How autophagy and related processes are coordinated and important in adaption to changed nutrient availability and cell damage

Lead Research Organisation: Babraham Institute
Department Name: UNLISTED

Abstract

The increase in life span of model organisms subjected to DR is dependent on autophagy83 but the exact molecular mechanisms linking autophagy to ageing remain elusive. A major complication is that autophagy is part of one of the hallmarks of ageing namely loss of proteostasis while also contributing to several others such as deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence and stem cell exhaustion. Of note, up-regulation of autophagy by transgenic expression of ATG5 in mice extends health and life span2. The core process of autophagy is the generation of a double membrane bounded organelle that can engulf cell constituents and traffic them into the lysosomal compartment for recycling. Two protein machines control the initiation of autophagy, the ULK and Vps34 (class III PI3K) complexes. Together they remodel the ER to generate early autophagosomes that expand in an LC3- lipidation-dependent fashion. Autophagy operates in different contexts. If nutrients are scarce non-selective autophagy is induced by activation of AMPK and inactivation of mTORC1 and engulfs cytoplasm and/or organelles in autophagosomes of diverse size. There are forms of autophagy that proceed in the presence of ample nutrients (“selective” autophagy, eg, mitophagy (autophagy of mitochondria), are targeted by cargo-selective autophagic receptors and appear to be insensitive to changes in mTORC1 or AMPK activity. Both nutrient-supply-sensitive and “selective” autophagy are probably important for dietary-restriction-induced life span extension. Recent work has shown that molecular components of the autophagy pathway, including the machinery that lipidates LC3, have roles in other cell processes that can internalise and deliver extracellular material to lysosomes, eg phagocytosis, entosis and macropinocytosis. The molecular mechanisms that coordinate this non-canonical use of the autophagy apparatus, their roles in cell biology and how they dovetail with conventional autophagy are unknown.

Publications

10 25 50
 
Description 1) Autophagy is an essential cellular process involved in recycling of cellular constituents to release energy when the cell is short of nutrients. Non-canonical autophagy is a closely related process that is clearly important but is very poorly understood. ATG16 is a protein that is essential for the processes of autophagy and non-canonical autophagy through its role in the conjugation of lipid modified proteins essential in those processes. We have identified key domains and residues in ATG16 that are required for non-canonical autophagy but not autophagy. This has allowed us to create tools that will allow us to understand the role of non canonical autophagy in physiological processes. We have created cells and mice expressing mutant versions of ATG16 that will enable us to progress this work.
2) We have identified tool compounds that activate non-canonical autophagy and will allow us understand the regulation of the process.
3) We have resolved the longstanding debate about the status of autophagy during mitosis by showing unequivocally that autophagy is repressed in mitosis. This because CDK1 (a protein kinase that controls mitosis) inhibits mTORC1 and takes over its functions to phosphorylate key autophagy regulators. This ensures that autophagy stays repressed during nuclear membrane breakdown to protect the genome during cell division. This may be an important control mechanism to support genome stability
4) mTOR inhibitors can increase lifespan and healthspan so we have investigated how cells adapt to chronic mTOR inhibition. These cells amplify eIF4E to maintain protein synthesis but we have now discovered that they also remodel key regulators of autophagy causing down regulation of ULK1 and the transcription factor TFEB, which normally drives expression of genes involved in lysosome function and biogenesis.
5) We have demonstrated that the ubiquitous autophagy cargo receptors p62/SQSTM1, that is involved in the transport of proteins that are destined for destruction to the autophagosome, is phosphorylated at multiple sights in response to activation of the DYRK stress kinases. In addition, multiple other proteins known to be involved in proteostasis and autophagy have been identified as DYRK-inducible phosphoproteins.
6) We have revealed the mechanisms regulating the processes by which dysfunctional mitochondria are targeted by autophagy (mitophagy) and find both differences and similarities with normal autophagy. This suggests it may be possible to selectively interfere with mitophagic v autophagic processes.
Exploitation Route The above results will be taken forward as described in our ISPG. Our collaborators are already building the conclusions of our work into their planning.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description We have communicated our results to commerical collaborators in this area (eg Axol Bioscience) and they are developing a new therapeutic strategy based on these results. Work on the repression of autophagy during mitosis may be relevant to the use of certain anti-mitotic agents in chemotherapy and we are discussing this with clinical and charity sector colleagues. Our increasing interest in the process of non-canonical autophagy has led to collaboration with industry targeting lysosomal storage diseases. This work has the potential to have substantial benefit for a number of poorly treated diseases.
First Year Of Impact 2016
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description Babraham Institute Representative on Translational Research at EU Life, a consortium of EU Life Sciences Institutes
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
URL http://eu-life.eu/
 
Description Membership of Scientific Advisory Board for Cancer Research Technology
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Scientific Advisory Board for CRUK Programme Grant awarded to Northern Institute for Cancer Research, Univeristy of Newcastle
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Participation in a advisory committee
 
Title ATG16L1 K490A mouse 
Description We have developed a novel transgenic mouse, where a single point mutation was introduced into the protein ATG16L1 using CRISPR/Cas9 technology. This mutation renders the mouse defective for a specific autophagy-related pathway (non-canonical autophagy LC3-associated phagocytosis), while the canonical autophagy pathways remain unaffected. 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Year Produced 2019 
Provided To Others? No  
Impact Using this novel mouse line, we can for the first time specifically inhibit the non-canonical autophagy pathway and explore its function in vivo. Preliminary results suggest this pathway has an important role in how dendritic cells mount an immune response to exogenous stimuli. 
 
Title DYRK1B and DYRK2 CRISPR KO cells lines 
Description HEK293 cells with CRISPR/Cas9-mediated deletion of DYRK1B or DYRK2 Fully sequenced and characterisation ongoing 
Type Of Material Cell line 
Year Produced 2019 
Provided To Others? No  
Impact Initial characterisation has revealed some striking phenotypes that are currently being investigated. In the interim these cell lines are available for collaborators 
 
Title Inducible DYRK1B cells 
Description HEK293 cells lines engineered to exhibit Tet-inducible expression of the DYRK1B protein kinase 
Type Of Material Cell line 
Provided To Others? No  
Impact New knowledge of the biological function of the DYRK1B protein kinase, including new substrates. New research papers New collaborations 
 
Title Inducible DYRK2 cell line 
Description HEK293 cells lines engineered to exhibit Tet-inducible expression of the DYRK2 protein kinase 
Type Of Material Cell line 
Provided To Others? No  
Impact New knowledge of DYRK2 Identification of new substrates of DYRK2 
 
Title DYRK1B phosphoproteomics data set 
Description Using HEK293 cells exhibiting inducible expression of the DYRK1B protein kinase (HD1B cells) we have performed Phospho-SILAC mess spectrometry to identify DYRK1B-inducible phosphoproteins. Some of these turn out to be direct DYRK1B substrates 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact This data set has allowed us to identify new DYRK1B substrates and so has provided new insights into the function of this protein kinases in controlling gene expression and autophagy. The dataset will ultimately be released and freely available when the first mansucript is published 
 
Title DYRK1B transcriptome gene data set 
Description RNA-seq data set derived from HEK293 cells which exhibit Tet-regulated DYRK1B expression Reports genome wide changes in abundance and splicing patterns in response to DYRK1B expression 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Too soon for impacts. Data currently being analsyed 
 
Title DYRK2 Transcriptome gene data set 
Description RNA-seq data set derived from HEK293 cells which exhibit Tet-regulated DYRK2 expression Reports genome wide changes in abundance and splicing patterns in response to DYRK2 expression 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Too soon for impacts. Data currently being analysed 
 
Title DYRK2 phosphoproteomics dataset 
Description Using HEK293 cells exhibiting inducible expression of the DYRK2 protein kinase (HD2 cells) we have performed Phospho-SILAC mess spectrometry to identify DYRK2-inducible phosphoproteins. Some of these turn out to be direct DYRK2 substrates 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact This dataset has allowed us to identify DYRK2-inducible phosphoproteins, including new substrates, providing new insghts into the function of the DYRK2 protein in gene expression, autophagy/proteostasis and cell motility 
 
Description A mouse model to study non-canonical autophagy 
Organisation University of East Anglia
Department Biomedical Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We are providing technical assistance and expertise on non-canonical autophagy experiments. We are sharing preliminary data regarding the autophagy protein Atg16L1.
Collaborator Contribution Our collaborators are generating and have generated mouse models which can be used to study non-canonical autophagy.
Impact We have had meetings to discuss the work and shared cell reagents. This work has resulted in a publication in the EMBO Journal, 2018.
Start Year 2015
 
Description Axol Bioscience 
Organisation Axol Bioscience Ltd
Country United Kingdom 
Sector Private 
PI Contribution We have conducted research into the role autophagy in tumour progression that is relevant to their objectives
Collaborator Contribution Reagents, commerical advice and perspective.
Impact Progressing towards publications
Start Year 2016
 
Description Colaborration with Japanese 
Organisation University of Tokyo
Country Japan 
Sector Academic/University 
PI Contribution Paper together with Prof Noboru Mizushima
Collaborator Contribution Paper together with Prof Noboru Mizushima
Impact paper together visit of scientist
Start Year 2011
 
Description Collaboration with Casma Thereapeutics 
Organisation Casma Therapeutics
Country United States 
Sector Private 
PI Contribution We have provided intelectual knowledge and insights into the non-canonical autophagy pathway. We have shared reagents and performed experiments.
Collaborator Contribution Casma have contributed reagemts, experiments and data.
Impact Thus far this collaboration has resulted in a presention of data as an invited speaker at a Gordon Research Conference.
Start Year 2019
 
Description Hosted a visiting ERASMUS student 
Organisation European Commission
Country European Union (EU) 
Sector Public 
PI Contribution My lab hosted a visiting student (Celine Judon) on an ERASMUS scholarship between 02/2016 to 07/2016. She gained experience and training in laboratory techniques and wrote a final report on her project.
Collaborator Contribution ERASMUS provided a living allowance for the student.
Impact Work and data from the student was used in a publication (Jacquin et al. Autophagy. 2017). The student was a named author on the publication.
Start Year 2016
 
Description Hosted an AMGEN scholar summer student 
Organisation Amgen Foundation
Country United States 
Sector Charity/Non Profit 
PI Contribution My lab hosted an AMGEN scholar summer student (Pablo Romero Clavijo) from 07/2017 to 09/2017. We provided training and mentorship through a research project.
Collaborator Contribution The AMGEN student (Pablo) was involved in an active research project and contributed to generation of biological lab reagents and in presenting his data during lab meeting.
Impact The AMGEN student has proceeded to apply for PhD studentships within the UK, using his experience from his time in our lab for teh applications.
Start Year 2017
 
Description In vitro ATG8 lipidation 
Organisation University of Oslo
Country Norway 
Sector Academic/University 
PI Contribution We have provided experimental data and design based on our current work. We are providing mass spectrometry analysis of final samples.
Collaborator Contribution The lab of Anne Simonsen are performing in vitro ATG8 lipidation assays suing purified proteins and liposomes.
Impact N/A
Start Year 2019
 
Description Mitophagy in human patients 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Examining human fibroblasts from patients with mitochondrial dysfunction to identify those with mitophagy alterations
Collaborator Contribution Provision of patient fibroblasts and patient histories
Impact still in progress
Start Year 2018
 
Description Nano-particles and autophagy 
Organisation Oslo University Hospital
Country Norway 
Sector Hospitals 
PI Contribution We are providing a set of cell lines in which key autophagy proteins have been edited by CRISPR/Cas9. We are also providing technical assistance in experimental design.
Collaborator Contribution Our collaborators are providing different nano-particles with distinct chemistry, and expertise in functional analysis of nano-particles.
Impact Our collaboration formed part of a successful grant application for our collaborators in Norway.
Start Year 2017
 
Description Roger Williams 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Academic/University 
PI Contribution Exchange of reagents and cell lines
Collaborator Contribution Exchange of reagents and cell lines
Impact Publications and grants
Start Year 2012
 
Description Role of non-canonical autophagy in influenza A infection 
Organisation University of Cambridge
Department Microelectronics Group
Country United Kingdom 
Sector Academic/University 
PI Contribution We have generated a range of cell systems to distinguish between canonical and non-canonical autophagy.
Collaborator Contribution Our partners have extensive experience in influenza research and are able to use our cell system in their experiments.
Impact We are in the process of submitting a manuscript based on this collaboration. This mauscript has now been published in the EMBO Journal, 2018.
Start Year 2016
 
Description Sharon Tooze 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Exchange of reagents and cell lines
Collaborator Contribution Exchange of reagents and cell lines
Impact Publications Meetings
Start Year 2009
 
Description Synuclein clearance 
Organisation National University of Cordoba
Country Argentina 
Sector Academic/University 
PI Contribution Hosted student to study clearance of synuclein fibers by autohagy
Collaborator Contribution Model system
Impact publication
Start Year 2017
 
Description Tamotsu 
Organisation Osaka University
Country Japan 
Sector Academic/University 
PI Contribution Papers together
Collaborator Contribution Papers together
Impact Published 2 papers together
Start Year 2009
 
Description BioScience Lites 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I gave a short seminar to a group (8) of teachers on the research interests in my group and how it uses different microscopy techniques. This was followed by a practical demonstration on one of the microscopes. This increased the teachers understanding of how microscopy techniques are used and of the different types there are available.
Year(s) Of Engagement Activity 2019
 
Description Cambridge Science Festival , David Barneda 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Cambridge science festival presentation/ discussion on the role of science in society
Year(s) Of Engagement Activity 2019
 
Description College Career Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Members from the lab presented a poster dispaying they types of work/job they so in reasearch. Lab members then reviewed college student poster presentations.
Year(s) Of Engagement Activity 2019
 
Description Deep dive autophagy discussion 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Provided expert opinion on whether autophagy is a good investment area
Year(s) Of Engagement Activity 2019
 
Description Escape Room Installation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A 'Signalling' Escape Room was designed by students within the Signallign Laboratory, working with the Public Engagement team. This was then presented by studnets and post-docs, including members of the Cook lab at both the Cambridge Science Festival and the Latitude Music Festival.
Year(s) Of Engagement Activity 2019,2020
 
Description Escape room installation used in 2 events 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A "signalling" escape room installation that was presented at the Latitude Music Festival, and the Cambridge science Festival
Year(s) Of Engagement Activity 2019,2020
 
Description How to read research papers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Discussion with Bristol university PhD studetns about reading and analysing research papers.
Year(s) Of Engagement Activity 2018
 
Description Launchpad filming 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Filming associated with Launchpad activity
Year(s) Of Engagement Activity 2020
 
Description Lifelab 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact The event attracted a total audience of 1765
Year(s) Of Engagement Activity 2018
 
Description Member of visiting group at University of Athens Biology Department 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Part of the five-year evaluation of the Biology undergraduate and graduate programme at University of Athens. 4-member panel, one week visit,
Year(s) Of Engagement Activity 2018
 
Description Participated in Babraham Institute exhibit at Royal Society Summer Science Exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Babraham Institute prepared an exhibit - The Ageing Clock - which exemplified aspects of our ageing research portfolio for a public audience. Tjis was selcted tp be part of the prestigious Royal Society Summer Science Exhibition and I was involved in presentign this exhbit to the Public togehter with colleagues.
Year(s) Of Engagement Activity 2018
 
Description Participation in Public Engagement event on genome editing - part of the Cambridge Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A debate/dialgoue open to the pulbic entitled 'Genome editing: How far should we go'
Year(s) Of Engagement Activity 2018
 
Description Royal society summer exhibition 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Exhibits interactively presenting the work in the signalling programme where presented at the Royal Soc, audience of approx 10000 over 7 days
Year(s) Of Engagement Activity 2018
 
Description Schools day 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Schools day projects presented, executed and discussed with students
Year(s) Of Engagement Activity 2018
 
Description Schools day 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact School children from across the country attended an event at Babraham
Year(s) Of Engagement Activity 2018
 
Description Schools day event at BI 2020 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Schoold event where we presented to teachers and students a project involving human neutrophil biology.
Year(s) Of Engagement Activity 2020
 
Description Sophianum (dutch school) visit to BI 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Visit from dutch school to learn about international context of research and BI and its impacts.
Year(s) Of Engagement Activity 2020
 
Description SysMod 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I organised the 2nd meeting of the ISCB Community of Special Interest SysMod. Up to 270 people attended depending on the talk.
Year(s) Of Engagement Activity 2017
 
Description Talk to a local community group. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I spoke to a local community group about the Babraham Institute and specifically about the types of research my group performs. This was followed up by a visit of the group to the institute at a later date.
Year(s) Of Engagement Activity 2017
 
Description Visits by Teachers 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I hosted 6th form Biology teachers (one PhD trained, the other MSc trained) who were visiting my Institution during Half Term to update their knowledge as part of their CPD
Year(s) Of Engagement Activity 2016,2017,2018,2019,2020
 
Description eLife Community Webinar - Refreshing approaches to researcher evaluation 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I animated a webinar discussing various ways to bypass the traditional publication-based evaluation of researchers.
Year(s) Of Engagement Activity 2017
 
Description stem insights teachers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact STEM teachers attended an event at Babraham designed to give them insight into the process of research and careers in research.
Year(s) Of Engagement Activity 2018