This project will seek to understand and modify viral permissivity and antiviral defence mechanisms in developing brain and brain tumours, focusing on stem cell intrinsic pathways. In the first place we will  address the hypothesis that immune selection pressure on glioma stem cells during tumour development results in expansion of a mesenchymal/injury-response cell population (https://www.cell.com/cell/pdf/S0092-8674(21)00351-2.pdf) refractory to virus infection, then proceed to examine underlying mechanisms.

You will be working with human patient-derived and mouse defined mutation glioma cell models, treated with viruses and viral mimetic compounds. You will be assaying transcriptional identity and responses using qPCR and RNA sequencing, immunofluorescence and RNA smFISH, and cytokine secretion using immunoassays. The lab has access to the state-of-the-art Cambridge Stem Cell Institute imaging, FACS, sequencing and bioinformatic facilities, and to additional specialist facilities (e.g. imaging mass cytometry) in the CRUK Cancer Institute next door. We will validate results in mice in vivo and/or slice cultures prepared from  human developing brain and patient brain tumour tissue, models we have established and use routinely in the lab.

Emerging evidence suggests an exciting link between metabolism, chromatin and transcription. Metabolism can regulate post-translational modifications of histones which in turn regulate transcription of target genes. Highly proliferative cancer cells re-wire their metabolism to fuel growth, and in turn modify histones to alter gene expression. Identifying mechanisms by which cancer cells re-wire their metabolism and gene expression will identify key vulnerabilities to target using small molecule therapeutics.

Our recent work at NIH has demonstrated links between histone lactylation, gene expression and cancer metabolism (histone lactylation depends on elevated cellular lactate, the end product of glycolysis – a preferred metabolic pathway in cancer). Work in Cambridge has further linked the molecular chaperone HSP90 with gene expression and metabolism in the context of cancer. Harnessing the complementary strengths in the two labs at NIH and Cambridge, the collaborative work will delineate molecular pathways linking small-molecule therapeutics targeting the chaperone HSP90 with cancer metabolism and with specific small-molecule inhibitors of glycolysis. The data we obtain delineating the metabolic dependence of gene expression in cancer will uncover novel and exciting treatment strategies to treat cancers’ metabolic vulnerabilities.