Research projects

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Investigating Immune Pathways in Cardiovascular Diseases

Supervisor: Dr Pasquale Maffia

Project outline:Immune responses play key roles in cardiovascular diseases (CVD) such as atherosclerosis and hypertension. By using a broad range of vascular, immunological and omics techniques we aim to study the net contribution of specific immune pathways to CVD in humans and experimental models.

Techniques to be used: The project will provide training in both vascular biology and immunology, including flow cytometry, microscopy and single-cell omics.

References

1. Maffia P, Mauro C, Case A, Kemper C. Canonical and non-canonical roles of complement in atherosclerosis. Nat Rev Cardiol. 2024 Apr 10. doi: 10.1038/s41569-024-01016-y.
2. Guzik TJ, Nosalski R, Maffia P, Drummond GR. Immune and inflammatory mechanisms in hypertension. Nat Rev Cardiol. 2024;21(6):396-416.
3. MacRitchie N, Grassia G, Noonan J, Cole JE, Hughes CE, Schroeder J, Benson RA, Cochain C, Zernecke A, Guzik TJ, Garside P, Monaco C, Maffia P. The aorta can act as a site of naïve CD4+ T-cell priming. Cardiovasc Res. 2020;116(2):306-316.
4. Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ. Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin Beta Receptors. Immunity. 2015;42:1100-15.

School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA

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Investigating the molecular mechanisms underlying the cellular decision to initiate inflammation

Supervisors: Thimo Kurz, Ruaidhri Carmody

Project outline: The ability of the innate immune system to discriminate between stimuli that pose little danger and those that threaten the host is a key determinant of human health. The concentration of microbial-associated molecules that activates an innate inflammatory response is determined by the activation threshold of key signalling pathways. This is an important mechanism used by innate immune cells to distinguish between threats that should be tolerated and those that require a strong inflammatory response.

This project is based on our recent findings that the stability of TPL-2 (MAP3K8), a key activator of the mitogen activated protein kinase (MAPK) pathway, controls the cellular decision to respond to inflammatory stimuli. Our studies so far have identified the nucleus as the key site regulating the stability of TPL-2.

This project will investigate the regulation MAPKs in the nucleus during innate immune cell responses; explore novel functions of MAPKs in the nucleus; and investigate the impact of altering MAPK activation on cellular responses to inflammatory stimuli. The findings will provide fundamental insights into the regulation of the cellular response to inflammatory stimuli and contribute to the development of novel strategies for the therapeutic control of inflammation.

Summary aim: This project will investigate regulation and function of MAPKs in the nucleus during innate immune cell activation.

Techniques: CRISPR/Cas9 gene editing, molecular biology (including site directed mutagenesis), chromatin immunoprecipitation, immunoblotting, cell culture, real-time PCR

References

1. Somma D, Kok FO, Kerrigan D, Wells CA, Carmody RJ. (2021) Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of NFKB1 Knockout THP1 Cells. Frontiers in Immunology (12) 669906.
2. Kok FO, Wang H, Riedlova P, Goodyear CS, Carmody RJ. (2021) Defining the structure of the NF-ĸB pathway in human immune cells using quantitative proteomic data. Cell Signalling (88) 110154.
3. Mitxitorena I, Somma D, Mitchell JP, Lepistö M, Tyrchan C, Smith EL, Kiely PA, Walden H, Keeshan K, Carmody RJ. (2020) The deubiquitinase USP7 uses a distinct ubiquitin-like domain to deubiquitinate NF-ĸB subunits. Journal of Biological Chemistry 295(33):11754-11763.
4. Sarrou E, Richmond L, Carmody RJ, Gibson B, Keeshan K. (2020) CRISPR Gene Editing of Murine Blood Stem and Progenitor Cells Induces MLL-AF9 Chromosomal Translocation and MLL-AF9 Leukaemogenesis. International Journal Molecular Sciences 21(12):4266.
5. Collins PE, Somma D, Kerrigan D, Herrington F, Keeshan K, Nibbs RJ and Carmody RJ (2019) The IκB-protein BCL-3 Controls Toll-like Receptor-Induced MAPK Activity by Promoting TPL-2 Degradation in the Nucleus. Proceedings of the National Academy of Sciences USA 116 (51), 25828-25838.
6. Smith EL, Somma D, Kerrigan D, McIntyre Z, Cole JJ, Kiely PA, Keeshan K and Carmody RJ. (2019) The regulation of sequence specific NF-ĸB DNA binding and transcription by IKKβ Phosphorylation of NF-ĸB p50 at Serine 80. Nucleic Acids Research 47 (21), 11151-11163.
7. Butcher A, O’Carroll C, Wells CA and Carmody RJ (2018) Toll-like receptors drive specific patterns of tolerance and training on restimulation of macrophages. Frontiers in Immunology doi.org/10.3389/fimmu.2018.00933.

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T cell/APC interactions and immunological decisions

Supervisors: Prof James Brewer, Prof Paul Garside

Project outline: It is becoming clear that the duration, frequency, and intensity of T cell/APC interactions, determines the induction of immunological tolerance versus priming. However, the detailed molecular mechanisms regulating cellular interactions in vivo remain unclear. We contend that spatiotemporal context has a critical influence on T/APC interactions and consequently the induction, maintenance and/or control of immune responses. For example, we have recently shown that the duration and magnitude antigen presentation and the subsequent T cell/APC interaction can influence differentiation of T cells to the Tfh phenotype responsible for driving B cell antibody production. Consequently, cellular and molecular interactions must be carefully choreographed in space and time to provide normal immune function giving protection against infection while avoiding autoimmunity. On the other hand, dysregulated spatiotemporal expression of molecules involved in T cell/APC interactions may result in pathology.

Summary aim: 

1. What are the molecular mechanisms controlling T/APC interactions during priming and tolerance in vivo?
2. How do these pathways impact on the duration, frequency and intensity of T cell/APC interactions in Lymph Nodes (LN)

Techniques to be used: High content (INCELL) imaging, Live in vitro microscope, Intravital multiphoton microscopy

References

1. Zinselmeyer, B. H. et al. In situ characterization of CD4+ T cell behavior in mucosal and systemic lymphoid tissues during the induction of oral priming and tolerance. J. Exp. Med. 201, 1815–23 (2005).
2. Millington, O. R. et al. Malaria impairs T cell clustering and immune priming despite normal signal 1 from dendritic cells. PLoS pathogens 3, 1380–7 (2007).
3. Celli, S., Lemaître, F. & Bousso, P. Real-time manipulation of T cell-dendritic cell interactions in vivo reveals the importance of prolonged contacts for CD4+ T cell activation. Immunity 27, 625–34 (2007)

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The NF-ĸB transcription factor

Supervisor: Ruaidhri Carmody

Project outline: The NF-ĸB transcription factor is a master regulator of the immune response and plays a critical role in inflammatory disease by mediating the expression of pro-inflammatory factors. The NF-ĸB-directed transcription of genes that promote cell survival and proliferation also implicates it as an important factor in cancers and neurodegenerative disorders. The key roles for NF-ĸB in the pathogenesis of these and other diseases have established it as an important therapeutic target, which to date remains unharnessed. Previous strategies focussed on inhibiting the IKK kinases, critical activators of NF-ĸB, have failed to make clinical impact due to severe side-effects, and so new approaches to targeting NF-ĸB for therapeutic benefit are required. This project aims to exploit the regulation of NF-ĸB by the ubiquitin proteasome system in order to inhibit NF-ĸB mediated inflammatory responses. The ubiquitin-triggered proteasomal degradation of NF-ĸB is a major limiting factor in the expression of pro-inflammatory genes. We have previously identified the deubiquitinase USP7 as a key regulator of NF-ĸB transcriptional activity by reversing NF-ĸB ubiquitination and preventing its proteasomal degradation. We have extended these initial findings to identify a distinct NF-ĸB binding site in USP7 that selectively mediates the interaction of USP7 with NF-ĸB. We hypothesise that this binding site could be targeted to selectively inhibit NF-ĸB-directed inflammatory responses by promoting its ubiquitination and degradation. This project is a structure-function based study of the USP7 and NF-ĸB interface that will define the NF-ĸB binding site and the functional impact of its disruption. The results will facilitate the rational structure-led design of substrate-selective inhibitors of USP7 to inhibit NF-kB mediated inflammatory responses.

Summary aim: This project will investigate the potential to inhibit inflammation by inhibiting the deubiquitination of NF-κB by USP7.

Techniques to be used: CRISPR/Cas9 gene editing, molecular biology (including site directed mutagenesis), protein purification and X- ray crystallography, proteomics and transcriptomics.

Contact: ruaidhri.carmody@glasgow.ac.uk, Sir Graeme Davies Building, School of Infection and Immunity, University of Glasgow, Room B/316, 120 University Place, Glasgow, G12 8TA Tel: 0141 330 5945

Also see www.carmodylab.org

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Understanding the regulation of inflammation by the ubiquitin system

Supervisors: Thimo Kurz, Ruaidhri Carmody

Project outline: Inflammatory responses rely on an intricate network of signalling events, which ensure that cells respond appropriately to insults, such as infections, toxic compounds, or cell damage. These responses need to be tightly controlled to prevent over- or under activation that could lead to disease. The ubiquitin pathway, which is a versatile post-translational protein modification system, is a major regulator of inflammatory signalling and this project is aimed at understanding the molecular details of how the ubiquitin system regulates inflammation.

We have identified a number of components of the ubiquitin system that are directly involved in the inflammatory response. With this project we will investigate where in the pathways this regulation occurs and how it is mediated on a molecular level, with the ultimate aim to identify new nodes of intervention to treat inflammatory disease.

The successful candidate will be trained in state-of-the-art technology, including CRISPR gene editing, protein mass spectrometry and primary human cell culture under the joint supervision of two experts in the field of inflammation and ubiquitin signalling, respectively.

References

1. Keuss MJ, Hjerpe R, Hsia O, Gourlay R, Burchmore R, Trost M, Kurz T. (2019) Unanchored tri-NEDD8 inhibits PARP-1 to protect from oxidative stress-induced cell death. EMBO J. 38(6):e100024.
2. Yann Thomas , Daniel C Scott , Yosua Adi Kristariyanto , Jesse Rinehart , Kristopher Clark , Philip Cohen , Thimo Kurz (2018) The NEDD8 E3 ligase DCNL5 is phosphorylated by IKK alpha during Toll-like receptor activation. PLoS One 13(6):e0199197.
3. Hjerpe R, Bett JS, Keuss MJ, Solovyova A, McWilliams TG, Johnson C, Sahu I, Varghese J, Wood N, Wightman M, Osborne G, Bates GP, Glickman MH, Trost M, Knebel A, Marchesi F, Kurz T. (2016) UBQLN2 Mediates Autophagy-Independent Protein Aggregate Clearance by the Proteasome. Cell. 166(4):935-949.
4. Keuss MJ, Thomas Y, Mcarthur R, Wood NT, Knebel A, Kurz T. (2016) Characterization of the mammalian family of DCN-type NEDD8 E3 ligases. J Cell Sci. 129(7):1441-54.
5. Somma D, Kok FO, Kerrigan D, Wells CA, Carmody RJ. (2021) Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of NFKB1 Knockout THP1 Cells. Frontiers in Immunology (12) 669906.
6. Mitxitorena I, Somma D, Mitchell JP, Lepistö M, Tyrchan C, Smith EL, Kiely PA, Walden H, Keeshan K, Carmody RJ. (2020) The deubiquitinase USP7 uses a distinct ubiquitin-like domain to deubiquitinate NF-ĸB subunits. Journal of Biological Chemistry 295(33):11754-11763.
7. Collins PE, Somma D, Kerrigan D, Herrington F, Keeshan K, Nibbs RJ and Carmody RJ (2019) The IκB-protein BCL-3 Controls Toll-like Receptor-Induced MAPK Activity by Promoting TPL-2 Degradation in the Nucleus. Proceedings of the National Academy of Sciences USA 116 (51), 25828-25838.
8. Smith EL, Somma D, Kerrigan D, McIntyre Z, Cole JJ, Kiely PA, Keeshan K and Carmody RJ. (2019) The regulation of sequence specific NF-ĸB DNA binding and transcription by IKKβ Phosphorylation of NF-ĸB p50 at Serine 80. Nucleic Acids Research 47 (21), 11151-11163.

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Overview

The immune system provides vital protection against infection, and can be manipulated by vaccination to provide life-long resistance to pathogens. However, immune and inflammatory responses also make a major contribution to a spectrum of human pathologies, from chronic inflammatory disease, allergy and autoimmunity, neuroinflammatory disorders and brain immune interactions, to heart disease and cancer. 

Research in the Centre for Immunobiology within the School of Infection and Immunity is focused on generating a molecular and cellular understanding of the immune system in health and disease, and applying this knowledge to the development of novel therapeutics. This is built on close interactions between an excellent cohort of scientists and clinicians within the Centre, and on the networks of collaborators they have established with researchers in the rest of the School, elsewhere in the university, and further afield.

Our staff and students benefit from access to state-of-the-art laboratory facilities in the Sir Graeme Davis building at the heart of the university and in clinical units in hospitals across Glasgow. We have expertise in a broad range of techniques, including molecular biology, ‘Omics, cell biology, multiparameter flow cytometry, intravital imaging, and in vivo models of disease, and these approaches allow us to explore the immune system at the molecular, cellular and whole organism level.

The PhD programme in immunobiology is based on individual research projects covering an exciting range of topics, with specific areas of interest including (in alphabetical order):

• atherosclerosis
• bioinformatics
• cancer and leukaemia
• chemokines and cell migration
• cytokine biology
• dendritic cell biology
• imaging the immune response
• infectious disease
• intestinal immunity
• intracellular signalling and transcriptional regulation
• lymphocyte biology
• neuroimmunology, including repair strategies forbrain repair following immunologically mediated injury (Multiple Sclerosis, Guillain-Barré syndrome)  and spinal cord injury using glial/stem cell transplantation and antibody profiling
• osteoimmunology
• rheumatology
• tissue injury and repair; focus on regenerative medicine

Study options

PhD

• Duration: 3/4 years full-time; 5 years part-time

Individual research projects are tailored around the expertise of principal investigators.

Integrated PhD programmes (5 years)

Our Integrated PhD allows you to combine masters level teaching with your chosen research direction in a 1+3+1 format. 

International students with MSc and PhD scholarships/funding do not have to apply for 2 visas or exit and re-enter the country between programmes. International and UK/EU students may apply.

Year 1

Taught masters level modules are taken alongside students on our masters programmes. Our research-led teaching supports you to fine tune your research ideas and discuss these with potential PhD supervisors. You will gain a valuable introduction to academic topics, research methods, laboratory skills and the critical evaluation of research data. Your grades must meet our requirements in order to gain entry on to your pre-selected PhD research project. If not, you will have the options to pay outstanding MSc fees and complete with masters degree only.

Years 2, 3 and 4

PhD programme with research/lab work, completing an examinable piece of independent research in year 4.

Year 5

Thesis write up.

MSc (Research)

• Duration: 1 year full-time; 2 years part-time

MD (Doctor of Medicine)

• Duration: 2 years full-time; 4 years part-time (for medically-qualified graduates only)