Ella-Louise Hubber

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Academic and Work Experience Prior to Sept 2016 Programme Start

I obtained my bachelor's degree in Biomedical Science at the University of Sheffield where I also completed a project at the Centre for Stem Cell Biology during a Wellcome Trust funded placement. Following my degree I worked for Axol Bioscience, a biotech start-up specialising in iPSC culture and differentiation, and Charles River, a contract research organisation which provides many services for the development of pharmaceuticals.

PhD Programme – Year 1 – MRes and Project Rotations

During the first year of the programme I explored transplantation research in the context of three different tissues, in labs which ranged from basic science to more clinical research;

1. Assessing the expression of pro-survival growth factors by cardiac stem cells after transplantation into mice with myocardial infarction with Dr Georgina Ellison. Here I had the opportunity to collaborate with the Francis Crick Institute using laser capture microdissection.

2. Investigating the transfer of mitochondrial from mesenchymal stromal cells (MSC) to pancreatic islets prior to islet transplantation with Professor Peter Jones.

3. Investigating which MSC would provide the best support to primary human hepatocytes with the aim of improving hepatocyte transplantation with Dr Anil Dhawan and Dr Celine Filipi.

Public Engagement of Science at the Evelina Inspiring Youth Conference

Daria Belokhvostova gets into her stem cell embroidery at the Stitch’n Stem activity table as Ella Hubber demonstrates how transplantation of pancreatic islets in different organs in the body can act as a treatment for type 1 diabetes.

This group is much closer to the clinic, with several clinical trials in process, and gave me excellent insight into how research is translated. My competency as a researcher has improved significantly thanks to the combination of reports, presentations and workshops during year 1 and the planning and direction of my final project has greatly benefited from being exposed to different researchers in similar fields, each with their own way of approaching challenges.

PhD Programme – Years 2 to 4 – Doctoral Studies

For my thesis project I have chosen to join the department of diabetes with Professor Peter Jones. The replacement of β-cells through the transplantation of isolated pancreatic islets is a promising treatment for type 1 diabetes. However, this therapy has been limited by the progressive decline in islet function and viability during isolation and post-transplantation.

Co-culture of islets with MSCs prior to transplantation can improve islet function and transplantation outcomes. This project will take two distinct approaches to elucidate mechanisms of MSC-mediated support of islets. The first will identify differentially expressed genes in MSC co-cultured islets. Through gene knockdown and overexpression, we will determine if genes of interest are biologically relevant to islet function.

The second approach will focus on a mechanism known as mitochondrial transfer. Our pilot study revealed that MSC-derived mitochondria can be found within the outer cells of islets following co-culture. We aim to confirm and quantify transfer and determine if it is functionally beneficial to islets. Together, these investigations will support the development of an MSC-free culture approach where secreted factors, pharmacological pathway simulators and other biological components (i.e. isolated mitochondria) can be applied directly to islets in culture without the need for heterogenous MSC populations.

Emily Read

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Academic and Work Experience Prior to Sept 2016 Programme Start

I completed a Bachelor’s degree in Biological Sciences with a Year in Industry at Imperial College London. During my third year of this degree, I completed an Industrial Placement in the Allergic Inflammation Discovery Performance Unit at GlaxoSmithKline in Stevenage.

PhD Programme – Year 1 – MRes and Project Rotations

During my first year of the Wellcome Trust 'Cell Therapies and Regenerative Medicine' Four-Year PhD Programme I completed three very different rotations:

1. I first investigated the heterogeneity of mesenchymal stem cells in a murine tooth model in Professor Paul Sharpe’s group. 

2. Under the supervision of Dr Joana Neves and Professor Graham Lord, I then optimised a microinjection platform in murine small intestinal organoids, allowing us to study how bacteria interact with intestinal epithelial cells and gut-resident innate lymphoid cells in vitro. 

3. During my final rotation with Dr Francesca Spagnoli, I studied hepatic and pancreatic lineage determination using a genetic lineage tracing system in mouse embryonic stem cells. Throughout this year I have also thoroughly enjoyed taking part in public engagement by talking about my research with pupils from local schools who have visited the Centre for Stem Cells & Regenerative Medicine.

PhD Programme – Years 2 to 4 – Doctoral Studies

The gut contains a diverse community of bacteria, crucial for improving the digestion of food and training of the immune system. Epithelial cells lining the gut and gut-resident immune cells face the forefront of interaction with these bacteria. Imbalance of the gut bacteria, alongside damage to the gut epithelium and changes to the inflammatory status of gut-resident immune cells are associated with the development of chronic inflammatory disorders of the gut, such as inflammatory bowel disease (IBD).

During my PhD, I will generate a novel 3D co-culture system which allows us to model bacterial, gut epithelial and gut-resident immune cell interactions in a dish. Using this system, we will investigate the impact of IBD-associated bacteria, such as Fusobacterium nucleatum (F. nucleatum), on the integrity of the gut epithelium and the inflammatory status of gut-resident immune cells. F. nucleatum is an oral commensal, however intestinal colonisation is associated with colorectal cancer and IBD.

By identifying and characterising pathways that govern the interactions between bacteria, gut epithelial cells and immune cells, this project aims to discover novel targets that modulate gut inflammation and promote gut epithelial repair. This could have therapeutic promise for the treatment of IBD.

Gabriella Clarke

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Academic and Work Experience Prior to Sept 2016 Programme Start

I completed a BSc in Biological Sciences at Imperial College London, with a year in Industry where I worked in R&D at GlaxoSmithKline in Stevenage.

PhD Programme – Year 1 – MRes and Project Rotations

In my first year, I wanted to explore many different areas and techniques in stem cell biology. During my first rotation with Dr Tamir Rashid, I investigated the role of the IFNy/STAT1 axis on the culture of iPSC-derived hepatic progenitor cells with a view to explore this novel cell population, and improve iPSC-derived hepatocyte transplants in liver disease.

In my second rotation with Professor Eric So, I aimed to determine molecular and phenotypic differences in leukemic stem cells derived from two different cells of origin; haematopoetic stem cells versus chronic myeloid progenitors. In my final rotation with Dr Ivo Lieberam, I learned how to differentiate wildtype and mutant iPSCs into cortical neurons in order to examine Alzheimer’s-associated phenotypes in a cellular model of disease.

Overall, these three rotations improved my experience with cell culture, functional assays, molecular biology, cloning and imaging, and confirmed my desire to work in neuroscience.

Bloom

by Gabriella Clarke

Explanation: Neurons growing out from the middle of a ‘neural rosette’ during differentiation of mouse embryonic stem cells into cortical neurons in a dish. This rosette has been stained to show expression of the neural progenitor markers in green (nestin) and cell nuclei (blue).  Neural progenitors mature into cortical neurons which can be used to study Alzheimer’s disease.

PhD Programme – Years 2 to 4 – Doctoral Studies

For my PhD project I have joined Professor Chris Shaw’s Lab and will be working closely with Dr Ivo Lieberam as my second supervisor. My project will focus amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease characterised by loss of motor neurons and muscle wasting. ALS can be driven by a plethora of distinct genetic mutations. I will be investigating one such novel mutation in iPSC-derived motor neurons.

We predict that the respective mutant protein may respond to excitotoxicity (a widespread phenomenon in ALS), and contribute to the pathological protein aggregation that is a hallmark of approximately 97% of cases of ALS. In my project I will use optogenetics to accurately photostimulate wildtype and mutant iPSC-derived motor neurons, thereby recapitulating excitotoxicity. Any phenotypic responses to this stimulation will be assessed by live imaging.

Starry Starry Night

by Gabriella Clarke

Explanation: Young hiPSC-derived motor neurons grown in vitro. Cell bodies group together (cytoplasm green, nuclei blue) and form long overlapping networks of axons (red MAP2, orange BIIITub). This neuronal culture can be used to model disease phenotypes of amyotrophic lateral sclerosis in vitro.

First, we aim to determine if our target mutant protein accumulates in response to excitotoxicity. Second, we aim to assess whether these aggregates are dysregulated and pathogenic. Finally, we aim to not only determine the cellular response in motor neurons alone, but also to explore how any changes affect neuromuscular junctions using a novel compartmentalised microfluidic device developed by the Lieberam group. In conclusion, this work should improve the in vitro modelling of ALS, and uncover novel pathological mechanisms of action of our target mutant protein for the first time.

Peter Harley

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Academic and Work Experience Prior to Sept 2016 Programme Start

I completed my undergraduate degree in developmental biology (MSci) at the University of Manchester, where I worked with Professor Sue Kimber to develop iPSC models of rare skeletal disorders. During this time, I also undertook a BBSRC funded studentship to investigate wound healing in diabetes. 

PhD Programme – Year 1 – MRes and Project Rotations

1. During my first rotation project I worked with Dr Davide Danovi and Professor Fiona Watt as part of the human induced pluripotent stem cell initiative (HipSci). During this project I grew kidney organoids from patient iPSCs to model Bardet-Biedl syndrome.

2. In my second rotation project I worked with Dr Ivo Lieberam to develop in vitro neuromuscular circuits in order to model the loss of nerve-muscle connectivity in ALS. 

3. In my final project I worked with Dr Franziska Denk and Professor Stephen McMahon to understand how neuro-immune interactions contribute to sex-specific differences in chronic pain.

Impulse

by Peter Harley

Explanation: A motor neuron in blue (Tubb3) made artificially in the lab from stem cells taken from patients with motor neuron disease. The orange sections (Ankyrin-G) are the main sites where nerve impulses are generated.

PhD Programme – Years 2 to 4 – Doctoral Studies

Amyotrophic lateral sclerosis (ALS) is a rapidly fatal neurodegenerative disorder, characterised by progressive loss of motor neurons (MNs) in the brain and spinal cord. Surmounting evidence suggests that peripheral axonal and neuromuscular junction (NMJ) defects precede overall cell death in the disease pathogenesis. However, the molecular mechanisms underpinning these critical early events remain poorly understood.

A major reason for this is the difficulty in accessing live neuromuscular junctions for study. To overcome this, we intend to engineer functional human neuromuscular junctions in vitro. Motor neurons derived from wildtype human induced pluripotent stem cells (hiPSCs) and hiPSCs harbouring an ALS-linked TDPeter HarP-43 mutation will be plated, along with astrocytes, into a microfluidics device. Axons will be able to project through micro-channels into a separate muscle compartment, where they will be able to form neuromuscular connections. Optogenetics will be used to stimulate motor neuron activity and trigger myofiber contraction, mimicking the voluntary movement that is lost in ALS.

Using this platform, we will be able to apply various live imaging techniques to the study of human neuromuscular junction pathology that has not previously been possible. As such we feel this approach will provide unique insights into how TDP-43 mediates some of the earliest pathological events in ALS. Ultimately, through a collaboration with AstraZeneca, we intend to use this platform for drugs discovery. 

A Song of Fire and Ice

by Peter Harley

Explanation: We directed stem cells to become motor neurons (blue=Tubb3) and astrocytes (orange=GFAP). Normally astrocytes provide a comfortable environment for the neurons to live, but in a number of diseases, such as motor neuron disease, they can create a toxic environment that kills the neurons.

Congratulations to Peter Harley for receiving the:

• Susan Tucker Award for the most outstanding student in the Biomedical and Translational Sciences MRes programme. October 2018. 

• Centre for Stem Cells and Regenerative Medicine Award for the student scoring the highest Biomedical and Translational Science MRes degree mark and continuing to a PhD in Stem Cells and Regenerative Medicine.  November 2018.

Teodora Manea

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Academic and Work Experience Prior to Sept 2016 Programme Start

I completed my undergraduate studies at the University of York, graduating with a BSc Biochemistry degree. During my bachelor's degree, I gained research experience by participating in the iGEM (International Genetically Engineered Machine) competition as a member of the team representing my university. I spent the third year of my four-year degree on an industrial placement at the Earlham Institute, improving my knowledge of bioinformatics and learning more about gene expression analysis and tissue culture.

PhD Programme – Year 1 – MRes and Project Rotations

In my first year of the Wellcome Trust ‘Cell Therapies and Regenerative Medicine’ Four-Year PhD Programme, I explored diverse aspects of the field of stem cells and regenerative medicine through my three rotation projects.

I undertook my first rotation under the supervision of Professor Graham Lord and Dr Joana Neves, investigating plasticity triggers between different types of innate lymphoid cells within a 3D intestinal organoid co-culture system.

During my second rotation, in Dr Eileen Gentleman’s group, I worked to characterise the effects of PEG hydrogels with different mechanical properties on iPSC differentiation towards the three germ layers, focusing in particular on the role of hydrogel stiffness, adhesiveness and degradability.

Throughout my third rotation, carried out in Dr Rocio Sancho’s lab, I aimed to elucidate the role of Fbw7, an E3 Ubiquitin Ligase, in the proteasomal degradation of proendocrine transcription factors Pdx1 and MafA.

As these transcription factors, alongside Ngn3, are essential in β-cell development, it is hoped that by identifying ubiquitin ligases involved in their degradation and impairing their function, we can enhance β-cell generation.

PhD Programme – Years 2 to 4 – Doctoral Studies

In Type 1 Diabetes, insulin-producing β-cells in the pancreas are destroyed due to an autoimmune reaction, resulting in impaired insulin production and dysregulated glucose metabolism. Transplantation of pancreatic islets from healthy donors has been attempted, aiming to compensate for lost β-cells in diabetic patients, but a shortage of islets available for transplantation and the fact that the transplant must be accompanied by immunosuppression currently limits the clinical applications of this therapy.

To circumvent these issues and boost β-cell generation, attempts have been made to identify triggers that could induce the ex vivo transition from the abundant exocrine pancreatic cells to β-cells. While inducing overexpression of β-cell development factors Pdx1, Ngn3 and MafA in exocrine cells through adenoviral infection was found to transdifferentiate them into β-like cells, this strategy does not result in fully functional β-cells, partly due to the incorrect regulation of the three transcription factors.

My project, carried out within Dr Rocio Sancho’s lab, will investigate ways to stabilise Pdx1, Ngn3 and MafA levels post-translationally, focusing on the role of ubiquitin ligases Fbw7 and Huwe1. As preliminary data from the lab suggests that these ubiquitin ligases play a role in the degradation of at least some of the transcription factors of interest, we hypothesise that impairing their function could lead to stabilisation of Pdx1, Ngn3 and MafA, thus enhancing  β-cell generation.