Sources transmission and effects of transcriptional noise in C. elegans ageing

Lead Research Organisation: King's College London
Department Name: MRC Ctr for Developmental Neurobiology

Abstract

Ageing is a variable process affected by the environment, genes and random chance. The activity of several genes that affect lifespan and ageing are affected by the environment. The goal of this project is determine (1) what leads to fluctuations in the activity level of these genes and (2) the relationship between fluctuations in gene activity and variability in lifespan and ageing. In many species, similar genes and environmental factors contribute to ageing in similar ways. Moreover, variability in gene activity is a universal phenomenon, due to physical laws. Thus research in simple animals such as roundworms can provide general insights on these processes relevant to many species, including humans. We will use powerful experimental tools in the roundworm to dissect the causes of fluctuations in the activity of genes that affect lifespan and ageing, and discern how these fluctuations are linked to variation in lifespan and ageing. These experiments would be very difficult and expensive in other animals such as mice or humans. As an experimental system, roundworms have an established track record of providing insights to many biological processes, including human ageing. We will first measure the fluctuations in gene activity, classify the sources of these fluctuations and determine how these fluctuations are affected by food and temperature. Because these genes communicate with each other in the nervous system, we will next test how the communication process affects the fluctuations. Finally, we will determine whether fluctuations in gene activity lead to variability in ageing. To obtain the large amount of data needed for this work, we will engineer new computerised microscopy systems capable of collecting data ~50x faster than manual work by humans, and other tools to measure muscle decline with age. Together, this research will reveal how fluctuations in gene activity originate and affect ageing and lifespan.

Technical Summary

Aging varies from individual to individual due to environmental, genetic and stochastic factors. Powerful genetic and in vivo imaging tools in C. elegans offer unique advantages to study this process. Specific C. elegans neurons respond to environmental cues by changing expression of genes that modulate lifespan and ageing. The transcriptional noise in these processes is completely uncharacterized. How does environmental and transcriptional noise contribute to heterogeneity in aging and lifespan? What are the sources of noise? Are the noises shaped by signalling pathways? Addressing these questions will likely provide fundamental insights into variation in aging in both animal models and humans. Our goal is to determine how transcriptional noises in environmental responses translates to heterogeneity in lifespan and aging in C. elegans, to define factors that contribute to the noises, and to understand how feedback mechanisms shape transcriptional noises. First, we will use a high-throughput quantitative imaging approach to transcriptional noise in three genes implicated in environmental sensing and aging as a function of food, temperature and age. Next, we will identify how signalling among these genes transmit noise, and how feedback mechanisms shape noise in this system. Finally, we will determine if variance in gene expression is correlated with variance in lifespan and other age-related phenotypes, and if expression levels can predict individual ageing and lifespan phenotypes. We will assess ageing by creating new quantitative assays to investigate muscle structure and function with age. Together, these aims will create a conceptual framework for understanding how transcriptional noise created in and shaped by signalling circuits that influence lifespan, and whether these sources of noise are buffered or lead to variation in ageing and lifespan.

Planned Impact

This work will advance our knowledge on ageing, and thus has the potential to improve health in ageing populations such as the UK and USA. Similarities in the factors that influence aging indicate that our work will be relevant to mammals including humans. Our work is likely to reveal environment-dependent physiological states that cannot be predicted by genotype alone. In the long term, this may lead to individualized treatments or lifestyle modifications that promote healthy aging in humans, allowing the general populace will benefit from possibilities of enhanced health and quality of life in the face of age. Public health policy makers can use the scientific knowledge of factors that affect age-related declines to increase the effectiveness of their services and policy. A healthier population will have a positive impact on the nation's wealth and culture. The staff working on the projects will be afforded a rare multidisciplinary training opportunity combining molecular genetics, engineering, quantitative imaging and analysis. This diverse training, along with collaborative work and problem solving will be highly applicable to both academic and industry employment. This work will not only strengthen collaborative links between the UK and USA, but also highlight the synergistic interactions between engineers and biologists. Ageing, behaviour and the highly visual aspect of our research has much public appeal and can generate broader interest in science, engineering and research among the public. Dr. Ch'ng has a track record of working with a science museum (The San Francisco Exploratorium) to set up an exhibit. We will publish our work in international journals. We are committed to public engagement and will disseminate our work in layman's terms to reach a wider audience by working closely with our public relations departments. We look forward to sharing our work with the public.
 
Description We discovered how food levels are encoded in the nervous system. By looking at expression of specific genes in specific nerve cells, we can infer the food level that the animal was exposed to, and we can determine the overall accuracy of this neural code. The nervous system is largely thought to encode information using electrical activity; here we show that gene expression can also encode information in the nervous system. By combining these results with further experiments, we discovered that this ability to encode food is maintained despite big changes in temperature. These results show how biological systems can maintain their function across a range of environmental conditions, which is a fundamental feature of many complex biological systems.
Exploitation Route This work opens up studies of gene expression as an alternative mechanism of encoding information in the brain. The genes that we study that encode food levels to modulate lifespan are conserved from roundworms to humans, thus our work will also open up studies of food encoding in lifespan modulation across other species, which will have implications for human ageing as well as metabolic disorders. We are now poised to extend our analysis to additional pathways that encode food levels to modulate lifespan, and the ability of these pathways to integrate multiple environmental cues, such as food and temperature. Our understanding of how the gene networks ensure robustness of food encoding across different temperatures can help inspire similar mechanisms in AI, where similar convolutional networks are used in deep learning.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Healthcare

 
Description Our findings have been taught in several undergraduate and postgraduate lectures, and formed the basis for projects for summer undergraduates, as well as high-school interns. These provided an increased understanding of basic molecular genetics, and of the regulation of physiology. We have also trained personnel in transferable skills that allow them to contribute to other sectors in the economy (see next destination for personnel on the grant). The large-scale imaging data we acquired forms the basis for a PhD project funded by NPIF-BBSRC using deep learning to automate neuron identification in C. elegans.
Sector Creative Economy,Digital/Communication/Information Technologies (including Software),Education
Impact Types Societal,Economic

 
Description London Interdisciplinary Doctoral Programme (LIDo-DTP)
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact My interdisciplinary experience enabled me to serve effectively in the management of the London Interdisciplinary Doctoral Programme (LIDo-DTP). Currently, LIDo graduates ~50 PhD students per year, and is the largest BBSRC-funded DTP in the UK. I am a member of the LIDo Management Committee involved in the oversight and programme strategy, and the LIDo Research & Training Committee involved in PhD admissions, training, pastoral care and research projects.
URL http://lido-dtp.ac.uk
 
Description Automated High throughput Analysis of Gene Expression Codes in a Food Sensing Neuroendocrine Network
Amount £107,034 (GBP)
Funding ID BB/S507519/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
Description Project Grant
Amount £432,226 (GBP)
Funding ID BB/M00757X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2015 
End 01/2018
 
Title Automated high-throughput imaging of C. elegans 
Description In collaboration with the Lu Lab (Georgia Institute of Technology), we established a system to measure gene expression in single neurons at ~100 animals/hour. This involves integrating microfluidic devices, software controls for the microscope, image processing / analysis, and C. elegans strains with single copy integrants of transcriptional reporters bearing native regulatory sequences for a given gene. 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Year Produced 2015 
Provided To Others? Yes  
Impact Using this approach, we uncovered a gene expression based neural code for food levels in C. elegans that modulates lifespan. Our large scale approach allows us to measure the signals and variability of these responses by considering the entire response distributions. We can thus infer how accurately this neural code encodes food levels. We also discovered that the accuracy of this neural code is tuned by intercellular signalling. Serotonin limits the accuracy of this code by limiting the dynamic range of the gene expression responses, while TGF-beta promotes the accuracy of this code by reducing response variability. We have published a paper in eLife describing these novel findings. 
 
Title Image processing tools for quantifying gene expression reporters in single cells 
Description In collaboration with the Lu Lab, we have exploited the transcriptional reporters generated in our lab as training sets for image processing software that automates cell identification and fluorescence quantification of these reporter. 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Year Produced 2015 
Provided To Others? Yes  
Impact We have published a paper in PLOS Computational Biology describing this image processing method and uploaded the software to Github for distribution. 
 
Title Methods for broad range dietary restriction in C. elegans 
Description We detailed experimental protocols that allow one to assess the effects of food abundance. Prior work typically test animals over 2-3 orders of magnitude differences in food levels; our protocol spans over 11 orders of magnitude, which as allowed us to successfully identify new gene-food interactions. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2015 
Provided To Others? Yes  
Impact Our original paper describing this method has had been cited 14 times, and has been followed by a detailed description of the methods in the Journal of Visualised Experiments. 
 
Title Single copy reporters for gene expression 
Description Single copy reporters for daf-7/TGF-beta and tph-1/serotonin synthesis enzyme genes were integrated at precise regions in the genome and used for measuring expression levels of these respective genes. 
Type Of Material Technology assay or reagent 
Year Produced 2015 
Provided To Others? Yes  
Impact Published papers in eLife and Plos Computational Biology using these reagents. Provided these reagents to other labs worldwide for their analysis of gene expression. 
 
Title Applying neural decoding to gene expression data 
Description Neural decoding algorithms have largely been used for studying neural encoding via electrical activity. We applied this method to analysing gene expression in groups of single neurons from our large-scale imaging data. 
Type Of Material Data analysis technique 
Year Produced 2014 
Provided To Others? Yes  
Impact We have published a manuscript describing this analysis, which reveal how gene expression in specific neurons encode food levels to modulate lifespan. 
 
Title Modelling regulatory interactions in a gene expression circuit the encodes food 
Description Starting with our gene expression data, we have now developed simple linear models to describe the gene expression responses to different food levels. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact This work is still in the initial stage, but will likely provide deeper quantitative and mechanistic insights into the functions and design principles of our food sensing neural circuit. 
 
Description Long-term collaboration with Lu Lab 
Organisation Georgia Institute of Technology
Department Chemical & Biomolecular Engineering
Country United States 
Sector Academic/University 
PI Contribution We provide expertise in the molecular genetics of C. elegans, neurobiology and systems biology.
Collaborator Contribution The Lu lab provides expertise in image processing, microfluidics and computational analysis. They developed a high-throughput imaging system for C. elegans which allows us to perform large-scale imaging experiments not possible otherwise.
Impact This is a multidisciplinary collaboration between an engineering lab and a neurobiology lab. We developed and refine systems for high-throughput imaging of C. elegans, along with image processing pipelines. We have used it to understand how food is encoded by multi-neutron gene expression in C. elegans. At present we have published three papers.
Start Year 2015
 
Description Long-term collaboration with Lu Lab 
Organisation Georgia Institute of Technology
Country United States 
Sector Academic/University 
PI Contribution We provide expertise in the molecular genetics of C. elegans, neurobiology and systems biology.
Collaborator Contribution The Lu lab provides expertise in image processing, microfluidics and computational analysis. They developed a high-throughput imaging system for C. elegans which allows us to perform large-scale imaging experiments not possible otherwise.
Impact This is a multidisciplinary collaboration between an engineering lab and a neurobiology lab. We developed and refine systems for high-throughput imaging of C. elegans, along with image processing pipelines. We have used it to understand how food is encoded by multi-neutron gene expression in C. elegans. At present we have published two papers.
Start Year 2010
 
Description British Society for Research in Ageing Meeting (Norwich) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We gave a talk our collaborative work with the Lu Lab as part of the BBSRC-NIA transatlantic initiative, which led to many questions and discussions.
Year(s) Of Engagement Activity 2013
 
Description C. elegans Ageing Meeting (Madison, Wisconsin, USA) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a poster on our work, which drew a broad audience.
Year(s) Of Engagement Activity 2014
 
Description Interdisciplinary Approaches in C. elegans Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The seminar was attended by a wide range of biologists who were excited by our combination of experimental and computational approaches and are interested in apply them to their own work.
Year(s) Of Engagement Activity 2015
 
Description Internship for high school students 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Two high schools students from Southbank International came to perform an internship in the lab. One spent 5 months doing a full time internship after she graduated, learning genetics and molecular biology, and contributing original work to our research. The other came for a few hours weekly for 2 months, and learn molecular biology techniques.
Year(s) Of Engagement Activity 2015
 
Description Invited Seminar Speaker - Department of Cell and Developmental Biology, University College London, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I presented our work as an invited speaker to the seminar series at the Department of Cell and Developmental Biology at University College London. Afterwards, many audience members asked questions about our novel perspective on using genetic circuits in the nervous system to study information processing in biological systems. In particular, I received a lot of interested questions from PhD students, who were keen on taking a combination of computational and experimental approaches like what we have done in our work.
Year(s) Of Engagement Activity 2017
 
Description Invited Speaker - Modulation of Neural Circuits and Behavior, Gordon Research Conference, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gordon Conferences are known for being highly interactive. My talk stimulated a lot of interest from conference participants ranging from lab heads, postdoctoral researchers, and PhD students, who asked me a range of questions from aspects of the information processing functions in the neural circuits that we study to applications of our novel combination of computational approaches. At the conference, I initiated a collaboration with Prof Yun Zhang (Harvard University) and we have now applied for a NIH grant together.
Year(s) Of Engagement Activity 2017
 
Description Laboratory visit for year one students as part of the Skills for Biosciences module 
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 Undergraduate students
Results and Impact 5 students visited the lab to see our facilities. We described our research. Afterwards, students came to me asking for opportunities to work in my lab.
Year(s) Of Engagement Activity 2014,2015,2016
 
Description Lecture on Ageing to LIDo-DTP PhD students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Approximately 25 PhD students in the LIDo-DTP programme attended my class each year in the Principles of Biology course. This class provided opportunities for discussion and working out complex problems in biology using ageing as an example.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019
 
Description Lecture to 1st year PhD students in the London Interdisciplinary Doctoral Programme funded by BBSRC 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact 18-30 students attended the class, which was designed to be interactive and fostered discussion. Feedback form the students indicated that they enjoyed the topic and interactive format, as well as the general application to other areas of biology.
Year(s) Of Engagement Activity 2013,2014,2015,2016,2017
 
Description Lectures 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I cover our research in lectures to MSc and PhD students, which sparked questions and discussion about the how neuroendocrine circuits encode the environment to modulate lifespan.

Students gain knowledge and expressed interest in the systems biology of ageing and neural information processing.
Year(s) Of Engagement Activity 2011,2012,2013,2014
 
Description Lectures to Neuroscience MSc students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact 20-30 students in the Neuroscience MSci programme attended the lecture, which led to questions and discussions about how the nervous system modulates lifespan. Students came up to me afterwards to ask about working on our projects.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014,2015,2016,2017,2018
 
Description Podcast with eLife/Naked Scientist 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Did a interview about our research on how food modulates lifespan via the nervous system with Naked Scientists in conjunction with our eLife paper. This interview was recorded as a podcast that is disseminated on the Naked Scientist website and the eLife website.
Year(s) Of Engagement Activity 2014,2015,2016
URL http://www.thenakedscientists.com/HTML/interviews/interview/1001293/
 
Description Summer research students 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Two undergraduates spent 6-8 weeks doing original research in the lab, which provided first-hand research experience for them. Afterwards the students reported that it was a positive learning experience: they understood the science and the research process better, and inspired an interest in further scientific research work.
Year(s) Of Engagement Activity 2015
 
Description Symposium "New approaches in adipose tissue biology and metabolism" (Potsdam, Germany) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The generated interest in biologist in other fields who are also studying metabolism and physiology. We are now applying for EU COST funding to start a network of researchers in the field of adipose tissue biology and metabolism.
Year(s) Of Engagement Activity 2015
 
Description Talk at UCL (Developmental Neurobiology Club) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I presented our work combining experimental and computational approaches. This led to many questions from the audience and stimulated discussion afterwards in during an informal drinks session.
Year(s) Of Engagement Activity 2016
 
Description Talk to high school students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact The talk was attended by 20-30 baccalaureate students from Southbank International. The talk stimulated all kinds of questions about our research.

There was great interest in our work from the students. One of them will come to my lab to do an internship for a couple of months.
Year(s) Of Engagement Activity 2014
 
Description Visit from researcher from Chronos Therapeutics 
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 Industry/Business
Results and Impact A researcher from Chronos Therapeutics came to visit my lab to learn about our published approaches in high-throughput imaging using microfluidics, and in microscopy/imaging. We informally shared our expertise in these areas, allowing him to gain a deeper understanding of quantitative imaging, microscopy/optics, microfluidics, and automation.
Year(s) Of Engagement Activity 2016