Immunity in health and ageing: dissecting the role of the 'non-canonical autophagy' pathway

The immune system plays an important role in maintaining health and defending the body against invading pathogens, such as bacteria, fungi and viruses. As we age, this critical protective mechanism becomes compromised. As a result, elderly individuals have an increased risk of infection and do not respond to immunizations as well as younger people. The reasons behind this age-related decline in the immune system are not fully understood. One biological pathway that influences how we age is 'autophagy', meaning 'self-eating'. Autophagy allows the cells of the body to clear out and recycle unwanted or damaged material within cells. This process keeps cells healthy and is known to support a functional immune system. Recently, a related but distinct new autophagy pathway has been discovered called 'non-canonical autophagy'. Experimental evidence from our lab, and others, suggest this new autophagy pathway also has the potential to significantly impact the immune system, but it hasn't yet been studied in detail. One specific example of this relates to the way specialised immune cells, called dendritic cells, identify pathogens and communicate their presence to the rest of the immune system, to mount a protective response. Usually, dendritic cells 'eat' some of the pathogens, and then display parts of them on their surface; this allows other components of the immune system to recognise the pathogens and mount an attack on those that remain. Our new experimental data reveal that 'non-canonical autophagy' plays a key role in this process. This project will investigate exactly how the non-canonical autophagy pathway regulates the immune system, with a focus on these dendritic cells, and explore how this declines over lifespan. To do this, we will take advantage of our recent work in developing unique models, using both cultured cells and mice, in which the 'non-canonical autophagy' pathway is specifically turned off. We will gain a detailed understanding of this pathway and how aging impacts it, opening up the potential to modify and manipulate the novel 'non-canonical autophagy pathway' for therapeutic benefit.

A major consequence of the aging process is dysregulation of the immune response, but the mechanisms associated with this decline remain to be fully understood. The autophagy pathway is a key catabolic process that plays a significant role in both immunity and aging. Autophagy supports cellular health and energy status through the sequestration and transport of intracellular material to lysosomes, via LC3 decorated autophagosomes. We have recently described a distinct, but related pathway termed "non-canonical autophagy", which conjugates LC3 to intracellular single-membrane compartments of the endolysosomal system. An example of non-canonical autophagy occurs during LC3-associated phagocytosis (LAP), which modulates the killing of engulfed pathogens. This form of LC3 conjugation relies on some core autophagy proteins (e.g. ATG16L1), but is independent from upstream regulators of canonical autophagy. This raises the intriguing possibility that immune dysregulation observed in the absence of autophagy proteins, and with aging, may in fact be due to impaired non-canonical autophagy and LAP. Our central hypothesis for this proposal is that non-canonical autophagy plays a role in immunity and aging by regulating dendritic cell function. To explore this, we will (1) determine the role of non-canonical autophagy in dendritic and macrophage cell function, (2) define the molecular mechanisms regulating non-canonical autophagy and (3) establish the effect of aging on non-canonical autophagy. To achieve these aims, we will apply a combination of imaging, proteomics, flow cytometry and sequencing techniques, both in vitro and in vivo, using primary immune cells from a unique mouse model in which non-canonical autophagy has been specifically inhibited. Overall, our proposal seeks to understand the role of non-canonical autophagy in immune function and its relationship to aging, offering potential new avenues for intervention.

Impact summary

This grant proposal deals with the impact of the non-canonical autophagy pathway on the innate immune system and its role in the age-associated decline in immune responses. This has the potential for significant impact among a range of stakeholders.

Academia
i) The academic research community
The results generated from this proposal will advance our basic understanding of how the immune system declines with age, and discover new molecular mechanisms that regulate the recently described non-canonical autophagy pathway. This work will benefit researchers in the fields of autophagy, immunity and aging by increasing knowledge and generating new systems, tools and resources that can be shared.

ii) Internal collaborators
Within BI, the work in this proposal will directly inform our departmental colleague, Dr Nick Ktistakis, who researches autophagy. In neighbouring programmes at BI, the work on antigen presentation and aging will benefit Dr Michelle Linterman (Lymphocyte Signalling ISP), and drive a new collaboration between our groups. We will share resources and exchange knowledge through joint meetings.

iii) External collaborators
This work will build on and develop our collaborations with Dr Rupert Beale in the Virology department of the University of Cambridge and Prof. Tom Wileman at University of East Anglia, with whom we will share valuable knowledge and resources. The E230 mouse model generated will also seed important new, international collaborations, for instance, with Skip Virgin at Washington University, USA, who is highly experienced in the comprehensive phenotyping of autophagy related mouse models.

Industry
The autophagy proteins are well established drug targets, with efforts directed to inhibit the pathway in cancer and activate it in aging models of neurodegeneration. The non-canonical branch of this pathway can be modulated by many pharmacological agents, as described in our recent publications, but has yet to be targeted specifically. This represents a compelling niche, given the roles of this pathway in immunity and aging. The scientific knowledge generated from this proposal will benefit industry by providing a framework from which new interventions may be designed, and could also identify lead compounds for the creation of new products.

BBSRC
This proposal would contribute to key BBSRC strategic priorities (see Case for Support) and synergise with BBSRC core funded work at BI on the overlapping themes of autophagy, immunity and aging.

Staff
The PDRA associated with this grant will receive specialised technical training, experience in grant and manuscript writing and mentoring from Dr Florey and an additional PI or senior post-doc. The PDRA will also acquire and develop a range of transferable skills, selecting from courses that include statistics, public engagement and lab management.

General public
The discrepancy between lifespan and healthspan represents a major societal issue. This manifests in a reduction in wellbeing and quality of life for the population and increased costs to the health services. This issue constitutes a major focus of the BBSRC and a critical component of the future economic competitiveness of the UK.
The work outlined in this proposal would address the decline in immune function with age, and could thus guide strategies to modulate non-canonical autophagy with anti-ageing and immunity applications. In the long term, this may open the possibility for new interventions, which could reduce burden on the healthcare system, with economic benefit.
More broadly, this grant would mediate job creation and training, supporting economic prosperity, and increase public awareness and understanding of science through outreach and educational activities.