UKRMP/Immunology: Defining the role of tissue-resident immune cells in alveolar epithelial cell regeneration

The lung is a distinct organ in terms of self-renewal and regeneration. Under normal circumstances, cell turnover is low, but when injured, it possesses tremendous ability to regrow - a whole new lung segment can regenerate after partial pneumonectomy via the activity of adult stem cells. Yet, in end-stage lung diseases like chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), regeneration potential is low or occurs abnormally. Organ regeneration occurs within a complex micro-environment (or 'niche'), unique to each organ, in which the adult stem cells and its daughter cells communicate with each other and with the surrounding structural and supporting cells (e.g. fibroblasts - cells that make scars, endothelial cells - cells that lines blood vessel) and immune cells. The activity of these cellular constituents' impact on the ability of the stem cells to regenerate, and the kind of daughter cells they produce, a process called differentiation. Despite a lot of work on the niche, little is known of how immune cells, in particular those that stably reside in the niche (tissue-resident immune cells), influence regeneration. We are interested in the role of these tissue-resident immune cells (TRICs) in promoting regeneration after injury; specifically, in their interaction with the alveolar epithelial progenitors and the signalling mechanisms they employ. These studies will contribute to the detailed picture of the niche in which cells regenerate and pave the way for developing of new therapies to promote re-growth of a patient's own lung in diseases like IPF and potentially other chronic tissue-destructive diseases affecting other organs.

The goal of our research is to understand the contribution of tissue-resident immune cells (TRICs) to regeneration of an injured alveolar epithelium. Intense work is ongoing to examine the role of stroma and mesenchymal cells but very little is known on how immune cells maintain self-renewal during homeostasis and promote regeneration after injury. We will use a multi-faceted but cohesive approach as follows: (i) immune cells including TRICs are mapped to regenerating alveolar epithelium in human idiopathic pulmonary fibrosis lungs (a disease of aberrant alveolar regeneration) to determine the types of TRICs that colocalise to normal and aberrant alveolar regeneration in human lungs (ii) types, frequency, function and signalling pathways of TRICs are interrogated at injury, repair and regeneration or fibrosis time points in murine model of injury and appropriate regeneration compared to injury with fibrosis and (iii) test the hypothesis that a subset of regulatory T cells, Jag1+ Tregs, interact with CD103+ dendritic cells via Jag-Notch signalling to enable regeneration of type II alveolar epithelial cells after injury. These studies will complement each other and provide a detailed and robust examination of the immune cells in the regenerating alveolar niche in human lungs, ex vivo lung models and murine models. We will use advanced technology to aid of quest, including tissue and cell CYTOF, multi-colour high resolution immune-profiling, single-cell RNA sequencing, crispr-Cas9 gene-editing and judicious use of targeted genetically engineered murine models including the high definition confetti-reporter technology for lineage tracking.

(i)Impact on Regenerative Medicine research and UKRMP hub research
This is an exciting time in regenerative medicine research as the basework is laid for future translation to therapy. Work on non-autologous stem cell transplantation highlights the advantage of endogenous tissue regeneration which bypass the problem of immunogenicity and lack of cell numbers. Our work targets this sphere of the regenerative niche, focusing on the gap in this area - the role of immune cells in influencing tissue regeneration. In addition, there is a gathering momentum on discovery of multiple alveolar progenitors and the mechanisms by which the differentiate, transdifferentiate and de-differentiate. Our contribution would be in the uncovering of the key tissue-resident immune cells (TRICS) involved in alveolar regeneration and the mechanism by which they do this. Within the TRIC biology community, there is a small number of groups focusing on the non-conventional functions of these cells in tissue sites and currently no labs specifically study TRIC interactions with tissue stem cells. Indeed, transformative regenerative medicine outcomes at scale will not be attained until the immune system issues and specifically the adverse and potentially beneficial role of immune cells in the regenerating niche is understood and overcome. The immediate impact on the Hub might be in the enhancement of the small molecules used to cause regeneration in the lungs currently tested by Prof Janes' group in the ECE Hub. Although we have ensured that we work in a different regenerative niche in order to prevent duplication, our findings could enable new approaches to be undertaken which may synergise and enhance endogenous growth in bronchial epithelium.

(ii)Impact on Pharmaceutical Industry/Biotech companies/medicinal chemists.
The development of relevant inhibitors /activators to enhance or inhibit lung stem cell differentiation could in the long term stimulate economic growth. Furthermore, given the implication of Tregs in orchestrating immune responses in multiple tissues and organs, biological mediators could be utilized for other therapeutic purposes.
Impact on transferable skills gained by staff working on the project. The post-doctoral scientist and technicians employed on this project and other PhD/Rotation/Master's students attached to our labs will develop extensive scientific knowledge and acquire a skill set highly desirable for future employment prospects. With our mentorship, they will also gain additional general project management skills that are obtained from running a research project, which are transferable to many other disciplines in addition to the scientific employment sector. The recruits will gain communication and supervision/teaching skills that will be transferable to any management discipline.

(iii)Impact on Technology
We are among a handful of centres in UK which has the Hyperion tissue CYTOF platform and no studies have yet been published using IPF Lungs. The map of the alveolar niche will be a world first if we achieve this and also move this technology forward for diseased lungs. In addition, the use of single cell transcriptomics in the lungs that are regenerating and those that are fibrosing will also be a first and will provide a wealth of information on the novel groups of cells which may be involved, particularly rare cells which may be been missed with standard technologies.

(iv)Impact on Patients - hopes, inspiration and the future
IPF is a devastating disease, and prognosis is worse than many cancers. Treatment only slows down the progress but does not reverse the disease nor allow patients to regain any function. Endogenous alveolar regeneration provides hope (particularly for the younger subset of patients) for life-prolonging and disease-halting treatment and will have a significant impact on their day to day view of the future.