"We're developing better ways to study cells in the brain, such as microglia, and their role in dementia." Zameel Cader
UK DRI Momentum Award, Oxford

Associate Professor in Clinical Neurosciences at the University of Oxford, Prof Zameel Cader is leading the way in cutting edge translational medical research. After completing his clinical training at the University of Birmingham, he went on to obtain a DPhil in Neuroscience from the University of Oxford. He now bridges the gap between drug discovery research and the clinic, as Consultant Neurologist at the Oxford University Hospitals NHS Trust. As a Momentum Award holder at the UK DRI, Zameel leads an exciting programme of research investigating microglia, taking advantage of innovative stem cell-based approaches.

1. At a glance

The big impact of microglia

The UK DRI is funding an ambitious programme of research at the University of Oxford, through a Momentum Award. This programme of research centres on a particular type of cell in the body, called microglia. Microglia live in the brain and spinal cord, and make up 10-15% of all cells within the brain. They play a crucial role in the body’s immune response – it’s ﬁrst line of defence against infection and threats. It is becoming increasingly clear that microglia also play a role in neurodegenerative diseases; studying them could lead to breakthroughs in therapeutics.

There is a shortage of suitable human brain tissue for the study of cells, such as microglia, and so a number of techniques have been developed in the lab to get around this. Stem cells can be programmed to become any type of cell in the body, but there are issues with their use in neurodegenerative disease research. Cells in adult brain disorders are ‘mature’ – they have been through a lot! Programmed stem cells have not undergone this maturation and so may not accurately mimic human adult cells as desired.

Through three projects, researchers at Oxford aim to tackle these issues, developing better ways to study cells in the brain, such as microglia, and their role in dementia.

1. Stem cells, epigenetics and microglia

This project aims to understand how well stem cells model adult brain tissue. Researchers will collect blood samples and brain tissue from people undergoing surgery, such as for a tumour; the blood from the individual will be used to create stem cells in the lab to generate 'young' microglia, and these will then be paired with ‘mature’ microglia from the surgical brain tissue. Because they have been taken from the same individual, researchers will be able to see how similar they are, comparing ‘young’ and ‘mature’.

2. Creating a stem cell toolbox for researchers

Using highly novel techniques, this project aims to create a ‘toolbox’ of modiﬁed stem cell-derived microglia that are able to 'report' on the activity of microglia. This toolbox could then be used by researchers in further studies, to investigate the role of microglia in neurodegenerative diseases.

3. Using machine learning to understand microglial responses and interactions

Diﬀerent cell types are involved in the development of neurodegenerative diseases, however, it can be hard to understand how they interact. This project aims to address this, by ﬁnding features of cells using machine learning. Cells will be imaged, and hundreds of measurements taken which describe their size, shape and texture. Using these features, machine learning will be used to identify those features which might predict cell-cell interactions, drug responses or disease pathology. This will lead to better understand of the role of microglia in disease development, and test the possibility of targeting them as a new therapeutic approach.

2. Scientific goals

Through three projects and one cross-cutting theme, researchers will generate hypotheses and new ways to study microglia.

Projects (Leading researchers in italics):

1. The Epigenomic Landscape of Human IPSC and Primary Brain Cultures (Cader)

The epigenomic landscape of the brain has barely been explored, particularly for the study of brain disorders, as there is a scarcity of suitable brain tissue. Human induced pluripotent stem cell (iPSC) models circumvent some of these challenges, but research has shown that these cells have a ‘fetal’ identity, meaning the epigenomic network is also likely to be immature. Thus, their applicability to age-related diseases may be limited. There is a real need to understand the potential gap between iPSC models and adult brain tissue.

This project aims to fulﬁl this knowledge gap by pairing human iPSCs with adult brain cells from the same individual. Researchers will collect viable brain cells from patients undergoing surgery, such as for epilepsy or a brain tumour. Then, peripheral blood cells will be taken from the same patient and reprogrammed in to iPSC, speciﬁcally excitatory cortical neurons, astrocytes and microglia. These iPSCs can then be paired with the brain cells from the same individual, and used to test the applicability of iPSC models to epigenetic hypotheses in dementia.

2. Reporter toolbox for analysis of iPSC-microglia function in co-culture with neurons (Cowley)

The developmental pathway for human microglia begins in week 4.5 of gestation, before the blood-brain barrier forms. They mature into lifelong brain-resident microglia through intimate cross-talk with the neuronal environment.

Researchers in this lab have developed a novel protocol technique for differentiating microglia from human induced Pluripotent Stem Cells, which has been found to most closely represent the prenatal pathway of microglia development. Using this technique, iPS cell lines incorporating fluorescent reporters are being used in imaging studies to assess the activation state of microglia, including phagocytosis. iPS-microglia are also being used to explore responses to activation signals at the single-cell transcriptome level.

3. Novel image analysis methods for complex dynamic neural culture systems (Nicholls)

Neurodegenerative phenotypes are subtle and involve a number of cell processes, but imaging these diﬀerent phenotypes is currently hindered as assays are generally one cell type, or observed at a speciﬁc snapshot in time. This means that potential for discovering drug targets and understanding disease mechanisms is limited, but, advances in imaging, computer vision and machine learning oﬀer opportunities to distinguish phenotypes automatically. This has a number of beneﬁts, for example avoiding human bias.

Through close collaboration between engineers and biologists, this project will develop cell imaging and analysis systems to expand the range of observable phenotypes at single cell level. Using advanced imaging methods, hundreds of measurements of individual cells will be taken, such as shape size and texture. Then, using unsupervised machine learning techniques, a clustering algorithm will ﬁnd groups of cells that share the same properties, going beyond current methods to identify disease relevant phenotypes. This will enable the development and testing of treatments against novel but robust phenotypes.

3. Team members

Dr Sally Cowley, Dunn School of Pathology, Oxford
Dr Francesca Nicholls, Nuffield Department of Medicine, Oxford
Dr John Davis, Nuffield Department of Medicine, Oxford Daniel Ebner, Nuffield Department of Medicine, Oxford
Prof Jens Rittscher, Ludwig Institute, Oxford
Prof Simon Lovestone, Department of Psychiatry, Oxford
Prof Kevin Talbot, Nuffield Department of Clinical Neurosciences, Oxford

4. Collaborations

Within UK DRI:

Prof Caleb Webber, UK DRI at Cardiff
Prof Paul Matthews, UK DRI at Imperial

Beyond UK DRI:

Professor David Owen, Imperial College London
Orion Pharma
Roche
Eli Lilly

5. Topics

Microglia, iPSC, single cell transcriptomics, epigenetics, functional genomics, big data

6. Techniques

Machine learning, CRISPR, iPSC

7. Key publications

Fang EF, Hou Y, Palikaras K, Adriaanse BA, Kerr JS, Yang B, Lautrup S, Hasan-Olive MM, Caponio D, Dan X, Rocktäschel P, Croteau DL, Akbari M, Greig NH, Fladby T, Nilsen H, Cader MZ, Mattson MP, Tavernarakis N, Bohr VA. Mitophagy inhibits amyloid-β and tau pathology and reverses cognitive deficits in models of Alzheimer's disease. Nat Neurosci. 2019 Mar;22(3):401-412.

Volpato V, Smith J, Sandor C, Ried JS, Baud A, Handel A, Newey SE, Wessely F, Attar M, Whiteley E, Chintawar S, Verheyen A, Barta T, Lako M, Armstrong L, Muschet C, Artati A, Cusulin C, Christensen K, Patsch C, Sharma E, Nicod J, Brownjohn P, Stubbs V, Heywood WE, Gissen P, De Filippis R, Janssen K, Reinhardt P, Adamski J, Royaux I, Peeters PJ, Terstappen GC, Graf M, Livesey FJ, Akerman CJ, Mills K, Bowden R, Nicholson G, Webber C, Cader MZ, Lakics V. Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study. Stem Cell Reports. 2018 Oct 9;11(4):897-911.

Haenseler W, Sansom SN, Buchrieser J, Newey SE, Moore CS, Nicholls FJ, Chintawar S, Schnell C, Antel JP, Allen ND, Cader MZ, Wade-Martins R, James WS, Cowley SA. A Highly Efficient Human Pluripotent Stem Cell Microglia Model Displays a Neuronal-Co-culture-Specific Expression Profile and Inflammatory Response. Stem Cell Reports. 2017 Jun 6;8(6):1727-1742.

Handel AE, Chintawar S, Lalic T, Whiteley E, Vowles J, Giustacchini A, Argoud K, Sopp P, Nakanishi M, Bowden R, Cowley S, Newey S, Akerman C, Ponting CP, Cader MZ. Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single- cell transcriptomics. Hum Mol Genet. 2016 Mar 1;25(5):989-1000.

Morrison M, Klein C, Clemann N, Collier DA, Hardy J, Heisserer B, Cader MZ, Graf M, Kaye J. StemBANCC: Governing Access to Material and Data in a Large Stem Cell Research Consortium. Stem Cell Rev. 2015 Oct;11(5):681-7.

Zameel Cader