Genome stability established through epigenome plasticity during ageing and rejuvenation

Lead Research Organisation: University of Cambridge
Department Name: Cancer Research UK Cambridge Institute

Abstract

Epigenetic alterations and genome instability are hallmark of ageing. However, partially due to a lack of robust models and technologies, the precise nature of these age-associated genetic and epigenetic alterations and their functional relevance in the plasticity of the phenotype are unclear. We have developed a new mouse model, in which we are able to switch on/off basal autophagy in adulthood and have found that reduced autophagy accelerates ageing and that this premature ageing phenotype can be 'segmentally' rescued by subsequent autophagy restoration. Strikingly, this 'rejuvenation' is accompanied by increased tumorigenesis. We reason that age-associated metabolic stress (reduced basal autophagy) induces genomic and epigenomic alterations, the latter of which could be either reversible or irreversible, and that those alterations collectively provide a selective pressure under optimal conditions (i.e., upon age-reversal). Taking advantage of our new immunoprecipitation-free epigenome profiling method, which is capable of assaying the epigenomic profiles from low-input tissues, we will determine the dynamic nature of the age-associated epigenetic changes and genetic mutations during ageing and age-reversal in mice. This technology will also be applied to detect the age-associated genetic changes that occur adjacent to specific epigenetic marks: we envisage that functionally relevant mutations may be enriched or diminished after the age-reversal. These approaches will provide an insight into the mechanism behind the establishment of genomic instability through these epigenomic states. In parallel, we will also develop a high-throughput single-cell epigenome sequencing platform to refine cell type specificity, which, together with our rejuvenation model, will potentially identify functional components as well as 'passenger' (epi-)genetic events in ageing at a single-cell level.

Planned Impact

Genetic instability and epigenetic drift are hallmarks of ageing but their individual and combined functional relevance are highly elusive. This is largely due to a lack suitable animal models and versatile low-input epigenomic technologies. Our proposal covers these elements, taking advantage of our new age-reversal mouse model and a single-cell epigenetic profiling technology, ChILT. These will be highly beneficial to researchers not only in the ageing field, but also any researchers who are interested in 'cellular heterogeneity'. In addition, we will utilise microfluidics to develop high throughput epigenomic techniques, which will also inspire microfluidics and microgel researchers. Since the mouse model utilises autophagy perturbation, this will also be benefit to researchers in the field of autophagy research.

We will strengthen the active collaborations between the Japanese and UK teams, or within each team. This is an interdisciplinary project, and all researchers directly involved in the projects will have a unique opportunity to further develop and extend their career paths. Through combined teaching efforts in the international team, students (both under- and post-graduates) will be exposed to cutting-edge research methods and concepts.

We aim to publish our new results in Open Access, peer-reviewed, high impact scientific journals and will regularly present our data at high-profile meetings. Genomic data will be disseminated through open access repositories such as GEO Datasets. Any new mouse models will be available to the research community. Communication of significant findings will be enhanced with support from dedicated PR teams at the University of Cambridge and CRUK, in addition to social media platforms, such as Twitter (@CRUKCambridge, @narita_lab).

Cambridge benefits from a thriving biotech environment from small-medium enterprise (SME) to large pharmaceutical companies such as AstraZenica, who currently occupy space within the CRUK CI facility. We will look to leverage the results of this study and foster academic-industrial links with segments of this community to accelerate translation into the clinic and society.
Through this study, we will actively seek to identify a molecular signature, which controls the ageing process and that is potentially pharmacologically exploitable. Therefore, our study may eventually benefit the general public.

Publications

10 25 50
 
Description Why do we age? Deterioration of our DNA, our blueprint, is one of the main hallmarks of ageing. However, partially due to a lack of robust models and technologies, the precise nature of these age-associated genetic (DNA), and epigenetic (DNA associated factors), alterations are unclear. Another emerging explanation is that cellular recycling decrease as we age. We have developed a new mouse model, in which we are able to switch on/off cellular recycling, autophagy, in adulthood and have found that reduced autophagy accelerates ageing and that this premature ageing phenotype can be 'segmentally' rescued by subsequent autophagy restoration. Strikingly, this 'rejuvenation' is accompanied by increased cancer incidence. We reason that age-associated metabolic stress (reduced basal autophagy) induces genomic and epigenomic alterations, the latter of which could be either reversible or irreversible, and that those alterations collectively provide a selective pressure under optimal conditions (i.e., upon age-reversal). Taking advantage of our new immunoprecipitation-free epigenome profiling method, which is capable of assaying the epigenomic profiles from low-input tissues, we will determine the dynamic nature of the age-associated epigenetic changes and genetic mutations during ageing and age-reversal in mice. This technology will also be applied to detect the age-associated genetic changes that occur adjacent to specific epigenetic marks: we envisage that functionally relevant mutations may be enriched or diminished after the age-reversal. These approaches will provide an insight into the mechanism behind the establishment of genomic instability through these epigenomic states. In parallel, we will also develop a high-throughput single-cell epigenome sequencing platform to refine cell type specificity, which, together with our rejuvenation model, will potentially identify functional components as well as 'passenger' (epi-)genetic events in ageing at a single-cell level.
Exploitation Route Developing simple, low-cost and high throughput epigenomic system will enhance studies involving heterogeneity: not only in ageing but also other fields. Single cell RNA-seq is becoming increasingly feasible but single cell epigenomics is still technically challenging. Our method will provide substantial flexibility to a wide range of research fields.

Our mouse model has been shared with the research community.
Sectors Pharmaceuticals and Medical Biotechnology

 
Description This project will strengthen the active collaborations between the Japanese and UK teams. This is an interdisciplinary project, and all researchers directly involved in the projects will have a unique opportunity to further develop and extend their career paths. Through combined teaching efforts in the international team, students (both undergrad & post-graduates) will be exposed to cutting-edge research methods and concepts. Cambridge benefits from a thriving biotech environment from small-medium enterprise (SME) to large pharmaceutical companies such as AstraZenica, who currently occupy space within the Cancer Research UK Cambridge Institute. We will look to leverage the results of this study and foster academic-industrial links with segments of this community to accelerate translation into the clinic and society. Through this study, we will actively seek to identify a molecular signature, which controls the ageing process and that is potentially pharmacologically exploitable. Therefore, our study may eventually benefit the general public.
First Year Of Impact 2019
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description Hiroshi 
Organisation Osaka University
Department Graduate School of Frontier Biosciences
Country Japan 
Sector Academic/University 
PI Contribution Using the monoclonal antibodies provided in our research on senescence. Dr. Kimura and I regularly discuss epigenetics projects and indeed, I will stay with him for a month as a vising scientist this year (2017).
Collaborator Contribution My group shares our experimental resources (published and unpublished) with Dr. Narita, these include ChIP-grade monoclonal antibodies against various chromatin factors and genetically encoded probes for specific histone modifications. Dr. Narita and I regularly discuss epigenetics projects and indeed, he stays with us for a month as a vising scientist this year.
Impact Publication. Mol Cell 2012.
Start Year 2009
 
Description Professor Tuomas Knowles 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution The Narita lab showed the first functional relevance for autophagy in senescence in culture. Now the lab has generated a highly unique autophagy mouse model, Atg5i (Autophagy, 2018), which will be utilised in this proposal.
Collaborator Contribution Prof. Knowles (UK Co-Investigator, BBSRC-JSPS grant; Dept Chemistry, University of Cambridge) is a world expert on biophysics and microfluidics. The Knowles lab has developed a microfluidic inDrop single-cell RNA-sequencing system, which we will adapt to our high-throughput single-cell Chromatin Integreation & Labelling (scChIL) technology.
Impact The primary impact of the project will be to increase knowledge of the genetic and epigenetic alterations that occur during ageing and age-reversal. This project will be of direct benefit to researchers working in the fields of ageing and age-related disorders as well as epigenetics. Since our mouse model uses autophagy perturbation, this will also be benefit to researchers in the field of autophagy. We will utilise microfluidics to develop high throughput epigenomic techniques, which will also inspire microfluidics and microgel researchers.
Start Year 2018
 
Description Professor Yasuyuki Ohkawa 
Organisation Kyushu University
Country Japan 
Sector Academic/University 
PI Contribution The Narita lab showed the first functional relevance for autophagy in senescence in culture. Now the lab has generated a highly unique autophagy mouse model, Atg5i (Autophagy, 2018), which will be utilised in this proposal.
Collaborator Contribution Low-throughput manual single-cell Chromatin Integration & Labelling (scChIL) has been successfully developed by the Ohkawa/Kimura team. Also, the Ohkawa lab has constant access to 26 months old mice (1-17M old mice are commercially available in Japan).
Impact The primary impact of the project will be to increase knowledge of the genetic and epigenetic alterations that occur during ageing and age-reversal. This project will be of direct benefit to researchers working in the fields of ageing and age-related disorders as well as epigenetics. Since our mouse model uses autophagy perturbation, this will also be benefit to researchers in the field of autophagy. We will utilise microfluidics to develop high throughput epigenomic techniques, which will also inspire microfluidics and microgel researchers.
Start Year 2018
 
Description Twitter channel 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Narita Lab Twitter channel was started in 2017 as a means for sharing the impact of work in the field, both from the lab and from other labs pursuing similar interests, as well as outreach activities involving members of the lab. This channel promotes sharing of published work, allowing discussion and supports other research engagement activities carried out within the Institute and in wider Cambridge.
Year(s) Of Engagement Activity 2017
URL https://twitter.com/narita_lab