Response to mechanical stress in ageing tissue

Lead Research Organisation: University of Manchester
Department Name: School of Biological Sciences

Abstract

The defining qualities of our cells - their physical features and function - can be determined by their surroundings, but the tissue environment can be demanding. Just as our muscles regenerate and are conditioned by exercise to maintain health, our cells have developed mechanisms to protect against damage induced by mechanical stress. Perhaps a predictable response to increased load would be to 'bulk up' the structural components within the cell. However, changes in the regulation of metabolism, the consumption of small molecules that fuel cells and form the building blocks of growth and regeneration, could be equally crucial in repairing damage. A fundamental response to stress is the production of 'chaperone' or 'heat shock' proteins within our cells. These molecular machines act to limit and reverse damage by refolding proteins unwound by stress back into functional structures. However, these mechanisms are thought to deteriorate in old age. This loss of function may be compounded by other factors affecting aging tissue: the matrix - the material in which cells are embedded - is known to stiffen with age and the tissue has a reduced potential to regenerate its cells through mechanisms such as the proliferation of stem cells.

This proposal describes work to examine the extent to which heat shock proteins are needed to protect the cytoskeleton, the network of structural proteins that give our cells the robustness necessary to withstand mechanical stressing. It will consider the consequences of an impaired stress response, as seen in our cells as they age, by blocking or removing the activity of heat shock proteins. The effects of this perturbation will be measured in model systems that reflect the conditions found in mechanically stressed tissues such as muscle and heart. These systems will also be tuned to model the changes in matrix composition and stiffness that manifest in aging tissue. I will also examine the effects of mechanical stress and impaired heat shock response on the ability of tissue to repair itself by looking at the effect on the regenerative capacity of stems cells. By better understanding the stress response, the proteins it is designed to protect and how they alter during stress and aging, I will be able to suggest better pathways to target in developing future therapies for heart and muscle wasting. Findings of this work may also caution against inhibiting the stress response machinery when treating other diseases such as cancer in patients particularly at risk of heart disease.

In recent years, scientists have developed powerful methods to characterize the genetic programing, protein contents and metabolic activities of cells. My proposal will combine these methods with new tools, developed during my post-doctoral work, to examine protein interactions and changes in 'fold' or shape. Determining which proteins interact is particularly important for this study in order to uncover the identities of the damaged 'client' proteins that heat shock proteins are targeting. Likewise, a measure of protein fold is necessary to identify which proteins have been stressed into the incorrect shape. I will look for mechanisms of regulation by searching for protein modifications in stressed systems: chemical alterations such as phosphorylation have potential as mechano-sensitive 'flags' for signaling, whereas modifications such as oxidation may be markers of an overloaded stress response machinery. A combination of these methods will give a complete picture of the cellular response to stress and thus give a new perspective on the stiff-tissue disorders associated with old age.

Technical Summary

I will test the hypothesis that heat shock proteins (HSPs) are necessary for maintenance of the cytoskeleton and to explore the consequences of the degeneration of the stress management machinery during aging on the health of stiff tissues, such as muscle and heart. Cells in stiff tissue have a well developed cytoskeleton to maintain the structural integrity of the cell. However, the role of HSPs, which can account for a significant fraction of total cellular protein, in managing mechanically-induced damage to the cytoskeleton is poorly understood. Furthermore, the loss of heat shock response in aging tissue is accompanied by changes in matrix stiffness and composition, and a loss of regenerative capacity (e.g. through stem cells); I propose to investigate the links and coupling between these factors. Initial experiments will use cardiomyocytes and mesenchymal stem cell systems, with stress applied to model systems by varying the stiffness of the underlying matrix, by applying stain-cycling and by subjecting cultures to shear flow. Later work will be expanded to test lineages derived from pluripotent stem cells, thus exploring aspects of tissue regeneration. I will consider the effects of drug inhibitors of HSP activity, such as are currently in trials for cancer therapy, examining whether such treatments have deleterious side effects in aging tissue. The cellular response to stress will be examined by a combination of proteomic, transcriptomic and metabolomic profiling tools. I will apply new techniques developed during my post-doc to study in situ protein conformation and complex formation. The first of these methods uses a cysteine-reactive probe in combination with mass spectrometry (MS), used previously to analyze folding of the nuclear cytoskeleton protein, lamin. The second method uses cross-linking and immuno-precipitation, followed by MS, to identify interacting proteins - a tool that will be essential in determining the role of HSPs in stressed cells.

Planned Impact

This project will bring potential benefits to a broad range of people in the UK and throughout the world. The work aims to deliver an understanding of how our cells deal with mechanical stress, why this is particularly important as we age and how exercise and activity may help to strengthen the resistance of our cells to damage. The need for a better understanding of these problems is particularly important in the UK, which has an aging population. It is imperative to maintain a high-quality of life for the elderly and a better knowledge of the aging process will help us manage the resources of state care. I am confident that my research can make an important and meaningful contribution to understanding stress-management and regeneration mechanisms in stiff tissue (e.g. heart and muscle) during the five year fellowship period. These findings might also suggest certain regulatory pathways as important targets for future drug developments, or warn against certain combinations of drugs (e.g. inhibitors of heat shock response in cancer treatment) in patients with predisposition towards heart disease. Results, findings and recommendations will be delivered in the final two years of the fellowship period through means of peer-reviewed publications and the presentation of conference papers. Additionally, the work will find significant interest as it seeks to develop new and emerging technologies and methodologies. Studies of proteomics, transcriptomics, metabolomics and variations on such technologies are becoming increasingly central to modern biological science and new developments are keenly anticipated.

It is important to engage the public to reinforce both the implications of this work and the continuing relevance of scientific research. I will achieve this aim by contributing to KCL's planned Science Gallery, scheduled to open on the Guy's campus in late 2015. This exciting development seeks to inspire interest from the public by bringing a combination of science, art and engineering to a projected audience of some quarter-of-a-million visitors annually. Further interaction with the public will be achieved through an active web presence and contribution to the CSCRM's planned patient and visitor outreach centre.

Publications

10 25 50
 
Description The Fellowship was granted a no-cost extension until 21-Mar-2020. A final report will be prepared and submitted by 21-JUN-2020.
Exploitation Route The Fellowship was granted a no-cost extension until 21-Mar-2020. A final report will be prepared and submitted by 21-JUN-2020.
Sectors Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description A new role for intermediate filaments in the secretory pathway
Amount £481,165 (GBP)
Funding ID BB/T000945/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2019 
End 08/2022
 
Description BBSRC ICASE PhD studentship with industrial partner Biogelx
Amount £95,042 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
 
Description BBSRC mid-range equipment, Inverted and upright confocal microscopes for multidisciplinary research
Amount £282,781 (GBP)
Funding ID BB/R014361/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2017 
End 08/2018
 
Description Directors Discretionary Fund support for post doctoral researcher Jeremy Herrera, Idiopathic Pulmonary Fibrosis
Amount £127,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2017 
End 12/2019
 
Description EPSRC-MRC CDT Regen. Med. PhD studentship
Amount £91,956 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 04/2016 
End 04/2019
 
Description Helen Muir Fund -- "Visit to exchange methods for quantification of ECM changes in ageing brain tissue"
Amount £1,221 (GBP)
Organisation University of Manchester 
Sector Academic/University
Country United Kingdom
Start 02/2019 
End 03/2019
 
Description ISSF-3 Cross-Faculty Consortia Fund "Towards strategic oncology funding at the University of Manchester - developing models to understand the dynamic tumour microenvironment."
Amount £284,812 (GBP)
Funding ID 204796/Z/16/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2019 
End 03/2021
 
Description Institutional Strategic Support Fund - Research Consortia
Amount £49,499 (GBP)
Funding ID 105610/Z/14/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2015 
End 05/2016
 
Description Institutional Strategic Support Fund - Single Cell
Amount £11,260 (GBP)
Funding ID 105610/Z/14/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2015 
End 09/2016
 
Description Quantitative and Biophysical Biology Doctoral Training Programme Studentship
Amount £119,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2017 
End 09/2020
 
Description Summer Research Experience Placement, Molecular chaperone regulation in the cellular mechano-response
Amount £2,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 06/2017 
End 08/2017
 
Description University of Manchester BBSRC DTP Studentship
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2019 
End 09/2023
 
Description University of Manchester CASE DTP Studentship with industrial partner SCIEX
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2019 
End 09/2023
 
Description University of Manchester Wellcome QBB Studentship
Amount £120,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2019 
End 09/2022
 
Description Walgreens Boots Alliance -- Skin Ageing Project
Amount £1,716,486 (GBP)
Organisation Walgreens Boots Alliance, Inc 
Sector Private
Country United States
Start 01/2019 
End 12/2023
 
Description Wellcome Multi-User Equipment Grant
Amount £390,000 (GBP)
Funding ID 218306/Z/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2020 
End 01/2023
 
Description Wellcome Trust Centre for Cell-Matrix Research
Amount £4,975,692 (GBP)
Funding ID 203128/Z/16/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2016 
End 10/2021
 
Title BayesENproteomics 
Description For label-free proteomics, multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in levels of the parent protein. We compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein as well as providing pathway-level fold changes. Our results show that BayesENproteomics can quantify changes to proteins, PTMs and pathways across a broad dynamic range with greater accuracy and sensitivity than other regression methods. 
Type Of Material Computer model/algorithm 
Year Produced 2018 
Provided To Others? Yes  
Impact Technology underpins mass spectrometry analysis in papers produced by the lab and our collaborators. 
URL https://github.com/VenkMallikarjun/BayesENproteomics
 
Title Mass spectrometry proteomics data 
Description All mass spectrometry data associated with the Fellowship has been uploaded to the PRIDE database. 2020 Update: we have continued to upload all proteomic and transcriptomic data associated with publications and submissions to the BioRxiV preprint server. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Too early to tell how this data will be utilised by other researchers. 
URL https://www.ebi.ac.uk/pride/archive/
 
Title RNA-Seq transcriptomics data 
Description EMBO-EBI database of RNA-Seq data (ArrayExpress) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Data accompanies paper: Gilbert et al. (Nat Commun, 2019) 
URL https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7925/
 
Description A new role for intermediate filaments in the secretory pathway 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise on intermediate filament proteins, particularly in how they influence mechanical properties and the cell nucleus.
Collaborator Contribution Expertise in cell secretory pathways, mathematical modelling and biochemistry.
Impact Basis of successful application for BBSRC responsive mode funding. Hired post-doctoral research associate, starting 2020. Multi-disciplinary: cell biology; biophysics; biochemistry.
Start Year 2019
 
Description Age-associated changes in the mechanical properties of brain tissue 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Mass spectrometry proteomics and bioinformatic methods to analyse the composition of tissues (brain) and extracellular matrix secreted by cells in culture.
Collaborator Contribution Ageing is the leading cause and the major risk factor of neurodegenerative disorders, which is driven and accelerated by the resident progenitor cell arrest causing a diminished regenerative response. Emerging research supports the notion that the ageing brain extracellular matrix (ECM) not only provides structural support but also directs progenitor cell fate and function. Concurrently, the ECM biochemical and biophysical properties modulate the ageing progenitor cell phenotype. However, the mechanisms underlying changes in ECM properties and their link to deregulation of progenitor cell maintenance are not well understood. The purpose of the collaboration between Swift and Franklin groups is to disentangle the dynamic ECM changes by using mass spectrometry proteomics to analyse ECM extracts from brains of different ages. The first objective of the project will be to quantify the changes to ECM in samples of ageing rat brain. Furthermore, the Franklin lab has recently established a link between glial cells called astrocytes and an ageing ECM phenotype. When cultured on substrates that mimic the biophysical properties of the ageing brain, astrocytes produce ECM which is inhibitory to the resident progenitor cells. Therefore, the second objective will be to perform proteomics analysis of the ECM produced by astrocytes on substrates mimicking biophysical properties of brains from different ages. The end goal of the collaboration is to understand how the ECM changes with age and how it contributes to the ageing of brain progenitor cells. This, in turn, will provide attractive new therapeutic targets for the ageing brain disorders.
Impact Multi-disciplinary: cell biology and biophysics. A two-week visit to Manchester by a researcher from Cambridge, for methods transfer, was paid for by the Helen Muir Fund (£1.2k).
Start Year 2019
 
Description Cancer microenvironments 
Organisation Manchester BIOGEL
Country United Kingdom 
Sector Private 
PI Contribution Project proposes development of a pipeline to recreate mechanical, topological and compositional aspects of primary tissues in vitro. This draws on technology developed during the Fellowship to characterise primary tissues by mass spectrometry, and to produce stiffness-controlled cell culture systems that reproduce tissue mechanics.
Collaborator Contribution This is a cross faculty, multi-discipline application aimed at modeling the dynamic tumour microenvironment. By combining our diverse expertise in immunology, cancer biology, ECM, biomaterials, bioinformatics and drug discovery, we have an opportunity to develop novel approaches to understand and treat cancer. During the initiation and progression of cancer, fundamental changes occur to cellular microenvironments, irrespective of the tissue affected by the disease. These changes include remodelling of the biochemical and biomechanical properties of the extra-cellular matrix (ECM), the formation of hypoxic conditions and the recruitment of cancer-associated inflammatory cells (CAICs). We propose to develop a pipeline to study the dynamic cancer microenvironment. We will focus on glioma and breast cancer, in which our expertise will allow development and validation of the pipeline, and where we have established access to patient material.
Impact Multi-disciplinary: cell biology, biophysics, bioengineering. Collaboration with industrial partner Manchester BioGel and to support PhD studentship "Using 3D-matrices to understand mammary epithelial function". Wellcome Trust Institutional Strategic Support Fund (ISSF) backing (£284k) that will pay for three years of post-doc salary, materials and analysis costs. 2020 Update: two post-doctoral researchers have been hired and are working on brain and breast extracellular matrix characterisation, and development of 3D in vitro models. We are preparing a methods paper on the brain proteomics.
Start Year 2018
 
Description Consequences of LINC complex knockouts on mechanotransduction in mouse fibroblasts 
Organisation University of Minnesota
Country United States 
Sector Academic/University 
PI Contribution To characterise the mechano-responsiveness of mouse fibroblast cell lines with perturbations to protein complexes that tether nucleus and cytoskeleton, using stiffness-controlled substrates, microscopy and mass spectrometry.
Collaborator Contribution Provision of mouse fibroblast cell lines with knockout of linker of nucleo- and cytoskeleton (LINC) complex proteins such as SUN2.
Impact Newly established collaboration: no outputs or outcomes to report yet.
Start Year 2018
 
Description Determining how loss of cell-matrix regulation causes Idiopathic Pulmonary Fibrosis (IPF) 
Organisation Wellcome Trust
Department Wellcome Trust Centre for Cell-Matrix Research
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Co-supervise a project a new research collaboration to look at mechano-transduction pathways in fibrosis. Swift lab will provide expertise in mass spectrometry and morphometric analysis of cells in culture and under mechanical perturbation.
Collaborator Contribution Other members of the project management team provide expertise on immunology and mechanotransduction. Partners will provide primary tissue samples for mechanical and proteomic analysis.
Impact Funding provided by WT Director's Discretionary Fund to pay salary of post-doc and research costs for three years. 2019 Update: Herrera J, Forster C, Pengo T, Monteres A, Swift J, Schwartz M, Henke CA, Bitterman PB. Idiopathic Pulmonary Fibrosis: Registration of extracellular matrix components comprising the fibroblastic focus. JCI Insight (2019) 4(1), e125185. 2020 Update: methods paper on laser-capture microdissection of lung tissue was added to BioRxiV, currently under revision for Clinical Proteomics (Herrera et al. 2019).
Start Year 2017
 
Description Directing stem cell fate using tuneable biomimetic peptide hydrogels 
Organisation Biogelx
Country United Kingdom 
Sector Private 
PI Contribution Expertise in characterisation of pathways in mesenchymal stem cells: mechanobiology, mass spectrometry, transcriptomics, microscopy. Co-supervision of BBSRC ICASE PhD studentship (worth approx. GBP 95k over four years).
Collaborator Contribution BioGelx (Glasgow, UK) will provide an industrial placement for the PhD candidate and provide samples for testing. Primary supervisor Dr. Stephen Richardson will provide expertise on working with primary cells.
Impact Training to be provided as part of a BBSRC ICASE Studentship. Project combines aspects of biophysics and biology, with industrial and biomedical applications.
Start Year 2016
 
Description Directing stem cell fate using tuneable biomimetic peptide hydrogels 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in characterisation of pathways in mesenchymal stem cells: mechanobiology, mass spectrometry, transcriptomics, microscopy. Co-supervision of BBSRC ICASE PhD studentship (worth approx. GBP 95k over four years).
Collaborator Contribution BioGelx (Glasgow, UK) will provide an industrial placement for the PhD candidate and provide samples for testing. Primary supervisor Dr. Stephen Richardson will provide expertise on working with primary cells.
Impact Training to be provided as part of a BBSRC ICASE Studentship. Project combines aspects of biophysics and biology, with industrial and biomedical applications.
Start Year 2016
 
Description Effects of ageing on composition and mechanical properties of skin 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution We developed and applied mass spectrometry proteomics profiling to young, old and ovariectomy mouse skin samples, and made further comparisons to in vitro model systems.
Collaborator Contribution Characterisation of the mechanical properties of ageing skin. 2017 update:- characterisation of mouse skin mechanics and composition has been expanded to include a mouse model for Weill-Marchesani syndrome (ADAMTS10 mutation).
Impact Three manuscripts in preparation. Grant proposal under consideration at MRC. Multi-disciplinary: biology, bioengineering, biophysics. 2019 Update: methods established will be used in a partnership with Walgreen Boots Alliance (WBA).
Start Year 2015
 
Description How does ageing affect homeostasis in the marrow niche? 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Development of mass spectrometry methods to analyse the secretome of in vitro cell systems.
Collaborator Contribution Expertise in handling and analysis of haematopoietic stem cells (HSCs), for example by flow cytometry.
Impact Mass spectrometry methods development. Multi-disciplinary: Biology, Immunology, Biophysics.
Start Year 2015
 
Description Mechanisms of mechanical regulation of stem cell fate (investigation by proximity tagging proteomics) 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution This study will identify interacting networks of proteins responsible for transmission and transduction of mechanical signalling in cells. My laboratory will contribute experience in mass spectrometry proteomics and mechanobiology of the nucleus.
Collaborator Contribution Partnering laboratory at the University of Manchester has collected preliminary data using bioID proximity labelling strategies and has world-leading expertise in cell adhesion complexes.
Impact Basis of applications for BBSRC responsive mode and faculty strategic funding, currently under consideration. Multi-disciplinary: cell biology, biophysics, bioinformatics.
Start Year 2019
 
Description Pathomolecular mechanisms of intracerebral haemorrhage: functional analysis of collagen IV variants. 
Organisation University of Glasgow
Country United Kingdom 
Sector Academic/University 
PI Contribution The Swift lab will apply methods we have developed for mass spectrometry proteomics to analyse the matrix of brain tissue from mice with collagen IV mutations associated with intracerebral haemorrhage (ICH).
Collaborator Contribution "15% of stroke cases are due to intracerebral haemorrhage (ICH), and there is a need for specific treatments, indicating increased knowledge of its genetic and pathomolecular basis is required. Collagen IV is an extracellular matrix component that provides structural support to blood vessels and affects cell behaviour. Rare mutations in COL4A1 or COL4A2 (collagen IV alpha chain 1/2) cause familial ICH and importantly we have now established common COL4A2 variants are a risk factor for sporadic ICH, but their prevalence and disease mechanism are unknown. Here we will use sequence analysis of a large cohort of sporadic deep ICH cases to establish the identity and prevalence of novel rare mutations and common variants in COL4A1/4A2 in ICH. Functional analysis of selected identified common variants and novel rare mutations (e.g. predicted to enhance or decrease expression, alter protein composition) will be used to address our hypothesis that ER stress is a shared mechanism between sporadic and familial ICH: ER stress results from intracellular retention of secreted proteins, can be pathogenic when chronic and be modulated by FDA- approved compounds. We will address this using a combination of genome editing, molecular cell biology and complementary -omics approaches, and in so doing provide unparalleled insight into the nature of compositional matrix defects and ER stress response, and their effects on downstream cellular pathways, leading to endothelial cell dysfunction. Parallel analysis of "ER stress only" models will inform on the relative contribution of ER stress. Importantly, the relevance of identified mechanisms will be verified in brain samples of mice and patients with ICH. This will transform our knowledge of the genetic and pathomolecular basis of ICH in the general population, inform on patient stratification based on disease mechanism, and highlight future therapeutic avenues including the potential repurposing of FDA-approved compounds."
Impact Grant proposal funded by the MRC. 2020 Update: A follow-up grant proposal will be submitted to MRC summer 2020.
Start Year 2017
 
Description Remodelling of cells and extracellular matrix in response to uniaxial and biaxial strain 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Provide advice on sample preparation and analysis of data produced from mass spectrometry proteomics. Develop computer code to analyse proteomics data.
Collaborator Contribution Construction and characterisation of three-dimensional cell culture models that can be subjected to strain. Characterisation methods include antibody based staining and electron microscopy.
Impact The project brings together expertise in biology and bioengineering. It will form the basis of a paper and future applications for funding.
Start Year 2016
 
Description Systematized recoil of the retracting rear in migrating cells 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in producing stiffness-controlled hydrogel substrates.
Collaborator Contribution Characterisation of cells; molecular biology; microscopy.
Impact The work combines biophysics with molecular biology. Preliminary data will be used in support of future grant applications. Opportunity of transfer of expertise, with my group learning methods for time-resolved microscopy. 2019 Update: Hetmanski JHR, de Belly H, Nair RV, Sokleva V, Dobre O, Cameron A, Gauthier N, Lamaze C, Swift J, del Campo A, Paluch E, Schwartz J-M, Caswell PT. Membrane tension coordinates rear retraction in durotaxis and 3D cell migration. (2018) http://dx.doi.org/10.2139/ssrn.3249468 2020 Update: Paper published in Dev Cell.
Start Year 2016
 
Description The effect of circadian rhythm on the matrix of ageing cartilage 
Organisation AB SCIEX
Country United States 
Sector Private 
PI Contribution Application of analysis software developed by lab member Venkatesh Mallikarjun to mass spectrometry proteomic datasets of mouse cartilage tissue during circadian cycle.
Collaborator Contribution Development of mouse models to study effects of circadian cycle in tissues.
Impact Manuscript submitted 2018: Yeung C-YC, Garva R, Pickard A, Chang J, Holmes DF, Lu Y, Mallikarjun V, Swift J, Adamson A, Calverley B, Meng QJ, Kadler KE. Circadian clock regulation of the secretory pathway. BioRxiv.org (2018) https://doi.org/10.1101/304014 BBSRC CASE Studentship with industrial partner Sciex Ltd is based on this project. We have nominated a student to be interviewed for this position to start in September 2019. 2020 Update: Manuscript submitted in 2018 is now published in Nat Cell Biol (Chang et al 2020); another manuscript has been uploaded to the BioRxiv preprint server on circadian rhythm in cartilage (Dudes et al 2019). Student has been recruited to the BBSRC CASE position, starting September 2019.
Start Year 2016
 
Description The effect of circadian rhythm on the matrix of ageing cartilage 
Organisation Wellcome Trust
Department Wellcome Trust Centre for Cell-Matrix Research
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Application of analysis software developed by lab member Venkatesh Mallikarjun to mass spectrometry proteomic datasets of mouse cartilage tissue during circadian cycle.
Collaborator Contribution Development of mouse models to study effects of circadian cycle in tissues.
Impact Manuscript submitted 2018: Yeung C-YC, Garva R, Pickard A, Chang J, Holmes DF, Lu Y, Mallikarjun V, Swift J, Adamson A, Calverley B, Meng QJ, Kadler KE. Circadian clock regulation of the secretory pathway. BioRxiv.org (2018) https://doi.org/10.1101/304014 BBSRC CASE Studentship with industrial partner Sciex Ltd is based on this project. We have nominated a student to be interviewed for this position to start in September 2019. 2020 Update: Manuscript submitted in 2018 is now published in Nat Cell Biol (Chang et al 2020); another manuscript has been uploaded to the BioRxiv preprint server on circadian rhythm in cartilage (Dudes et al 2019). Student has been recruited to the BBSRC CASE position, starting September 2019.
Start Year 2016
 
Description The mechanics of the collagen fibrillar network in ageing cartilage 
Organisation Queen Mary University of London
Department Centre for Environmental and Preventive Medicine
Country United Kingdom 
Sector Hospitals 
PI Contribution The project aims to correlate the mechanical properties of ageing cartilage with changes in tissue composition. The Swift lab will use mass spectrometry proteomics to quantify protein content.
Collaborator Contribution Partners at QMUL have combined small-angle X-ray scattering (SAXS) with in situ mechanical testing to measure how the collagen fibrillar network in cartilage responds to loading. This will allow nanoscale characterisation of how ageing cartilage responds to mechanical stress.
Impact The team of collaborators currently have a grant proposal under consideration for BBSRC funding. Multi-disciplinary:- physics, engineering and biology.
Start Year 2017
 
Description Time-resolved analysis of stem cell responses to changes in substrate stiffness 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution To characterise interactions between stem cells and substrates with dynamic, tuneable mechanical properties as a model of ageing or diseased tissue.
Collaborator Contribution Development of polymeric substrates with mechanical properties that can be reversibly softened or stiffened by exposure to UV-light or temperature variation, thus mimicking physical changes that occur in ageing and disease.
Impact *Lee I-N, *Dobre O, Richards D, Ballestrem C, Curran JM, Hunt JA, §Richardson SM, §Swift J, §Wong LS. Photo-responsive hydrogels with photoswitchable mechanical properties allow time-resolved analysis of cellular responses to matrix stiffening. ACS Appl Mater Interfaces (2018), 10 (9), 7765-7776. Hiring and training of Research Assistant OD. Multi-disciplinary: tissue engineering; physical and materials sciences (chemistry); cell biology.
Start Year 2015
 
Description WBA Basic Science Discovery -- Skin Ageing 
Organisation Croda International
Country United Kingdom 
Sector Private 
PI Contribution The work packages described in the following are underpinned by mass spectrometry proteomics methods to characterise changes in the composition of skin during ageing. These experiments will be performed in collaboration with the Swift lab, using methods and analysis that we have developed over the BBSRC Fellowship.
Collaborator Contribution The basic science discovery programme will develop new methods to characterise skin changes in ageing and health. These, and existing methods, will then be used to better understand the mechanisms which drive ageing and damage and to hence develop new, WBA exclusive, treatments. We will develop methods to characterise the influence of ageing, disease and therapeutic interventions on skin composition (proteome, transcriptome and elemental analysis) and chemistry (by Raman and mass spectrometry spectroscopy). The five year work programme is divided into five complimentary streams: (i) to characterise the baseline regulation and composition of healthy skin; (ii) to characterise chemical signatures of skin damage and repair; (iii) to examine the roles of proteases as mediators of repair and the immune system, and how these pathways could be modulated therapeutically; (iv) to test specific anti-ageing formulations developed by WBA and Sederma; (v) to examine the role of circadian rhythm in skin regulation.
Impact Multi-disciplinary: biology, biophysics, biochemistry.
Start Year 2018
 
Description WBA Basic Science Discovery -- Skin Ageing 
Organisation Walgreens Boots Alliance, Inc
Country United States 
Sector Private 
PI Contribution The work packages described in the following are underpinned by mass spectrometry proteomics methods to characterise changes in the composition of skin during ageing. These experiments will be performed in collaboration with the Swift lab, using methods and analysis that we have developed over the BBSRC Fellowship.
Collaborator Contribution The basic science discovery programme will develop new methods to characterise skin changes in ageing and health. These, and existing methods, will then be used to better understand the mechanisms which drive ageing and damage and to hence develop new, WBA exclusive, treatments. We will develop methods to characterise the influence of ageing, disease and therapeutic interventions on skin composition (proteome, transcriptome and elemental analysis) and chemistry (by Raman and mass spectrometry spectroscopy). The five year work programme is divided into five complimentary streams: (i) to characterise the baseline regulation and composition of healthy skin; (ii) to characterise chemical signatures of skin damage and repair; (iii) to examine the roles of proteases as mediators of repair and the immune system, and how these pathways could be modulated therapeutically; (iv) to test specific anti-ageing formulations developed by WBA and Sederma; (v) to examine the role of circadian rhythm in skin regulation.
Impact Multi-disciplinary: biology, biophysics, biochemistry.
Start Year 2018
 
Description microRNA-dependent regulation of biomechanical genes mediate tissue mechanical homeostasis 
Organisation Yale University
Country United States 
Sector Academic/University 
PI Contribution Mass spectrometry analysis of samples from labs of Martin Schwartz (Manchester and Yale Universities) and Stefania Nicoli (Yale University).
Collaborator Contribution High throughput assays of microRNA activity.
Impact Moro A, Driscoll T, Armero W, Boraas LC, Kasper D, Baeyens N, Jouy C, Mallikarjun V, Swift J, Sang JA, Lee D, Zhang J, Gu M, Gerstein M, §Schwartz M, §Nicoli S. microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis. Nat Cell Biol (2019) 21(3), 348-358. Multidisciplinary: cell biology and biophysics.
Start Year 2017
 
Description Healthy Ageing and Technology Innovation Lab 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Academics from the University of Manchester worked with industry representatives to design solutions to problems identified in an ageing population. Joe Swift and Hamish Gilbert (Fellowship post-doc) collaborated with Unilever to develop a pitch for seed funding to investigate the effects of skin ageing on mental well-being. The event concluded with a "Dragons' Den"-style presentation.
Year(s) Of Engagement Activity 2019
 
Description Manchester Body Experience 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Raised awareness of biomechanics in disease (specifically, mechanical changes in tissue during breast cancer).

Engaging children (ages 4-11) and their parents with current questions in scientific research; positive feedback is noted on the website (link below). The event is repeated annually and I would like to increase my lab's participation.
Year(s) Of Engagement Activity 2014
URL http://www.ls.manchester.ac.uk/schoolsandcommunity/communityeventhighlights/bodyexperience/
 
Description PhD student EA awarded Widening Participation Fellowship & involvement with SIAM Three Minute Thesis competitions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact EA is a PhD student in my laboratory (Wellcome QBB programme). She has been awarded a University of Manchester Widening Participation Fellowship. She has additionally been involved in the SIAM Three-Minute Thesis competition, winning local and regional competitions.
Year(s) Of Engagement Activity 2019,2020
 
Description Why are bones strong and brains squishy? Manchester Museum 2016/17 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact The lab (five members) developed and presented a new exhibit for the Manchester Body Experience at the Manchester Museum. The exhibit featured hands-on activities designed to emphasise the importance of 'biophysics' in understanding how our bodies function. The event was attended by hundreds of members of the public (largely primary-school children and their families).
Year(s) Of Engagement Activity 2016,2017
URL https://storify.com/CeriHarrop/body-experience