Research Projects 2019/20 (applications open 3^rd September 2018)

Deadlines for applications for admission in the academic year October 2019 – September 2020 are as follows:

Gates US: 10^th October 2018

Graduate Funding Competition: 5^th December 2018

IMPORTANT – this included applications from applicants who wish to be considered for Cambridge Trust funding (both inside and outside the EU).

Please note that ALL supporting documents (references, transcript, CV) must be uploaded within 7 days of the date of applying

Short listing meetings for applications will be first week of January 2019, followed by interviews week commencing 21^st January 2019. Only those shortlisted for interviews will be contacted by e-mail.

*We are still considering applications for Easter 2019 but applicants need to have funding in place*

For more information about a specific project please contact the individual supervisor using the e-mail address provided, it is recommended that applicants contact supervisors prior to applying. However, please do not submit an application to the individual supervisor. All applications must be submitted following the process detailed on our How to Apply page.

Professor Franklin Aigbirhio (fia20@medschl.cam.ac.uk) – Wolfson Brain Imaging

• Synthesis and Evaluation of Novel Molecular Imaging Probes for Imaging Aggregated Protein Structures linked with Neurodegenerative Diseases (PhD only)

This project’s objective is to develop novel molecular imaging probes, including PET probes, that are selective to protein aggregates, which are neuropathological features of various neurodegenerative diseases, including Alzheimer’s disease and frontotemperal dementia. The project would involve organic synthesis and in vitro assays of compounds, combined with developing the radiosynthesis of the novel PET probes. Evaluation of the probes would involve in vitro radiographic methods and in vivo imaging in models of dementia using a high resolution PET scanner.

• Development and Application of Novel PET Markers of Neuroinflammation (PhD only)

This project’s objective is to develop novel in vivo PET probes for application as sensitive markers of neuroinflammatory processes which are key components of several pathologies, including stroke, traumatic brain injury, multiple sclerosis and dementias. The project would involve organic synthesis and in vitro assays of compounds, combined with developing the radiosynthesis of the novel PET probes. Evaluation of the probes would involve in vitro radiographic methods and in vivo imaging in models of neuroinflammation using a high resolution PET scanner.

• Novel Carbon-11 and Fluorine Radiochemistry for manufacture of PET Radiopharmaceutical (PhD only)

This project is focused on developing novel radiosynthetic methods for carbon-11 and fluorine-18 to widen the scope of radiolabelling method and produce simpler, more robust methods for the manufacture of PET radiopharmaceuticals. Novel technologies will be applied include flow chemical/microfluidic methods and micro-capillary films.

*NOTE: these projects are particularly suited to graduates in Chemistry.

Edward Avezov (ea347@medschl.cam.ac.uk) – UK Dementia Research Institute

(PhD or MPhil, PhD preferable)

• Endoplasmic Reticulum Transport and Morphoregulation in Neuron (Patho)Physiology

The Endoplasmic Reticulum (ER) is a multifunctional organelle, shaped as a contiguous network of membranous pipes extending throughout the cell periphery. Its morphology benefits intercellular communication, allowing controlled distribution of ER luminal solutes (e.g. Ca²⁺ in muscular/neuronal signaling) and membrane bound components to distant sites and adjoining organelles. Mounting data points to a critical role of ER morphology regulation in neuronal functioning. This is prominently exemplified by the direct association of ER morphogens (aka ER shaping proteins) with neuropathologies such as Hereditary Spastic Paraplegia and dementia related diseases. We seek understanding of how ER’s network integrity, morphological regulation and luminal transport support neuronal cell functioning, with a view to identifying new intervention targets for prevention of neurodegenerative avalanche. The projects involves editing of candidate genes in cells with potential to differentiate to neurons/glia, and analysing the consequences of the targeted mutagenesis on structure/function of neuronal ER using live cell microscopy techniques such as super-resolution imaging and single particle tracking (carried out in collaboration with optics physicists and computer scientists).

• Endoplasmic Reticulum Associated ROS and Redox Dynamics in Neurons

Reactive Oxygen Species (ROS) are utilized by cells as secondary messengers. Fine time-space regulation of ROS is vital to avoid their toxicity. Elevated ROS (oxidative stress) accompany dementia pathologies. Endoplasmic Reticulum (ER) and its insulated and regulated redox system emerges as key player in physiological and controlled supply of certain ROS and may be also a source of the pathological oxidative stress. The project aims to explore this notion and identify the factors endowing the ER with its ROS production, storage and supply capabilities. Work involves utilizing (and further development) of genetically encoded probes for live cell redox and ROS imaging in genetically and pharmacologically manipulated neurons.

• Monitoring Protein Aggregation and Aggregates’ Handling by Neurons

Cells maintain dynamic protein homeostasis, ensuring a manageable load of unfolded proteins and adequate availability of the protein folding machinery. In healthy proteostasis nascent proteins are chaperoned through the functional folding route avoiding misfolding and aggregation. Dementia related pathologies are associated with a disbalanced proteostasis manifested in aggregation of several particularly aggregation-prone proteins (e.g. TAU, a-betta, a-synuclein etc.). In this project we develop live-cell- imaging-compatible aggregation-sensing techniques to study cellular mechanisms and factors behind aggregation-predisposing cellular conditions, and those involved in aggregates’ turn-over.

Dr Peter Arthur-Farraj (pja47@cam.ac.uk) – Neurology/ John Van Geest Centre for Brain Repair

• Neuronal-Glia Communication during Axon Injury and Regeneration (PhD only)

(Co-supervised by Professor Michael Coleman)

The major glial cells of the peripheral nervous system, myelinating and non-myelinating Schwann cells, are reprogrammed after nerve injury into repair Schwann cells, specialized for maintaining survival of injured neurons, supporting axonal regeneration and nerve repair. This is regulated by Schwann cell-intrinsic signals, yet it is completely unknown whether extrinsic signals from injured axons initiate this process? Before injured axons can regenerate, the segment distal to the injury degenerates within a highly predictable time window. However, Schwann cells respond with changes in transcription long before axonal degeneration, at sites remote from the injury, suggesting potential axonal-Schwann cell signalling.

This project will use a number of cutting edge techniques as well as standard molecular and cell biology approaches to investigate this hypothesis. These include; live imaging of axon-Schwann cell interactions and calcium signalling in transgenic zebrafish models of nerve injury; live imaging of neuronal and Schwann cell populations from transgenic mouse lines in compartmentalized cocultures in microfluidic chambers; and the possibility to use transcriptomics and proteomics along with bioinformatic analysis to identify potential novel signals.

References:

Arthur-Farraj, P., Latouche, M., Wilton, D.K., Quintes, S., Chabrol, E., Banerjee, A., Woodhoo, A., Jenkins, B., Rahman, M., Turmaine, M., et al. (2012). c-Jun Reprograms Schwann Cells of Injured Nerves to Generate a Repair Cell Essential for Regeneration. Neuron 75, 633–647.

Conforti, L., Gilley, J., and Coleman, M.P. (2014). Wallerian degeneration: an emerging axon death pathway linking injury and disease. Nat. Rev. Neurosci. 15, 394–409.

Jessen, K.R., and Mirsky, R. (2016). The repair Schwann cell and its function in regenerating nerves. J Physiol. 594, 3521-3531.

Professor Manohar Bance (mlb59@cam.ac.uk) Cambridge Ear Institute

Hearing Related Projects:

• Developing New Tests for Site of Lesion in Hearing Loss

(PhD- suitable for clinical otology, audiology or auditory science backgrounds)

(co-supervised by Professor Brian Moore)

Hearing loss is often a black box, described by symptoms (such as sudden hearing loss) rather than the underlying biology. The aim of this project is to develop and apply newer and more sophisticated tests of auditory function tease out if the site of lesion is at the inner ear, synapse or auditory nerve.

This project will use and modify current tests in electrophysiology such as electrocochleography, ABR, and frequency following responses, and psychoacoustic tests such as amplitude modulated noise, reversed speech etc. in a series of patients with suspected or known pathologies in the cochlear basilar membrane mechanics, auditory nerve, synapse and outer hair cells to develop a panel of discriminatory tests that can pinpoint the site of pathology better in hearing impaired subjects. We will liaise with animal researchers using genetic knockout mice with known sites of pathophysiology to corroborate our findings in patients.

• Cochlear Implant Stimulation Spread in Patients and Models

 (PhD- suitable for clinical otology, audiology or auditory science backgrounds)

 (co-supervised by Dr. Bob Carlyon)

Cochlear implant results are severely impacted by current and stimulation spread inside the cochlea. This makes it very difficult to selectively stimulate different parts of the auditory nerve for to achieve frequency selectivity. This project will use sophisticated methods to interrogate the stimulus and response functions in-vivo in patients with implanted cochlear implants, to tease out those electrodes that are causing the most stimulation spread. Simultaneously, the project will work on a cadaveric model with implanted cochlear implants and directly measure stimulation spread within the cochlea

• Developing 3-D Reconstructed Models of the Human Cochlea, and using them to Develop the Material Properties for Cochlear Implants for a Range of Anatomies

 (MPhil/PhD- suitable for clinical otology, imaging, or anatomy backgrounds)

(co-supervised by Dr Andrew Gee & Dr Graham Treece)

There is a huge variation in the anatomy and size of the human cochlea. This project develops 3D models of the human cochlea from microCT scans, and using imaging statistical tools to develop models of variation. The different geometries are then 3D printed, and used as templates to develop the material properties for different types of electrode arrays that are optimized to differing geometries.

• Machine-Neural Interfaces in Auditory Implants (Phd engineering, cell biology or clinical backgrounds)

(Co-supervised by Profesor George Malliaras & Dr Roisin Owens)

We are working to develop the machine-neural interface in cochlear implants by modifying the cellular and microelectronic interfaces to try to increase the number of information channels that can be created.This is needed to improve bidirectional information flow to neural structures in the cochlea. This project combines work in materials engineering, microfabrication and cellular biology

• Measuring Acoustic Sound Fields that Hearing-Impaired Subjects Function in

 (PhD or MPhil- suitable for engineering, acoustics, otology or audiology backgrounds)

(Co-supervised by Dr Anurag Agrawal)

As one of the largest auditory implant centres in the country, we have clinical experience with thousands of patients. Their hearing experience at home is often subjectively not well correlated with the very controlled tests of hearing function that we use clinically. A large missing piece is what kind of acoustic environments the patients have to function in their real daily lives.

In this project, we are developing a wearable body technology that uses sophisticated probes of the auditory/acoustic environment during the patients daily activities. These will be correlated with the patient’s subjective and objective measures of hearing difficulty and effort of listening, to develop more realistic programming parameters for patient functioning.

Vestibular and Balance Related Projects

• Point of Symptom Measurements in Patients with Vertiginous Disorders.

(PhD, suitable for otology, audiology, engineering or biomechanics backgrounds)

 Patients with vertiginous disorders often have symptoms at home, and when seen in the clinic are quiescent. This makes it difficult to understand the biologic changes during the episodes, and differentiate the various disorders. We are developing wearable technologies to measure aspects of eye movement, pulse, EEG and hearing during attacks. This project will take groups of patients with intermittent symptoms of imbalance or vertigo, and help develop and validate the wearable technologies to log the underlying physiology changes during attacks, as diagnostic aids and measures of therapeutic interventions.

Developing new Imaging Technologies for the Temporal Bone and Lateral Skull Base

• Developing machine learning and complex algorithmic solutions for detecting lateral skull base tumors, automated segmentation and volume extraction, and prediction of growth (with Dr Steven Price, University of Cambridge) PhD only

Particularly with slowly growing benign tumors such as vestibular schwannomas, there are very long periods of follow-up, and it is difficult to predict what any individual tumor will do.

In this project, liaising with artificial intelligence experts, we will use our extensive collection of vestibular schwannoma imaging to train algorithms or develop new deep learning protocols to automate tumor segmentation, and to try to predict tumor behaviour

• New MRI Imaging Modalities for the Temporal Bone (with Dr Tomasz Matys, and Dr Josh Kaggi, University of Cambridge) PhD only

We are working on developing new imaging coils and sequences that will  i) allow better resolution imaging of the cochlea and inner ear ii) allow bone imaging simultaneously with soft tissue imaging. Both of these projects involve human and cadaveric testing of these technologies. 

Professor Roger Barker (rab46@cam.ac.uk) – Neurology/ John Van Geest Centre for Brain Repair

• Rescuing Vulnerable Neurons in Parkinson’s Disease (PhD only)

(Co-supervised by Dr. Wei-Li Kuan)

Although being traditionally considered as a movement disorder that is pathologically defined by the loss of midbrain dopaminergic neurons, the fact that pathological alpha-synuclein can “propagate” in a stereotypic spatiotemporal pattern, and the presence of non-motor symptoms years before motor impairment, suggest that the pathogenesis of Parkinson’s disease (PD) is much more systemic, potentially involving both the central and peripheral nervous systems. Intriguingly, selective population of neurons are very resilient to alpha-synuclein toxicity, and appear to be less affected even at an advanced stage of disease. We have recently found that a systemic delivery of misfolded alpha-synuclein induces a highly selective neuropathology in nontransgenic animals resembling early stages PD. In particular there were progressive gastrointestinal and olfactory impairments with corresponding cellular deficits in selective subsets of neurons. Using a combination of cellular and molecular biology techniques, the objective of this PhD project is to study the mechanism(s) driving such selective vulnerability in different neuronal subsets, with an aim to identify novel targets to treat PD.

Dr Dennis Chan (dc598@medschl.cam.ac.uk) – Neurology

(co-supervised by Professor Cecilia Mascolo, Department of Computer Science)

• Use of Wearable Technologies to detect Alterations of Behaviour in People at risk of Alzheimer’s Disease (PhD only)

The aim of this project is to use apps based on wearable technologies, such as smartphones and smartwatches, to detect changes in functions that precede the onset of dementia, such as navigation and sleep. In collaboration with Cecilia Mascolo, Professor of Mobile Systems at the University of Cambridge, we have developed and piloted the use of several apps, and this project will involve implementation of these apps in cohorts at risk of AD, comparison of their diagnostic classification accuracy against currently used cognitive tests and app validation against established markers of disease such as MRI brain scanning. The successful student will be encouraged to investigate additional options for passive sensing of everyday behaviour.

Applicants with a background in programming or computer science would be particularly encouraged.

Professor Marek Czosnyka (mc141@medschl.cam.ac.uk ) – Neurosurgery

• Mathematical Modelling of Brain Haemodynamics and Pressure-Volume Compensation  

Dynamical properties of cerebral blood flow (CBF) and cerebrospinal fluid circulation (CSF) can be modelled by a structure of nonlinear differential equations (1). Models describe such phenomena as autoregulation of blood flow, brain venous blood outflow, compensatory role of CSF circulation, etc (2). They are relevant to understanding of pathophysiological mechanisms after traumatic brain injury, subarachnoid haemorrhage, stroke, in hydrocephalus and in idiopathic intracranial hypertension. Database of recorded clinical signals is available for verification or identification of successful modelling structures. Project will be focused on further refinement of the existing models, including their application for non-invasive assessment of intracranial pressure (3), asymmetry of CBF and phenomenon related to collapse of cerebral venous sinuses. Project suits neuroscientists with strong computer skills (including writing own codes, advanced Matlab, etc).

Further readings (4). 1. Czosnyka et al. J Neurol Neurosurg Psychiatry. 1997 Dec;63(6):721-31. 2. Piechnik et al. J Cereb Blood Flow Metab. 2001 Feb;21(2):182-92. 3 Kashif FM et al. Sci Transl Med. 2012;4(129):129ra44. 4.http://www.neurosurg.cam.ac.uk/pages/brainphys/index.php

• Methodology of Clinical Tests for Assessment of Cerebral Autoregulation after Traumatic Head Injury

Various methods exist for assessment of autoregulation of Cerebral Blood Flow (CBF). They incorporate different modalities: arterial blood pressure, intracranial pressure, blood flow velocity, cerebral perfusion pressure, and brain tissue oxygenation (1). Dynamical tests of cerebral autoregulation include time series analysis, analysis of models based on transfer function, wavelet decomposition, non-linear decomposition, etc. The aim of the project is to compare various methodologies, various modalities and compare them from the point of view of clinical utility in a group of head injured patients. Strong emphasis will be put on feasibility studies of new and existing methodologies at the bedside: such as a concept of ‘optimal’ Cerebral Perfusion Pressure or individualized threshold of intracranial pressure. Also links between brain physics modalities and electrophysiology and biochemistry will be of interest Project is ideal for a person having medical or biological background with strong practical computer skills.

Further readings (4). 1. Czosnyka M et al. Neurocrit Care. 2009;10(3):373-86. 2. Aries MJ et al. Crit Care Med. 2012; 40(8):2456-63. 3. Lazaridis C et al. J Neurosurg. 2014 Apr;120(4):893-900. 4.http://www.neurosurg.cam.ac.uk/pages/brainphys/index.php

• Mechanisms controlling Cerebrospinal Fluid dynamics

In various pathologies, reasons for intracranial hypertension may be different. In hydrocephalus: disturbed outflow of Cerebrospinal Fluid (CSF); in idiopathic intracranial hypertension (IIH): obstruction of venous blood outflow; in head injury and stroke: brain edema, increased vasogenic component of ICP, failing regulation of cerebral blood volume or all three factors together, etc. (1) This is an interdisciplinary project requiring good background in clinical neurosciences, brain physics and computational methods (time series analysis, dynamic modelling). Clinical applications are envisaged (but not limited to) mainly in area of hydrocephalus (2) and IIH . Vast database of recorded signals and clinical material (over 5000 cases) can be used for mastering new methodologies of processing and modelling (3). Strong knowledge of brain imaging techniques will be essential. Project is ideal for a person having medical or biological background with strong practical computer skills.

Further readings (4). 1. Czosnyka M, Pickard JD. J Neurol Neurosurg Psychiatry. 2004;75(6):813-21. 2. Weerakkody RA et al. Acta Neurol Scand. 2011;124(2):85-98. 3. Varsos GV et al.

Professor Robin Franklin (rjf1000@cam.ac.uk) – Stem Cell Neurobiology/WT-MRC Cambridge Stem Cell Institute

The regenerative biology of adult CNS stem cells. In my laboratory our main area of research is aimed at understanding how adult CNS stem cells respond to injury and contribute to regeneration, chiefly the regeneration of new myelin sheaths – or remyelination (and area in which we are considered world leaders). Our lab is primarily a cell biology laboratory, pursing the underlying mechanisms on which future developments in therapy are based. Many of the projects are undertaken in collaboration with my colleague Dr. Chao Zhao.

There are many projects ongoing and available as PhD projects and precisely what form a project might take is very fluid. This is open to discussion with potential PhD students. Example of the sorts of projects available are as follows:

• Rejuvenating Ageing CNS Stem Cells by Partial Reprogramming

Therapeutic enhancement of remyelination is likely to be a highly effective means of preventing much of the axon loss that underpins the progressive phase of MS. Remyelination efficiency declines with ageing. This means that the need for remyelination therapies increases with disease progression. It may also imply that adult OPCs, the cells primarily responsible for remyelination, become refractory to such therapies with increasing age. We have generated data from ageing OPCs showing that this is indeed the case. Thus, in order to make endogenous adult OPCs in the ageing CNS more responsive to remyelination-enhancing therapies it may be necessary for them to be rejuvenated. New and exciting evidence shows that partial reprogramming can rejuvenate ageing cells and improve regeneration of ageing pancreas and skeletal muscle (Ocampo et al ., Cell 2016). In this project will be apply this approach to the problem of ageing adult OPCs and the age-associated decline in remyelination efficiency. The project is designed to be achievable by a committed PhD student.

• Adult Brain stem Cells, Ageing and Circadian Rhythms

This project concerns the cell biology of adult stem cell ageing, an especially ‘hot topic’ in current stem cell research. An area of current interest is how the biology of circadian rhythms controls the maintenance and properties of adult CNS stem cells and how disturbances in these rhythms with ageing can disrupt normal regenerative processes. We address questions of fundamental stem cell biology that underpin our understanding of disease and are needed to therapeutically harness the immense regenerative potential latent within the aging CNS.

• Do Ageing CNS Progenitors become Vulnerable to Autoimmune Damage with Disease Progression in Multiple Sclerosis?

The project has arisen from unpublished data generated during this collaboration, where, by proteomic analysis of CNS progenitors, we have discovered that as adult progenitors age they acquire expression of antigens known to be targets of the autoimmune process in MS. This raises the exciting and potentially transformative hypothesis that one of the reasons why the regenerative process of remyelination fail in MS is because the cells primarily responsible for remyelination themselves become vulnerable to destruction by the maladaptive immune process of the disease.

• What Role does Angiogenesis play in Remyelination and How does this Change within Ageing?

Given the central role of angiogenesis in many regenerative processes it is somewhat surprising that this has not been fully explored in the context of CNS remyelination. This project will first examine the role of angiogenesis using experimental approaches, and then use the information derived to analyse and interpret data obtained from MS tissue. It will use both in vitro approaches and experimental in vivo models of demyelination/remyelination to explore cross-talk between endothelial and oligodendrocyte lineage cells, the mechanisms within a remyelinating lesion that govern angiogenesis, and how these change with ageing.

Dr Rita Horvath (rh732@medschl.cam.ac.uk) – Neurology

• Identifying Novel Disease Genes in Patients with Hereditary Motor Neuropathies

(Co-supervised by Dr Rhys Roberts & Professor Patrick F. Chinnery)

Charcot-Marie-Tooth disease (CMT) is a group of inherited disorders of the peripheral nerves. Clinical diagnosis of CMT can be made fairly accurately, and the clinical classification is very helpful in the identification of new disease genes. All types of CMT thought to affect approximately 5 to 40 per 100,000 individuals. We have recently re-evaluated the prevalence of CMT in Northern England, which is compatible with other European countries. Thus far more than 80 genes have been implicated in CMT, and the recent next generation CMT panel screening enable the mutation detection in all known rare neuropathy genes. However, achieving a genetic diagnosis is still challenging in some forms of inherited neuropathies, including hereditary motor neuropathies (~40% detection rate).

We have already characterized the clinical presentation and electrophysiology in over 100 patients with hereditary motor neuropathy. CMT panel and whole exome sequencing has been performed in genomic DNA samples of these patients and the confirmation of the exome results by Sanger sequencing is currently ongoing. We have recently reported a novel disease gene SYT2, which is the first gene involved in motor neuropathy affecting synaptic transmission and the involvement of the neuromuscular junctions raised the possibility of a novel approach for therapy.  

This project will focus on genetic analysis of the exome results in hereditary motor neuropathies with the potential to identify further novel human disease genes. The evaluation of detected changes and the confirmation of pathogenicity may require further laboratory techniques, such as tissue culture studies, cDNA analysis and functional studies. We will explore the involvement of neuromuscular junction in the development of the neuropathy and will study whether the modification of the neuromuscular junction can be beneficial for these patients.

References:

1. Reilly MM, Shy ME. Diagnosis and new treatments in genetic neuropathies. J Neurol Neurosurg Psychiatry 2009;80:1304-14.
2. Foley C, Schofield I, Eglon G, Bailey G, Chinnery PF, Horvath R. Charcot-Marie-Tooth Disease in Northern England. J Neurol Neursurg Psychiatry 2012;83:572-3.
3. Bansagi B, Griffin H, Whittaker RG, Antoniadi T, Evangelista T, Miller J, Greenslade M, Forester N, Duff J, Bradshaw A, Kleinle S, Boczonadi V, Steele H, Ramesh V, Franko E, Pyle A, Lochmüller H, Chinnery PF, Horvath R. Genetic heterogeneity of motor neuropathies. Neurology. 2017 Mar 28;88(13):1226-1234.
4. Herrmann DN, Horvath R, Sowden JE, Gonzales M, Sanchez-Mejias A, Guan Z, Whittaker RG, Almodovar JL, Lane M, Bansagi B, Pyle A, Boczonadi V, Lochmüller H, Griffin H, Chinnery PF, Lloyd TE, Littleton JT, Zuchner S. Synaptotagmin 2 mutations cause an autosomal-dominant form of Lambert-Eaton Myasthenic Syndrome and non-progressive motor neuropathy.

• Studying the Molecular Mechanism of Mitochondrial Aminoacyl tRNA Synthetases in Neurons

(Co-supervised by Dr Michal Minczuk & Dr Andras Lakatos)

Aminoacyl-tRNA synthetases (ARSs) are essential and ubiquitous ‘house-keeping’ enzymes responsible for charging amino acids to their cognate tRNAs and provide the substrates for global protein synthesis. Mutations in each of the 19 human mt-ARSs genes have been reported in human disease. Glycyl- (GARS) and lysyl tRNA (KARS) synthetase genes encode both cytosolic and mitochondrial ARS enzymes, suggesting links between protein syntheses in these two distinct cellular compartments. Despite being ubiquitously expressed, mutations in these genes show an unexpected variety of phenotypes, including many neurological disorders affecting the white matter, causing epileptic encephalopathy, pontocerebellar hypoplasia, peripheral neuropathy or intellectual disability, while other characteristic phenotypes affect other organs. The cause of the selective vulnerability, or the exact molecular mechanisms leading to such tissue specific clinical manifestations are poorly understood.

In human cells, two distinct groups of ARSs encoded by separate genes can be distinguished by their cytoplasmic or mitochondrial localization however, GARS (glycyl tRNA synthetase) and KARS (lysyl tRNA synthase) are bi-functional enzymes functioning in both mitochondrial and cytosolic translation. Previous studies on different ARS enzymes showed multiple functions beyond translation including non-canonical functions. This project will investigate the molecular mechanism of tissue specific manifestations in mitochondrial and bi-functional tRNA synthetase associated mutations. We use human neuronal cell lines derived from patient fibroblasts to model the defect in neurons.  

References:

D’Souza AR, Minczuk M. Mitochondrial transcription and translation: overview. Essays Biochem. 2018 Jul 20;62(3):309-320.

Boczonadi V, Ricci G, Horvath R. Mitochondrial DNA transcription and translation: clinical syndromes. Essays Biochem. 2018 Jul 20;62(3):321-340. Print 2018 Jul 20. Review.

Boczonadi V, Meyer K, Gonczarowska-Jorge H, Griffin H, Roos A, Bartsakoulia M, Bansagi B, Ricci G, Palinkas F, Zahedi RP, Bruni F, Kaspar B, Lochmüller H, Boycott KM, Müller JS, Horvath R. Mutations in glycyl-tRNA synthetase impair mitochondrial metabolism in neurons. Hum Mol Genet. 2018 Jun 15;27(12):2187-2204.

Boczonadi V, Jennings MJ, Horvath R. The role of tRNA synthetases in neurological and neuromuscular disorders. FEBS Lett. 2018 Mar;592(5):703-717.

• New Genomic Approaches to explore the Neurogenetic Disease Burden of Consanguineous Marriages

(Co-supervised by Professor Patrick F. Chinnery & Professor David Rowitch)

This project aims to determine the burden of inherited neurogenetic conditions in consanguineous marriages in Turkey and thereby develop and improve genetic diagnosis and understanding of a group of severe and chronic disorders in childhood affecting primarily the brain, the nervous system and skeletal muscle.

Expert paediatric neurologists in Turkey carried out detailed clinical investigations of around 250 children with severe childhood disorders of the brain, nervous system or muscle and obtained blood and skin biopsy samples from these children as well as their unaffected parents and affected or unaffected siblings. DNA has undergone whole exome sequencing followed by in-depth computer analysis. Potential genetic causes in relevant genes have been identified and will be further explored to establish their function and see whether they are indeed the cause of the child’s condition.

The scientific work will be carried out in this project and involves the use of stem cell technology to transform skin cells into nerve cells, as well as genetic manipulation to change the genes of zebrafish embryos to recreate the problem seen in the child and help understand the function of the gene in the nervous system. Exploring these aspects in human cells and fish allows research towards the development of targeted and effective treatments for these diseases in humans. In addition to the expected discovery of new disease-causing genes, we will also generate and share valuable data for future research and will provide training in these new techniques. The information obtained will also contribute to future Turkish genome projects, and help understand the impact of consanguinity on severe childhood disorders in populations with high consanguinity rates.

References:

Burns DT, Donkervoort S, Müller JS, Knierim E, Bharucha-Goebel D, Faqeih EA, Bell SK, AlFaifi AY, Monies D, Millan F, Retterer K, Dyack S, MacKay S, Morales-Gonzalez S, Giunta M, Munro B, Hudson G, Scavina M, Baker L, Massini TC, Lek M, Ying Hu Y, Ezzo D, AlKuraya FS, Kang PB, Grifin H, Foley R, Schuelke M, Horvath R*, Bönnemann CG. Variants in EXOSC9 disrupt the RNA exosome and result in cerebellar atrophy with spinal motor neuronopathy. Am J Hum Genet 2018 May 3;102(5):858-873.

Bansagi B, Griffin H, Whittaker RG, Antoniadi T, Evangelista T, Miller J, Greenslade M, Forester N, Duff J, Bradshaw A, Kleinle S, Boczonadi V, Steele H, Ramesh V, Franko E, Pyle A, Lochmüller H, Chinnery PF, Horvath R. Genetic heterogeneity of motor neuropathies. Neurology 2017;28;88(13):1226-1234.

Boczonadi V, Müller V, Pyle A, Munkley J, Dor T, Quartararo J, Ferrero I, Karcagi V, Giunta M, Polvikoski T, Birchall D, Princzinger A, Cinnamon Y, Lützkendorf S, Piko H, Reza M, Florez L, Santibanez-Koref M, Griffin H, Schuelke M, Elpeleg O, Kalaydjieva L, Lochmüller H, Elliott DJ, Chinnery PF, Edvardson S and Horvath R. EXOSC8 mutations alter mRNA metabolism and cause hypomyelination with spinal muscular atrophy and cerebellar hypoplasia. Nat Commun 2014;5:4287.

Taylor RW, Pyle A, Griffin H, Blakely EL, Duff J, He L, Smertenko T, Alston CL, Neeve VC, Best A, Yarham JW, Kirschner J, Schara U, Talim B, Topaloglu H, Baric I, Holinski-Feder E, Abicht A, Czermin B, Kleinle S, Morris AAM, Vassallo G, Gorman GS, Turnbull DM, Ramesh V, Santibanez-Koref M, McFarland R, Horvath R, Chinnery PF. Whole exome sequencing defines the genetic basis of multiple mitochondrial respiratory chain complex deficiency. JAMA 2014;312:68-77.

Dr Mark Kotter (mrk25@cam.ac.uk) – Neurology

• Using Human Stem Cells for Modelling and Regenerating the Peripheral Nervous System

The peripheral nervous system (PNS) is key in transmitting signals from the outside world to our brain and vice versa. However, once this process is disrupted (i.e. trauma, inflammation, tumours), there is little can be done to regain loss of neurological functions. A promising option is using stem-cell derived cells to substitute and integrate missing components of the peripheral nerve to help with regeneration and functional restoration. This can also serve as a platform for answering key questions about the PNS, model diseases affecting the PNS, and for uncovering novel drug-based therapeutics. 

Previously, we reported a novel dual-targeting strategy for highly efficient expression of transcription factors in human stem cells, allowing us to reprogram them into mature cell types such as glutamatergic neurons and myocytes in a rapid and robust manner. Termed OPTi-OX, students will use this technology to generate human stem-cell derived motor and sensory neurons and integrate these cell types to generate an in vitro model of the peripheral nervous system. The prospective student will use a range of techniques, including: human stem cell culture; generation of mature human cell types through forward reprogramming; molecular biology, genome editing using zinc fingers and CRISPR-Cas. The student will have the optional opportunity to translate its work in vivo (rodent models) and collaborate with neuro-prosthetic experts to develop next generation of combined stem-cell/neural interface technology.

Dr Andrea Loreto (al850@cam.ac.uk) Neurology/ John Van Geest Centre for Brain Repair

• The Role of the Wallerian Axon-Death Pathway in Parkinson’s Disease (MPhil only)

(Co-supervised by Professor Michael Coleman)

Parkinson’s disease (PD) is a well-known neurodegenerative disorder affecting around 10 million people worldwide. Despite the availability of therapies to temporarily control the symptoms, we still lack disease-modifying treatments. This project will investigate mechanisms that lead to the death of neurons and why some neuronal populations are more vulnerable in people with PD.

We have characterised a preventable axon-death pathway (Wallerian pathway) controlling the degeneration of injured axons, a process known as Wallerian degeneration (Conforti et al., 2014). This study will assess whether this pathway is also involved in axonal and neuronal death caused by PD-related stimuli. In humans, a single, heavily branched axon projecting from a single dopaminergic neuron (the type that is preferentially affected in PD) is predicted to be around 4 meters long when all branches are included. The metabolic demand of supporting this extreme length is believed to contribute to the vulnerability of these neurons and, indeed, axons are the first neuronal sites to die in PD patients. Our preliminary data suggest a role for the Wallerian pathway in this process, partly reflecting its activation when mitochondria are impaired. The project will involve a combination of cellular and molecular biology techniques, live-cell imaging and confocal microscopy with expert training available in each case. These studies could greatly advance our understanding of mechanisms of neuronal death in PD, and in other disorders where axons degenerate such as multiple sclerosis, motor neuron disease and peripheral neuropathies. The project also has important clinical implications since the Wallerian pathway can be potently blocked, and will take place in an environment where there is extensive interaction between clinicians and basic scientists.

The successful applicant will be based in Professor Michael Coleman laboratory, at the John van Geest Centre for Brain Repair.

Conforti, L., Gilley, J., and Coleman, M.P. (2014). Wallerian degeneration: an emerging axon death pathway linking injury and disease. Nat. Rev. Neurosci. 15, 394–409.

Professor Hugh Markus (hsm32@medschl.cam.ac.uk) – Neurology

• Unravelling the Genetics of Cerebral Small Vessel Disease (PhD only)

Disease of the small blood vessels in the brain, which is called Cerebral Small Vessel Disease (SVD), causes a quarter of all strokes and is the most common cause of vascular dementia. Genetic risk is important although there is much that we do not understand about the molecular processes linking genetic risk to disease. SVD is the most common type of stroke caused by single gene disorders of which the most common is CADASIL but recently many others have been described including mutations due to HTRA1, COL4A1/2, and other genes. Our ability to investigate this area has been transformed by the advent of next generation sequencing (NGS).

The student will apply NGS techniques including whole genome sequencing (WGS) performed as part of the 100 000 Genome Project to investigate familial SVD. The project will involve analysing already acquired NGS data to both look at the frequency of mutations in known genes underlying SVD, and also determining the phenotypic characteristics in these patients, and also attempting to discover new genes underlying this important disease. The studentship could be adapted to suit a student wishing to undertake a primarily bioinformatics project, or to a student wishing to undertake a more clinically based project. Cambridge offers an exceptional environment to carry out this work as it has led the UK SVD whole genome sequencing project and has extensive expertise in bioinformatics analysis of WGS data.

Reference: Tan R, Traylor M, Rutten-Jacobs L, Markus H. New insights into mechanisms of small vessel disease stroke from genetics. Clin Sci (Lond). 2017 Apr 1;131(7):515-531.

• What Causes Apathy and Fatigue in Cerebral Small Vessel Disease? (PhD only)

Cerebral Small Vessel Disease (SVD) causes a quarter of all strokes and is the most common cause of vascular dementia and vascular cognitive impairment. Recently the importance of behavioural symptoms such as apathy and fatigue in SVD has been recognised. These present a major burden for patients and their families.

SVD causes damage to the white matter and increasing evidence suggests that disruption of distributed networks relying on the integrity of white matter tracts may underlie the genesis of both apathy and fatigue. White matter ultrastructural damage, and damage to specific white matter tracts, can be studied using magnetic resonance imaging (MRI), with diffusion tensor imaging (DTI). In previous studies we have shown that damage to white matter networks underlies apathy in SVD (Hollocks et al 2016). In this project, the student will take these studies further to investigate the relationship of apathy, and specific subcomponents of apathy, as well as fatigue, to white matter damage.

The project will study a group of patients with pure white matter damage occurring at an earlier age (due to a monogenic form of SVD called CADASIL) using this as a model of pure SVD; this overcomes a common problem in studying the elderly in that most elderly people have concurrent neurodegenerative and vascular pathology. The student will recruit patients from the National CADASIL clinic which is run in Cambridge (www.cadasil.co.uk). The project will provide the student with expertise in a variety of state of the art MRI imaging techniques primarily based on DTI, including voxel-symptom mapping, tractography, and structural network analysis. The project will also provide experience in cognitive and behavioural testing. It would suit a Psychologist or Neuroscientist with an interest both in working with patients, and in performing MR image analysis.

Reference: Hollocks MJ, Lawrence AJ, Brookes RL, Barrick TR, Morris RG, Husain M, Markus HS. Differential relationships between apathy and depression with white matter microstructural changes and functional outcomes. Brain. 2015 Dec;138(Pt 12):3803-15.

• Developing a New Model for Vascular Stroke using Human Induced Pluripotent Stem Cells (hiPSC) with the HDAC9 Risk Genetic Variant. (PhD only)  

(Co-supervised by Dr Alessandra Granata)

A quarter of all stroke is classified as large artery stroke, most of which are attributed to atherosclerosis. Together with conventional risk factors, there is evidence that a strong heritable genetic component contributes to large artery stroke risk.

In 2012, the Cambridge Stroke Research group published the first large genome wide study (GWAS) in ischaemic stroke, which identified a common variant in the Histone Deacetylase 9 (HDAC9) gene as the strongest genetic risk for large artery stroke to date. This offers the exciting possibility that inhibiting HDAC9 could prevent stroke. Consistent with this sodium valproate, a non-specific inhibitor of all HDACs, was found to be associated with lower stroke risk in human. However, the mechanisms linking this HDAC9 variant with increased stroke risk are still poorly understood. Better understanding these, and also developing relevant models containing the generic variant is essential, if we are to translate this genetic finding into improved patient care.  

In the proposed project, the student will use hiPSC containing the HDAC9 genetic variant derived from skin biopsies from patients with large artery stroke to generate cell types of the large artery including smooth muscle cells, endothelial cells and macrophages, which will be co-cultured to mimic the atherosclerotic plaque environment. This model will be used to investigate

1. How the variant influences HDAC9 regulation and which transcriptional factors are involved in controlling HDAC9 expression by performing chromatin-immunoprecipitation (ChIP) assay and gene reporter assay.
2. How the stroke variant affects the normal vascular cells functions in response to inflammation by performing a range of cell-based assay and omics studies in stroke risk hiPSC-derived vascular cells and CRISPR-edited isogenic cells.
3. And to test new specific HDAC inhibitors, with the aim of uncover new mechanisms/targets for the treatment of large-vessel stroke.

References:

• Bellenguez, C. et al. Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke. Nat.Genet. 44, 328–33 (2012).
• Markus, H. S. et al. Evidence HDAC9 genetic variant associated with ischemic stroke increases risk via promoting carotid atherosclerosis. Stroke. 44, 1220–5 (2013).
• Brookes, R. L. et al. Sodium Valproate, a Histone Deacetylase Inhibitor, Is Associated With Reduced Stroke Risk After Previous Ischemic Stroke or Transient Ischemic Attack. Stroke 49, 54–61 (2018)

 

• Studying CARASIL, a Monogenic form of Cerebral Small Vessel Disease, using an Induced Pluripotent Stem Cells (hiPSC)-derived in vitro model of the Blood Brain Barrier. (PhD only)

(Co-supervised by Dr Alessandra Granata)

CARASIL is an inherited disorder directly affecting the cerebral small blood vessels, caused by mutations in a gene encoding for HtrA serine peptidase/protease 1 (HTRA1). The main clinical manifestations of CARASIL are ischemic stroke, deterioration in brain functions and progressive dementia. Individuals with CARASIL usually develop symptoms between 20 and 30 years of age.

One of the major functions of HTRA1 is to regulate TGF-β signalling, which is essential for many critical cell functions. CARASIL-associated mutant HTRA1 exhibited decreased protease activity, which could alter the small blood vessel structure by preventing the effective regulation of TGF-β. However, the precise mechanism is not fully understood and currently there are no specific treatments for cerebral small vessel disease. Thus, studying HTRA1 mutations, which are responsible for rare but highly penetrant form of small vessel disease is particularly exciting because it can provide unique insights into the pathogenesis. In the proposed project, the student will be responsible for generating a human in vitro vascular disease model using induced pluripotent stem cells hiPSC lines with HTRA1 mutations generated from two CARASIL patients. In particular:

1. CARASIL patient-derived hiPSC will be used to generate the cells that forms blood brain barrier of cerebral small vessels, including brain endothelial cells, pericytes and astrocytes using protocols established in the lab.
2. The function of these cells and integrity of the blood brain barrier will be assessed by a range of cell-based and functional assays.
3. Transcriptomic and proteomics studies will be carried out in CARASIL hiPSC and CRISPR-edited isogenic cells to identify potential new therapeutic pathways/targets that can be assessed in this model.
4. References:

• Haffner, C. et al. Genetic factors in cerebral small vessel disease and their impact on stroke and dementia. J Cereb Blood Flow Metab 36, 158-71 (2016)

• Beaufort, N. et al. Cerebral small vessel disease-related protease HtrA1 processes latent TGF-β binding protein 1 and facilitates TGF-β signaling. PNAS 111, 16496-501 (2014)

Dr Will McEwan  (wm305@cam.ac.uk) – Neurology

www.mcewan-lab.com

• Control of Cytoplasmic Protein Aggregation by the Cell-Autonomous Immune System (PhD only)

Individual cells are capable of defending themselves against microbial and viral infection in the absence of direct co-ordination by the professional immune system. The effector proteins of this ‘cell-autonomous’ immunity provide a crucial last line of defence against infection against infection and are constitutively expressed in numerous cell types. Our lab investigates how this form of immunity can be brought to bear on self-propagating protein species that are implicated in neurodegeneration. We recently demonstrated that aggregates of tau, a protein which becomes aggregated in several progressive forms of neurodegeneration including Alzheimer’s disease, can be inactivated in this way (McEwan et al 2017 PMID: 28049840). Ongoing work in our lab has identified further cellular conditions where aggregation of tau is substantially reduced and genes of the cell-autonomous immune system are implicated. The aim of the project is to characterise the pathways involved in the suppression of protein aggregation. Given that there is currently little understanding of how cellular mechanisms can limit templated protein aggregation, the results may provide an important understanding of cellular pathways that limit disease progression. We will use a range of cell-based and molecular techniques to characterise the relevant genes and pathways involved. Students with an interest in infection and immunity as well as neurodegeneration are encouraged to apply. Knowledge of molecular biology and biochemical techniques is essential.

Professor David Menon (dkm13@cam.ac.uk) – Anaesthesia

• Neuroanatomical and connectomic substrates of neurobehavioral outcomes (PhD/MPhil)

CENTER-TBI is a large European project that aims to improve the care for patients with Traumatic Brain Injury (TBI) (www.center-tbi.eu/) and data used in this project will come from this study.  We will use both conventional statistics and machine learning approaches to undertake these analyses, in collaboration with the Computer Vision group at Imperial College (Dr Glocker) and the MRC BioStatistics Unit in Cambridge (Dr Wernisch)

TBI results in neurocognitive deficits (e.g. impaired sustained attention and working memory, and visuo-spatial associations) and neuroaffective abnormalities (30-70% of survivors develop depression; many exhibit increased impulsivity, poor decision making, and impulsive-aggressive behaviour). Data regarding the neural basis of and therapeutic options for these deficits remains limited, and most studies ignore the fact that TBI is a disease of neural systems as well as injury sites. This project will involve a range of approaches to relate neurocognitive deficits to: focal lesions (automated pathological segmentation); cortical, basal ganglia, and white matter loss (through conventional and DTI based VBM approaches); structural connectivity (TBSS and both probabilistic and streamline tractography); and functional connectivity (rs fMRI with seed based analysis, ICA, other techniques). These approaches may predict deficits, allow increasing monitoring in high-risk patients, and target rehabilitation to patients’ needs. Finally, discordant structural and functional connectivity could provide evidence of recovery potential or plasticity. Experience in neuroimaging, in particular MRI analysis, is required for this project. Skills in scientific computing and programming (e.g, Linux, Matlab, Python) are desirable.

• Neurological recovery/progression in TBI – subsets and imaging biomarkers (PhD/MPhil)

CENTER-TBI is a large European project that aims to improve the care for patients with Traumatic Brain Injury (TBI) (www.center-tbi.eu/) and data used in this project will come from this study. We will use both conventional statistics and machine learning approaches to undertake these analyses, in collaboration with the Computer Vision group at Imperial College (Dr Glocker) and the MRC BioStatistics Unit in Cambridge (Dr Wernisch)

This project will concentrate on patients who return for clinical evaluation at 12 and 24 months (expected n: ~300 and 250 each in the Admission and ICU strata, based on loss to follow up and mortality). Advanced imaging across the acute and chronic phase in large numbers of patients, will allow us to determine whether TBI is truly a chronic and progressive disease in a subset of individuals, and whether early clinical features, biomarkers or imaging features can identify such individuals, or at least characterize a subpopulation enriched for patients likely to have such a phenotype. This will allow detailed prospective characterization of the disease, and when combined with genetic analyses, provide insights into its underlying biology. Key interactions wiith other work packages in CENTER-TBI will allow for bidirectional relationships to be explored between physiological insults, biomarkers and lesion progression and volume. Genetic drivers of progression of structural injury may also be investigated. Critically, these correlative analyses may identify subsets of patients (e.g. mild TBI with persistent post-concussive symptoms, progressive late cognitive decline in severe TBI) who are candidates for trials that target early intervention. Experience in neuroimaging, in particular MRI analysis, is required for this project. Skills in scientific computing and programming (e.g, Linux, Matlab, Python) are desirable.

• Characterisation of individual, temporal and pathophysiological heterogeneity (PhD/MPhil) 

CENTER-TBI is a large European project that aims to improve the care for patients with Traumatic Brain Injury (TBI) (www.center-tbi.eu/) and data used in this project will come from this study. This project will investigate how early MRI and serial changes in MRI occur after TBI. This data will better characterize pathophysiology and individual, temporal, and regional pathophysiological heterogeneity. We will use both conventional statistics and machine learning approaches to undertake these analyses, in collaboration with the Computer Vision group at Imperial College (Dr Glocker) and the MRC BioStatistics Unit in Cambridge (Dr Wernisch)

Ability to identify patients likely to have a complicated clinical course will, along with stratification from multimodality physiological monitoring, be the first step in a personalized medicine approach to TBI, allowing us to limit the clinical risk and costs of complex and aggressive management interventions in patients who are unlikely to substantially benefit from them. At the very least, it may identify selected subsets of patients in whom the expected evolution of disease phenotype mandates greater vigilance and more detailed monitoring. Experience in neuroimaging, in particular MRI analysis, is required for this project. Skills in scientific computing and programming (e.g, Linux, Matlab, Python) are desirable.

Dr Stefano Pluchino (spp24.cam.ac.uk) – Neurology

Website; http://www.brc.cam.ac.uk/principal-investigators/stefano-pluchino/

• Making Human iNSCs from People with Progressive MS (PwPMS)

(Co-supervised by Dr Luca Peruzzotti-Jametti)

This project will involve the development of stably expandable, forward programmed neural stem cells (NSCs) from People with progressive MS (PwPMS). Somatic cells will be reprogrammed to stably expandable directly induced neural stem cells (iNSCs) and then differentiated and monitored for several markers of pluripotency/multipotency, checked for morphological, function and genomic stability as well as senescence over time period in vitro. This project will highlight potential issues of stability and suggest methods of mitigating these, should they arise.

The long-term goal of this investigation will be to evaluate the safety of iNSCs for use in a first-in-men clinical trial, which is being organised at Cambridge. The final objective of this investigation is the determination of whether or not the therapeutic use of iNSCs in PwPMS can be taken forward into clinical trials. In vivo characterization and manipulation of succinate dependent injury in neuroinflammation (co-supervised with Luca Peruzzotti-Jametti)

Despite the absence of clinically relevant immune-related attacks, a diffuse activation of the immune system is thought to be one of the major drivers of disease progression in MS. However, differently from relapsing remitting MS, in progressive MS the immune cells that mediate the damage are called mononuclear phagocytes. Mononuclear phagocytes are not harmful per se, but they become so because of a chronic change in the ways they consume and produce energy. Energy production in a cell (or metabolism) is important for its function. We found that mononuclear phagocytes undergo a “metabolic switch” that makes them chronically active and accumulate one specific metabolite called succinate.

The goal of this approach is to understand how different types of mononuclear phagocytes accumulate succinate during neuroinflammation and to interfere with their metabolism so that they stop damaging the brain. Moreover, thanks to a wide set of biological samples obtained from MS patients, we aim at finding out if succinate (or other metabolites) can be used as a marker to predict disability in MS patients.

• Single-cell RNAseq Analysis of Reactive Astrocyte Heterogeneity in Spinal Cord Injury (SCI)

(Co-supervised by Dr John Marioni)

Secondary injury mechanisms in traumatic spinal cord injury are exacerbated by morphological, molecular, and functional changes in astroglial cells (astrocyte reactivity/astrogliosis), which are still not fully characterized. Consequently, therapeutic approaches aiming at the modulation of astroglial reactivity remain controversial. The goal of this project is to investigate the molecular mechanisms of astroglial cell reactivity in SCI at unprecedented depth by employing the innovative technology of ex vivo single-cell RNA sequencing to obtain high-throughput gene expression profiling.

The candidate working at this project will aim at:

(i) Profiling the transcriptome of astrocytes isolated ex vivo from moderate and severe mouse models mouse models of moderate and severe contusion SCI at multiple stages (acute, subacute and chronic); and

(ii) Analysing and identifying pathways and genes that are critical to the beneficial and detrimental aspects of astroglial cell activation, with a focus on the comparison between the different severities and time points.

These results are expected to ultimately lead to the identification of novel therapeutic targets for future molecular approaches with significant translational value in complex SCIs and the potential to compare and contrast with other reactive astrocyte profiles in the future. Single-cell RNAseq analysis of reactive astrocyte heterogeneity in experimental autoimmune encephalomyelitis (EAE) (co-supervised with John Marioni). Multiple sclerosis (MS) is characterized by distinct disabilities in voluntary movement, cognition, and vision. Investigations of cell types in experimental autoimmune encephalomyelitis (EAE) have shown that non-neuronal cells have varying gene expression depending on the cell type and region. However, the heterogeneity within cell types in EAE models have yet to be characterized. The aim of this project is to investigate the heterogeneity within non-neuronal cell types in EAE at unprecedented depth by employing the novel, unbiased technology of ex vivo single-cell RNA sequencing to obtain high-throughput gene expression profiling.

The candidate working on this project will:

Profile the transcriptome of non-neuronal cells isolated ex vivo from EAE mouse models of progressive MS from several areas of interest; and identify genes/pathways detrimental to the neuroprotective role of non-neuronal cells. These results are expected to lead to the identification of novel therapeutic targets for future molecular approaches with significant translational value in MS. These results are expected to ultimately lead to the identification of novel therapeutic targets for future molecular approaches with significant translational value in chronic neuroinflammatory conditions, including multiple sclerosis, and the potential to compare and contrast with other reactive astrocyte profiles in the future.

• SUCNR1/GPR91 Antagonism in Mononuclear Phagocytes

(Co-supervised by Dr Luca Peruzzotti-Jametti)

Cell metabolism is a conserved biological process linked to diseases that span multiple areas of medicine. Studying the metabolism of immune cells in recent years has emphasized the tight link existing between the metabolic state and the phenotype of these cells. Mononuclear phagocytes (MPs) are a good example of this phenomenon. The differentiation of MPs into distinct phenotypes involves specific metabolic signatures and complex changes in mitochondrial metabolism. Inflammatory MPs have in fact the ability to switch their metabolism from oxidative phosphorylation to aerobic glycolysis for energy production, not dissimilar to the Warburg effect seen in tumour cells. As such, inflammatory MPs display a dysfunctional mitochondrial respiratory chain, and a broken Krebs cycle. This interrupted TCA cycle turns mitochondria into toxic factories where several metabolic intermediates with important signalling functions accumulate and are implicated in influencing MP phenotype and function.

We hypothesise that the metabolic intermediate succinate is a paracrine signal for chronic neuroinflammation, which accumulates in the CSF and functions as an alarmin by locally activating SUCNR1/GPR91-expressing MPs to initiate or exacerbate CNS compartmentalised immune responses.

The candidate working on this project will:

Provide high-dimensional, single-cell analysis of the type and state of non-neuronal cells expressing SUCNR1/GPR91 in post-mortem progressive MS cases and control post-mortem brain using Hyperion™ Imaging System, which brings together high-parameter CyTOF™ technology with imaging capability;

Investigate the role for SUCNR1/GPR91 in the pathogenicity of bone marrow-derived CNS infiltrating Ccr2+ macrophages or locally recruited Cx3cr1+ microglial cells in experimental autoimmune encephalomyelitis (EAE), taking advantage from state-of-the-art Sucnr1flox tg mice. Antagonise SUCNR1/GPR91 in MPs in vivo in animal disease models with in-house state-of-the-art pRNA nanotherapeutic-based delivery of Sucnr1 siRNAs;

The potential to identify the main cellular and molecular events upstream of succinate, as a metabolic signal in chronic neuroinflammation, and targeting these events in MPs to impact on disease is an extremely exciting prospect. Characterisation of a human-derived chemotherapeutic enzyme (in partnership with Cambridge Innovation Technologies Consulting Ltd, co-supervised with Jayden Smith and Luigi Occhipinti)

Cancer cells undergo complex metabolic changes, requiring the amino acid L-asparaginase (ASN) to grow. Starving cancers by depriving them of ASN is a powerful anticancer strategy, notably in the treatment of Acute Lymphoblastic Leukaemia (ALL), the most common cancer in children. The gold-standard treatment for ASN-avid cancers like ALL is the enzyme L-asparaginase (ASNase), which converts ASN into aspartate which cannot be metabolised by the cancer cells. Unfortunately, current ASNase drugs are bacterial in origin, leading to issues of immune intolerance in patients. Furthermore, these bacterial ASNases also elicit liver toxicity side-effects through off-target glutaminase (GLS) activity. Thus, there is a significant unmet clinical need for an efficacious and fully human-compatible ASNase with minimal side-effects.

HumaNase aims to address these needs by characterising a safer, human-derived alternative. The Pluchino Lab and CITC Ltd have recently described how extracellular vesicles derived from neural stem cells traffic GLS-free human Asparaginase-like protein 1 (hASRGL1). This project entails a thorough characterisation of hASRGL1 with respect to its (ASNase and GLS) activity and kinetics, stability, and in vitro anticancer efficacy, all with an eye towards future therapeutic use of the enzyme and development of a biomimetic delivery platform.

Dr Chris Rodgers (ctr28@cam.ac.uk) – WBIC

• Ultra-High Field (7T) Magnetic Resonance Imaging (MRI) Development (PhD only)

I founded a new ultra-high field (7T) MRI physics group in Cambridge in autumn 2017. We develop cutting-edge methods for studying the human brain and body using Cambridge’s new Siemens Terra 7T MRI scanner. Ours is the third 7T Terra to be installed worldwide; so we have access to state-of-the art hardware and software platforms for MRI. The group is growing rapidly: in the last 9 months, we have secured more than £1m of funding and three new researchers will join us imminently. We have active collaborations with clinicians in clinical neurosciences, psychiatry, oncology, and cardiology (Papworth), and with experts in cognitive neuroscience. I welcome PhD students to join the group. The following are areas of strong interest from our community, which would be suitable to develop a PhD project in discussion with me.

(i) Developing new spectroscopic imaging pulse sequences to map neurochemical profiles across the whole brain in a single scan. We have hardware available to apply these methods to study metabolites containing 1H (e.g. NAA, creatine, GABA, GSH) or 31P (e.g. PCr, ATP, in vivo pH mapping) or 13C (e.g. labelled glucose or succinate).

(ii) Developing new methods for neuroimaging, particularly for imaging blood flow in small vessel disease, or for rapid, motion-corrected fMRI in deep brain nuclei.

(iii) Developing new metabolic imaging methods for use in the human body. These would use a new 5-nucleus whole-body coil soon to be installed in Cambridge as part of a €3.1m EU Future and Emerging Technologies award for “Non-invasive Chemistry Imaging in the Whole Human Body”. Our initial focus is to characterise liver pathology in patients with colorectal cancer and liver metastases. Similar approaches would also work in the heart, kidney or pancreas.

If you are interested in these projects or other aspects of 7T MRI physics development, please email ctr28@cam.ac.uk and I will be happy to discuss the details with you.

Professor James Rowe (james.rowe@mrc-cbu.cam.ac.uk) – Neurology

• Understanding Disease Progression in Neurodegenerative Tauopathies with Structural Neuroimaging

(Co-supervised by Dr Timothy Rittman)

One of the challenges in understanding neurodegenerative disorders is to relate the effect of genetic and molecular changes associated with disease to the level of the whole brain. Increasing evidence points towards the vulnerability of macro-scale brain networks in the progression of neurodegeneration. In order to investigate disease progression in brain networks, this project will examine changes in structural networks in tau associated neurodegenerative diseases. These scans are drawn from a cohort study of people with the primary tauopathies of Progressive Supranuclear Palsy, Corticobasal Degeneration and Frontotemporal Dementia. Imaging data will be enriched with information available from post-mortem tissue to anchor the models in neuropathological changes, and with clinical cognitive data to gauge the influence of structural changes on clinical syndromes. There may be opportunities to extend this work with multimodal imaging techniques such as functional MRI. The successful candidate will use structural imaging techniques such as Diffusion Tensor Imaging and cortical thickness analysis (freesurfer) to understand the progression of tau associated neurodegenerative pathology through the brain. The candidate will build computational models that can be used to test hypotheses of tau spread and regional susceptibility. A familiarity with coding languages is essential and some experience of neuroimaging analysis is highly desirable.

The project will be supervised by Dr Timothy Rittman, a clinician scientist with extensive experience in neuroimaging applied to neurodegenerative diseases and genetics. This project supports the wider work of the Cambridge Centre for Parkinson’s Plus (https://ccpp.cam.ac.uk/)

Professor Stephen Sawcer (SJS1016@cam.ac.uk) – Neurology

• The genetic analysis of multiple sclerosis

Through genome-wide association studies and related follow up efforts we have identified over 100 genetic variants that influence the risk of developing multiple sclerosis. These variants map almost exclusively to regulatory regions of the genome that are active in immune cells suggesting that these variants primarily exert their effects by altering the expression of otherwise normal genes in critically important immune cell sub-types. In order to try and understand more precisely how these associated variants influence the development of multiple sclerosis we are undertaking a range of projects.
1) In work already completed we have established that at least two of the associated variants influence the expression of key immune signalling genes in B cell sub-types. These data confirm the importance of B cells in pathogenesis which is in keeping with the latest clinical trial data showing the positive effects of anti-B cell therapies. This project will focus on fine mapping the causal variants underlying observed associations by exploring the expression of key immune genes in B cell subtypes. The work will involve mapping of transcription and chromatin architecture, as well as protein expression and cell function.
2) The highly significant overlap in the genetic architecture of immune mediated inflammatory diseases (IMID) suggests that there are key pathways in the immune system that influence the propensity to autoimmunity. This project will use data from UK Biobank (500,000 genotyped individuals) to dissect out the genetic architecture of these common pathways. The project will then use genomewide methylation mapping to fine map associated variants epigenetically and determine the functional effects of these variants.
3) As part of the Cambridge Single Cell Analysis Core Facility we are undertaking single cell expression profiling in cells from the cerebrospinal fluid and blood of patients and controls. This project will allow a transcriptional based taxonomy of immune cells and identify master transcriptional regulators of relevance in multiple sclerosis. The project will also explore the epigenetic signature and functional effects of identified regulators.
The successful student will work closely with colleagues at the McGill University Epigenomics Mapping which is a leading institution in the International Human Epigenome Consortium (IHEC), the project may include the opportunity for willing students to spend a period of their research in Montreal.

Dr Peter Smielewski (ps10011@cam.ac.uk) – Neurosurgery

• Optimisation of Real Time Analysis of Multimodal Monitoring Data and its Application to Computer Guided Management of critically Ill Patients

In an established environment of neuro-intensive care large quantities of data can be captured from bed-side monitors. This data contains a wealth of information about the pathophysiology of the critically ill patient however; the extraction of this information often requires sophisticated signal analysis. Such analysis is usually performed using universal data analysis packages like Matlab but requires engineering/mathematics expertise and is only available in off-line mode and as such in not applicable in a clinical setting. Our own software ICM+ (http://www.neurosurg.cam.ac.uk/icmplus), which is by now used in many clinical centres worldwide, attempts to bridge the gap between laboratory and clinical application. It collects data from bedside monitors, calculates in real time ‘secondary’ parameters defined using highly configurable signal processing formulae and produces continuously updated charts. This way complex information coming off the bedside monitors can be summarized in a concise fashion and presented to medical staff in a simple way that alerts them to the development of various pathological processes. The projects offered will include the following stages:

1. Development of new methodologies of analysis of physiological signals acquired in the Neuro Intensive Care, including time and frequency domain, stationary and non-stationary methods, linear and non-linear approaches.
2. Validation of the new methodologies against retrospective and prospective data from the Neuro Intensive Care unit
3. Implementation of the novel algorithms into ICM+ plugins, packaged as Windows dll libraries, so that they can be used in real time by the bed side These projects would suit graduates in Biomedical Engineering, but also potentially Physics, Mathematics, and Computer Science.

Dr Emmanuel Stamatakis (eas46@cam.ac.uk) – Anaesthesia

 https://sites.google.com/site/ccigcambridge/

• The Default Mode Network in Consciousness (PhD/MPhil)

Brain injury management has improved considerably in recent years with resulting significant improvements in outcome. Nevertheless, a small but significant number of survivors do not fully emerge after acute coma and remain in prolonged disorders of consciousness (DoC), including vegetative and minimally conscious states. Long range brain networks, such as the default mode network (DMN), have been shown to be disrupted in DoC, and are partially or fully restored when patients recover cognitive capacity. The functional role of the DMN remains unclear. Although it was initially considered to be a task negative network, recent studies from our group and others have revealed DMN activity/connectivity during a wide range of self-referential and memory-based tasks, as well as altered DMN integrity in a variety of neuropsychiatric disorders. Such data provide support for inferences on the role of the DMN in cognitive capacity and consciousness. An emerging theory is that the DMN acts as global workspace integrating information from a variety of sources through associations, to make sense of the world at present. The major hubs of the DMN are multisynaptic and are connected to both cortical and subcortical regions rendering this network a suitable candidate for integrating information. Within this emerging theoretical framework this project will utilise fMRI/EEG to focus on the role of the DMN at rest but also importantly during tasks, in a cohort of DoC patients and healthy volunteers. Experience in neuroimaging and/or electrophysiology is required for this project. Skills in scientific computing and programming (e.g, Linux, Matlab, Python) are desirable.

• Functional MRI Imaging in Traumatic Brain Injury (PhD/MPhil)

CENTER-TBI is a large European project that aims to improve the care for patients with Traumatic Brain Injury (TBI). The work undertaken in Cambridge will examine the role of MRI in routine TBI imaging and this project will focus on the role of resting state functional MRI in TBI imaging. There is now abundant evidence from functional MRI suggesting that the resting brain is organised in coherent long range networks. The functionality of these networks is easily inferred since they typically track the functional anatomy of networks identified during activation studies. For this reason, the translational potential of resting networks, particularly in patients unable to participate in stimulus driven experiments (e.g. TBI), seems immense but is mostly unrealised. This project will evaluate the usefulness of resting state functional MRI imaging in TBI for understanding and tracking disease processes and prognosticating cognitive recovery. Additionally we will aim to relate functional connectivity patterns to cognitive measures, vulnerability for depression and to functional outcome in general. Experience in neuroimaging, in particular MRI analysis, is required for this project. Some programming experience (e.g, Linux, Matlab, Python) is desirable.

• Biomarkers for Risk and Clinical Outcome Prediction of Postoperative Cognitive Dysfunction (PhD/MPhil)

Postoperative cognitive impairment is increasingly prevalent in our aging society. This condition often has an acute phase of Postoperative Delirium (POD) which may then be followed by a more chronic phase of Postoperative Cognitive Dysfunction (POCD), which tends to persist over time. BIOCOG, a European FP7 funded project, aims to establish biomarkers for risk and clinical outcome prediction of POD/POCD. The study population are patients aged 65 to 80 undergoing major elective surgery. The work undertaken in Cambridge will focus on MRI imaging and will investigate whether brain network properties obtained from MRI diffusion tensor imaging (DTI) measures, relate to those obtained from resting state functional MRI data. Structural and functional network properties will be related to neuropsychological and clinical measures. Experience in neuroimaging, in particular MRI analysis, is required for this project. Skills in scientific computing and programming (e.g, Linux, Matlab, Python) are desirable.

Dr Deborah Vickers (d.vickers@ucl.ac.uk moving to Cambridge early 2019) – Neurology

• Evaluating the Clinical Effectiveness of the ‘Electrical Auditory Change Complex’ (eACC) in Guiding Electrode Discrimination Intervention Pathways to Improve Outcomes in Poorly Performing Cochlear Implant Users

Background

This study aims to address the issue of poor performance in cochlear implantation. Cochlear implants are electronic hearing devices for people with severe-to-profound deafness and are arguably the most successful neural prostheses to date, with over 16,200 UK users. However, the variability in outcomes is large and a significant proportion of users have poor speech understanding. In adults, this contributes to social isolation, depression, loss of independence, unemployment and cognitive decline. In children, poor hearing impacts their communicative development including speech, language, education and social skills. These users require continued technical and emotional support from professionals, thus putting a strain on health and care services, and the wider economy. One factor contributing to the poor performance is impaired electrode discrimination, which can distort the speech signal. This is rarely measured clinically due to current tests taking too long, uncertainty of using findings to guide interventions and task difficulty for some patients (particularly in cognitive impairment and for young children). However, an objective, cortically evoked electrophysiological measure, the ‘electrical auditory change complex’ (eACC), has been proposed as a clinically viable tool that can reliably measure electrode discrimination, is fast to administer and does not require active participation.

Aim: To examine the effectiveness of the eACC in guiding clinical interventions to improve electrode discrimination and help poorly performing cochlear implant users.

Objectives: To determine the effectiveness of intervention pathways (i, ii, iii below) based on the cochlear implant user’s electrode discrimination using the eACC and behavioural discrimination tests. Effectiveness will be assessed using outcomes of (a) everyday listening and (b) speech perception.

Intervention pathways:

1. deactivating indiscriminable electrodes based on eACC measured at comfortable listening level
2. increasing electrical threshold levels on indiscriminable electrodes based on eACC at lower stimulation levels

iii. electrode discrimination training on electrodes that are indiscriminable in the behavioural discrimination test

Methods: Forty-eight cochlear implant users experiencing poor performance will undergo eACC and behavioural tests to identify the main cause of poor electrode discrimination:

eACC will be measured at 100% and 40% of electrical dynamic range, behavioural electrode discrimination will be measured at 100% of the electrical dynamic range.

Everyday listening experience (primary outcome) and speech perception (secondary outcome) will be measured at baseline, after four weeks of intervention and after a further four weeks of consolidation.

Anticipated impact: The anticipated impact is improved outcomes for poorly performing cochlear implant users, thereby improving health. This will be achieved through development of evidence-based, clinical guidelines for (1) objectively measuring electrode discrimination in clinics, and (2) using findings to optimise everyday listening and speech perception.

Dissemination: Research findings will be disseminated through:

1. A Patient Advisory Group, involved throughout the project co-authoring lay summaries for distribution via charities and support groups
2. Manufacturer’s, university and hospital websites and social media

iii. Close collaboration with cochlear implant clinicians

1. Peer reviewed journal articles targeting professionals in the field of cochlear implants
2. Presentations at relevant national and international scientific meetings

The benefits of this research will reach patients and services within 1-3 years of completion.

Dr Caroline Williams-Gray (chm27@cam.ac.uk) – Neurology/John Van Geest Centre for Brain Repair

• Investigating the Immune Basis of Parkinson’s Disease (PhD only)

It is now well established that immune activation occurs in Parkinson’s disease, but its role in driving the disease process remains controversial, in particular whether it is a primary determinant of disease progression, or a secondary epiphenomenon. This is a critical question to address given that the immune system is a tractable target for disease-modifying therapy. This project will investigate markers of immune activation and immunosenescence in blood and CSF samples from patients with both prodromal and early stage Parkinson’s disease to establish whether immune activation precedes disease onset and whether it is predictive of longitudinal disease progression rates. Techniques will include multiplex immunoassays, immunophenotyping using flow cytometry, new techniques such as CyTOF (which allow labelling of large numbers of markers on a single cell), and functional lymphocyte and monocyte assays. This work will allow detailed characterisation of immune abnormalities in early PD to guide the development of future immune-based therapies and identify optimal immune-related biomarkers to track response to such therapies.

Dr Patrick Yu-Wai-Man (py237@cam.ac.uk) – Neuro-Ophthalmology and Genetics (PhD Applicants Only)

I am an academic neuro-ophthalmologist with a major research interest in mitochondrial genetics and inherited eye diseases. My research group is focused on new gene discovery and we are using a multipronged approach to dissect the disease pathways contributing to progressive neuronal loss and blindness, including zebrafish models and patient-derived induced pluripotent stem cells.

I coordinate a specialist clinical service for patients with mitochondrial eye diseases in Cambridge, Newcastle and London. Over the past 15 years, we have established a national cohort of patients with inherited optic neuropathies, and we are using this unique resource for deep phenotyping, biomarker profiling and to push forward with an active translational research programme, including gene therapy.

I have long-standing collaborations with other principal investigators in the Cambridge Centre for Brain Repair, the Cambridge MRC Mitochondrial Biology Unit and the UCL Institute of Ophthalmology in London. This extensive research network will provide the student with access to a wide source of expertise, tailored supervision and the opportunity to develop a broad skill set as the project evolves.

References:

1. Yu-Wai-Man P, Newman NJ. Inherited eye-related disorders due to mitochondrial dysfunction. Human Molecular Genetics. 2017; Epub ahead of print.
2. Yu-Wai-Man P, Votruba M, Burté F, La Morgia C, Barboni P, Carelli V. A neurodegenerative perspective on mitochondrial optic neuropathies. Acta Neuropathologica. 2016;132:789-806.
3. Burté F, Carelli V, Chinnery PF, Yu-Wai-Man P. Disturbed mitochondrial dynamics and neurodegenerative disorders. Nature Reviews Neurology. 2015;11:11-24.

PubMed Publications

https://www.ncbi.nlm.nih.gov/pubmed/?term=Yu-Wai-Man+P+or+Y-W-Man+P

Research Links

• http://www.neuroscience.cam.ac.uk/directory/profile.php?py237
• http://www.moorfields.nhs.uk/consultant/patrick-yu-wai-man
• http://www.newcastle-mitochondria.com/dr-patrick-yu-wai-man