Dr Emma Shepherd

Supervisor Details

Contact Details

Scientific Background

Scientific Inspiration

I am inspired by people who have achieved success by paving their own way. People such as Jane Cooke Wright (1919-2013) who was a doctor and trailblazing cancer researcher who worked to begin the use of cell culture to test individualised chemotherapy treatments.

Supervision Style

In three words or phrases: Supportive, collaborative and goal-driven.

Provision of Training

I prefer to take responsibility for your technical training and understanding of the premise of the project at first to ensure that you have the best platform to grow and steer in your project. Following this, I will help guide you towards independence at later stages and to help with developing your own problem-solving strategies to address research challenges

Progression Monitoring and Management

I will ensure that we have regular meetings to discuss progress and I expect you to come to these well prepared. The main driving force in your PhD will be you but I will help guide you to ensure that you keep on track. I endeavour to be a supportive and understanding supervisor who will encourage you to strive and grow as a researcher. The ultimate goal of my supervision is to help you develop the knowledge, skillset and mindset to flourish in your PhD and build a portfolio of transferable skills ready for continuing career development.

Communication

I think that work/life balance is important to promote sustained growth and therefore I do not answer emails outside of standard office hours or when I am on holiday. I have an open-door policy and am happy to respond to queries in person as they come up. I am happy to discuss any issues that are impacting your ability to fulfil your potential and my/our expectations. I will also signpost you to additional support or guidance where appropriate.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once a week

In year 1 of PhD study

At least once a fortnight

In year 2 of PhD study

At least once a month

In year 3 of PhD study

At least once a month

These meetings will be a mixture of face to face and video or phone call, and I am usually contactable for an instant response on every working day.

Working Pattern

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings), I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 week’s notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Investigating Matrix Regulation of Extracellular Vesicle Cargo Signalling

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Investigating Matrix Regulation of Extracellular Vesicle Cargo Signalling

Secondary Supervisor(s): Professor Andrew Devitt

University of Registration: Aston University

BBSRC Research Themes:

Understanding the Rules of Life (Immunology, Structural Biology)
Integrated Understanding of Health (Ageing)

Project Outline

The extracellular matrix (ECM) is a complex arrangement of molecules that provides structural and biochemical support to cells. Far more than just scaffolding, the ECM is also a key source of signals and signposts from neighbouring cells. Cells package molecules into small lipid-membrane-bound extracellular vesicles (EVs) and secrete them into the local microenvironment where they interact with the network of ECM proteins. Cells also receive feedback from the ECM and alter intracellular processes to control the biogenesis of EVs. Once secreted, various factors determine whether EVs are locally incorporated into the matrix or transported out of the matrix to be taken up by other cells or deposited into tissues.

Whilst we have a good idea of how these processes are regulated by chemical and physical damage stimuli, there is increasing evidence that the biophysical microenvironment also plays a key role. By combining the expertise of the Shepherd and Devitt labs, this project will investigate how the critical relationship between the ECM and EVs regulates regeneration in the liver.

This project will suit a PhD candidate interested in using cutting-edge technology to reveal new ways to explore interactions at the nanoscale. We hypothesize that the biophysical properties of ECM proteins in liver tissue alter the production and availability of EVs to regulate local cellular responses. To test this hypothesis, this project will characterise the composition of the liver ECM microenvironment, evaluate EV dynamics in these conditions and examine how these cues regulate EV orientation and availability to neighbouring immune cells. Understanding these mechanisms is crucial for developing new therapeutic strategies for improving wound healing and reducing fibrosis.

We have developed a system to incorporate decellularized ECM (dECM) from human liver for use in vitro to study how the matrix regulates liver cell phenotype in vitro. This project will incorporate this system to characterise EVs from cells cultured on dECM to reveal the role of the ECM composition directing macrophage phenotype. This research will advance our understanding of how environmental factors influence ECM dynamics and stress signalling, with broad implications for tissue engineering, regenerative medicine, and disease treatment. The findings could lead to novel therapeutic strategies for conditions such as fibrosis, cancer, and chronic inflammatory diseases.

Bioprinting soft matrices to reveal integrin-dependent adhesion processing 2

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Bioprinting soft matrices to reveal integrin-dependent adhesion processing

Secondary Supervisor(s): Professor Patricia Lalor

University of Registration: Aston University

BBSRC Research Themes:

Understanding the Rules of Life (Structural Biology)
Integrated Understanding of Health (Pharmaceuticals)

Project Outline

Integrin-mediated adhesions between cells and the extracellular matrix (ECM) are fundamental for cell and tissue function. One of the main functions of cell-matrix interactions is the detection of mechanical signals linked to the rigidity of ECM or the forces transmitted from it. The ECM of healthy human liver is relatively elastic but increased liver stiffness is associated with aging and chronic diseases such as liver fibrosis. In vivo models do not recapitulate the extent of ECM accumulation observed in chronically scarred human liver tissue and there are also key differences in gene regulation networks which impact translation to human physiology. Despite this, animal models remain the gold standard for investigating mechanisms of injury, fibrosis and repair due to a lack of viable alternatives. In vitro culture of ECM-producing human liver cells on 2D tissue culture plastic exposes cells to supraphysiological levels of stiffness which limits their use for understanding force-dependent mechanisms of regulation such as integrin-dependent adhesion. This can be partially addressed by culture methods such as soft, inert polymer gels or mouse cell-derived ECM (e.g. Matrigel®). However, there is a lack of models which represent biologically relevant matrix components and elastic modulus, and new systems are required to investigate human liver cell integrin-mediated biology. Thus, novel models that recreate the diverse constituents and stiffness features of human liver matrix are urgently required to extend the knowledge of mechanisms underpinning integrin-mediated adhesion.

The importance of how ECM is aligned (topography) and processed (crosslinked) has been described in a range of biological settings. By combining the expertise of the Shepherd and Lalor labs, this project will define and bioprint ECM roadmaps of human liver tissue to allow us to investigate how cues from the extracellular environment alter how cells use integrins and reveal if this is modulation as a therapeutic strategy. By modelling the biophysical properties of tissue in vitro, we will be better placed to screen drug libraries for efficacy in fibrotic conditions.

This project will suit a PhD candidate interested in using combining cell culture with biomaterials approaches to study how cells interact with their surrounding at the microscale. We have developed a system to incorporate decellularized ECM (dECM) from human liver for use in vitro to study how the matrix regulates liver cell phenotype in vitro. This project will incorporate liver scaffolds in a range of biomaterials that mimic the liver microenvironment to interrogate integrin-dependent cell adhesion and mechanotransduction mechanisms.

The outputs from this research will describe integrin interactions in real-world tissues to better inform the design and evaluation of new medicines targeting integrins to treat fibrotic diseases.

Co-supervisor on a project with Dr Anisa Mahomed.

Previous Projects (2024-25)

Primary supervisor for:

Developing 3D liver model systems for drug discovery

Previous Projects (2023-24)

Primary supervisor for:

Modelling liver cell: matrix interactions to identify new targets in tissue regeneration