A multidisciplinary approach to studying crypt-villus homeostasis and regeneration in the intestinal epithelium

Lead Research Organisation: University of Oxford
Department Name: Mathematical Institute

Abstract

We aim to study the mechanisms regulating the continuous renewal of the intestinal epithelium in physiological conditions and its recovery following injury. This understanding will contribute to the identification of strategies for maintaining the health and preventing diseases of the gastrointestinal (GI) tract.

The intestinal epithelium forms the first barrier between the gut lumen and the body. The epithelial cell monolayer lining the small intestine has a complex architecture, with invaginations into the intestinal wall called crypts located between finger-like projections into the lumen called villi. Several crypts surround a villus forming a crypt-villus unit; each crypt is involved in more than one unit, providing cells to more than one villus. Intestinal stem cells located at the base of each crypt proliferate and give rise to epithelial cells, which migrate to the tip of the neighbouring villi, from where they are shed into the gut lumen. In the healthy intestine, the dimensions and cell number on this crypt-villus unit remain remarkably constant during adult life. This implies that the rate of cell shedding from the villus tip is balanced by the rate at which new cells produced within the supporting crypts migrate from these crypts onto the villus.

Therefore, the maintenance of the functional integrity of the intestinal barrier requires a tight coordination of the numbers of crypts and villi, cell production in the crypts, cell migration along the crypt-villus axis, and cell shedding from the villus. Failure of regulation of these processes may result in cells escaping normal growth controls and tumour formation. Inflammatory processes are characterized by enhanced cell shedding that may fail to be compensated by the increase of cell proliferation within the crypts leading to the loss of the integrity of the intestinal barrier. In addition, the intestinal lesions in coeliac disease reflect a severe alteration of the balance between cell apoptosis on the villi and cell proliferation within the crypts. The subject of this proposal is gaining insight into the mechanisms underlying the maintenance of the equilibrium between crypts and villi in the intestinal epithelium and how this balance is regained after injury. This is essential to maintain the health of the GI tract and to develop novel preventive strategies for intestinal pathologies such as tumourigenesis, ulcerative inflammatory processes and coeliac disease.

However, such questions cannot currently be resolved by experimentation alone, since it is not possible to collect in vivo time course imaging of entire crypt/villus units over prolonged periods. To this end, mathematical and/or computational modelling represents an alternative framework within which to conduct in-silico experiments that complement the in-vitro experimental approaches. We plan to integrate computational models with experimental data to elucidate the biophysical mechanisms that may coordinate cell proliferation within the crypt, cell migration along the crypt-villus axis and cell shedding from the villus in order to preserve the numbers and size of crypts and villi within the small intestine. Computational simulations of the validated models will then be performed to predict the dynamics of epithelial recovery after injury. We will also identify potential early markers of altered epithelium.

Technical Summary

Using a combination of computational modelling and experimental measurements, we aim to understand the tight coordination between villi and crypts during the continuous renewal of the small intestinal epithelium and how the equilibrium is recovered after perturbations.

Experimental measurements will be gathered from healthy, altered and injured intestine. Counts and morphometric measurements of crypts and villi, cell proliferation, migration and shedding rates, cell size and cell density will be experimentally determined along the much studied murine small intestine in control conditions as well as after blocking cell proliferation by cytosine arabinoside, enhancing cell proliferation by glucagon-like peptide-2 and injuring the epithelium by bacterial lipopolysaccharide.

The spatio-temporal modelling of cell dynamics in the crypt-villus unit will be modelled by building on the individual cell models (IBMs) for the crypt already developed by the applicants. While it is feasible to simulate an IBM of one crypt-villus unit in a reasonable time, simulations comprising large populations of villi and crypts are likely to become computationally intractable. We will therefore investigate the relationship between populations of crypts and villi at the macroscopic level using 'mean-field' models. We will use the existing resources of Chaste, a software library for modelling soft tissues, to implement models and as a simulation suite.

Importantly, theory and experiments will be intertwined through the "predict-test-refine-predict" cycle to develop and test hypotheses regarding the regulation of cellular proliferation and migration along the crypt-villus axis, the mechanism of intestinal cell shedding and apoptosis and the relationship between these cellular phenomena and the maintenance of crypts and villi. Model simulations will be used to generate predictions on epithelium recovery after injury that will be tested experimentally, leading to refinement of the mode.

Planned Impact

This project proposal is targeting gut health to improve health and well-being across the life span by a multidisciplinary approach that integrates theoretical and experimental approaches. This is specifically targeted by the "Systems approaches to the bioscience" theme of the BBSRC research strategy priority "Exploiting new ways of working". Our project, specifically responds to the cross-council priority "Lifelong health and well-being" and the theme "Ageing research: lifelong health and well-being" of the priority "Basic bioscience underpinning health". BBSRC strategic priorities are devised to increase the impact of the BBSRC science on worldwide (and specifically on the UK) society and economy.

Our research focuses on understanding the basic mechanisms of regulation between intestinal villi and crypts and how their balance is recovered after injury and damage. As a result, we expect to gain continued and greater understanding of the fundamental aspects of this biological system. Our beneficiaries in the short term will be mainly those in the academic community while there is number of potential applications with economic and societal impacts in the long term.

Impact on Society

The public will be the first long term beneficiary of our research through enhanced gut health, gut tolerance to perturbations and recovery after injury, and the early detection of risk factors for GI-tract disease, leading to improved lifelong wellbeing and quality of life.
NHS and specialist services (e.g. gastroenterologists) will benefit from science-based advice and evidence to support improved strategies for a healthier gut. The output of our research may lead to develop novel prevention practices for intestinal tumourigenesis, chronic or inflammatory processes, intestinal ulcers and coeliac disease.
Enhancing the professional skills base. The staff working on the project and the participants in the workshops will be trained in a highly interdisciplinary area of knowledge. Knowledge in developing computing and modelling tools for Medicine and Biology is increasingly relevant to the public and private employment sector.

Inspiring young people. The integration of theoretical and experimental approaches that we propose, provides excellent opportunities for school and undergraduate science students to understand how biological systems work as a whole and to grasp the importance of multi disciplinary approaches to address unanswered scientific questions, contributing to the BBSRC public engagement priority by addressing young people in mathematics for biology.

Public opinion and policy makers. The generation of robust computing tools for in silico simulation of gut behaviour may provide an alternative platform to minimise the use of animals in research. Potentially, this will help policy makers address some public opinion concerns about animal testing.

Impact on Economy

A decreased UK Public spend might be envisaged from the reduced pressure on Health and Social care systems resulting from an improved gut health and wellbeing.

Industry, such as Biomedical industries and Biopharmaceutical companies, may benefit from strong evidence-based advice that may lead to the development of novel therapies and early markers for intestinal tumourigenesis, chronic inflammatory processes and coeliac disease. The output of this research on the kinetics of the intestinal epithelium renewal and regeneration might provide information to develop strategies to reduce the intestinal side effects of drugs treatments such as the highly used non-steroidal anti-inflammatory drugs. The small and large intestine account for 20-40% of all drug side effects [Best Pract Res Cl Ga 2010 24:133-141]. Thus, there is great potential to translate new ideas and results into exploitable outcomes and further strategic developmental proposals (EC, Human Frontiers programme) as well as attracting R&D investment from Global business into the UK economy.

Publications

10 25 50
 
Description The intestinal epithelium is a single layer of cells which provides the first line of defence of the intestinal to bacterial infection. Cohesion of this physical barrier is supported by renewal of epithelial stem cells, residing in tube-like invaginations called crypts, and by crypt cell migration onto protrusions called villi; if this mechanism is faulty, chronic inflammation may result. The impact that excessive or misplaced epithelial cell death may have on villus cell migration is currently unknown. In our research, we combined experimental studies with mathematical and computational modelling to investigate the mechanisms by which cells respond to disruption (acute or chronic) in the barrier. Statistical analysis of our models fitted to data from cell-tracking revealed that acute inflammatory cell death has a transient effect on epithelial cell dynamics, whereas cell death caused by chronic inflammation causes a delay in the accumulation of cells onto the villus. Furthermore, we found that the results depended on where in the intestine the injury was initiated. Hence, this investigation highlights which injuries (acute or chronic) may be regenerated and which cause disruption of healthy epithelial regulation. Furthermore, using a suite of mathematical models of increasing complexity we have extended our previous work to obtaina detailed cell-based mathematical model which can reproduce these results in a crypt-villus geometry. This model can now be used to perform in silico experiments to investigate how different interventions may affect crypt-villus regeneration and, in so doing, to generate testable predictions while also reducing the number of experiments that need to be carried out.
Exploitation Route Our results have implications for how wound healing occurs in the gut. Moreover, our validated computational model offers the potential for us to make testable predictions, allowing us to investigate how various interventions may affect crypt-villus regeneration, to identify those predictions that merit further experimental validation and, in so doing, to reduce the number of experiments we need to carry out.
Sectors Healthcare

 
Description Collaboration on statistical analysis with Dr Sarah Filippi (Imperial College, London) 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution We provided experimental data and models and she helped us with parameter estimation.
Collaborator Contribution She helped us with parameter estimation.
Impact One paper submitted (see publications) and one about to be submitted.
Start Year 2016
 
Description Keynote Lecture, Modern Drug Development - a Multi-scale Approach, RWTH Aachen University, Aachen, November 18, 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Keynote lecture to a group involving researchers from Bayer. This was in my role as member of the Scientific Advisory Board JRC Computational Biomedicine at RWTH Aachen.
Year(s) Of Engagement Activity 2016
URL https://www.mse.rwth-aachen.de/global/show_document.asp?id=aaaaaaaaaasveuv
 
Description Quantitative Systems Pharmacology: Is there a case for model reduction? UK QSP Satellite Meeting, Department of Physiology, Anatomy and Genetics, University of Oxford, June 29th, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk which led to discussions on model reduction and parameter identifiability - two of the major problems in mathematical biology at the moment.
Year(s) Of Engagement Activity 2016
 
Description School visit: Parker A., Pin C (2014) Mathematics in the Gut. Inside Science. 
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 Talk to GCSE students.
Year(s) Of Engagement Activity 2014
 
Description Bridging scales in models of cell to tissue behaviour: recent progress and future challenges; SEB Symposium, Oxford 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Daniele Muraro presented a talk on his research.
Year(s) Of Engagement Activity 2016
 
Description Public Engagement: Norwich Science Festival 2016 (Pin C., Parker A., Vaux L) 
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 Conveying new scientific ideas to 100s of members of the public.
Year(s) Of Engagement Activity 2016
URL http://norwichsciencefestival.co.uk/about/norwich-science-festival-gallery/
 
Description Public engagement: Parker A., Pin C., Vaux L. (2015) Science in Norwich day. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Conveying new scientific advances to members of the public.
Year(s) Of Engagement Activity 2015
 
Description School visit: Parker A (Norwich) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Mathematics, stem cells, and the gut/STEM careers session at a sixth form centre.
Year(s) Of Engagement Activity 2014,2016
 
Description Workshop on multiscale modelling approaches for gastrointestinal health and disease (Byrne and Fletcher: Oxford) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tissue renewal and regeneration are crucial for the survival and longevity of multicellular organisms. In the gut, a tightly coordinated programme of cell proliferation, migration and differentiation begins in glands called crypts. Mutations in crypt cells contribute to over 90% of colorectal cancers (CRC), one of the most common types of cancer. The past decade has witnessed remarkable progress in experimental studies of gut maintenance and CRC. Mathematical modelling offers a powerful complementary tool with which to study crypt cell dynamics, homeostasis, recovery following irradiation, and malignant transformation. While earlier models focused largely on a single level of organisation, more recent multiscale models have begun to study how processes at the level of a single cell affect the tissue-level behaviour of the gut epithelium.

With a critical mass of UK-based modellers now working in this area, quantitative data sets coming online due in part to improved organoid technology, and a rising population of patients suffering from intestinal diseases, now is the time to push forward multiscale modelling as a genuinely useful and predictive tool for improving our understanding of the healthy and diseased gut.

This workshop provided a timely opportunity for modellers and experimentalists with a common interest in gastrointestinal function to share their latest work in this area, identify new collaborations, and discuss key challenges inherent in multiscale modelling of the gut, as an archetypal model for quantitative understanding of cell to tissue level function more generally. These challenges included:

Modelling crosstalk: A number of signalling pathways are known to regulate crypt dynamics. While the Wnt pathway has been modelled extensively, there has been little attention of other pathways, such as Notch, which act in concert to guide cell behaviour.
Modelling tissue interactions: While most models focus on the intestinal epithelium and neglect the underlying stromal tissue, there is increasing evidence for mechanical and signalling interactions between these tissues, in particular during regeneration.
Exploiting tissue culture technology: Recent advances in 3D culture technology allow the generation of organoids that reflect key structural and functional properties of the gut. Such advances may eventually lead to patient-derived organoids and personalized treatment and offer a potential wealth of data with which to validate and test models.
Confronting models with data: While the majority of multiscale models have been used to obtain qualitative biological insights, some recent studies have attempted to place such models on a more quantitative footing. Key issues to be addressed include how to perform model selection, develop simplified 'emulators' to approximate such models for parameter inference, and efficiently compute or approximate statistical likelihoods.
High performance computing: The computational cost associated with analysing multiscale models remains a significant challenge. Overcoming this requires the use of parallel computing and specialised architectures, such as GPGPU.
Comparing and disseminating models: A barrier to the wider use of multiscale models is the lack of standards or benchmarks. Previously developed models are seldom re-used effectively, since they are typically not available as rigorously tested, open-source simulation software. A more systematic and comprehensive description of specific multiscale models in the literature is required.

The biological focus of this workshop - intestinal cell self-renewal and CRC - serves as a representative example of the more general study of stem cell dynamics, tissue homeostasis and carcinogenesis using multiscale modelling. We have invited a mix of mathematicians, engineers and experimental biologists at different career stages.


Participants

Axel Almet
PhD student,
mathematical biology
Oxford
axel.almet@maths.ox.ac.uk
Helen Byrne
Professor,
mathematical biology
Oxford
byrneh@maths.ox.ac.uk
Kit Curtius
PDRA,
tumour biology
BCI
k.curtius@qmul.ac.uk
Trevor Dale
Professor,
cancer biology
Cardiff
daletc@cardiff.ac.uk
Sara-Jane Dunn
Scientist,
computational biology
MSRC
sarajand@microsoft.com
Marianne Ellis
Senior lecturer,
biochemical engineering
Cardiff
m.j.ellis@bath.ac.uk
Alex Fletcher
Research fellow,
mathematical biology
Sheffield
a.g.fletcher@sheffield.ac.uk
David Gavaghan
Professor,
computational biology
Oxford
david.gavaghan@dtc.ox.ac.uk
Tim Ingham-
Dempster
PhD student,
computational biology
Sheffield
taingham-dempster1@sheffield.ac.uk
Lucia Marucci
Lecturer,
engineering mathematics
Bristol
lucia.marucci@bristol.ac.uk
Philip Maini
Professor,
mathematical biology
Oxford
maini@maths.ox.ac.uk
Daniele Muraro
PDRA,
mathematical biology
Oxford
Daniele.Muraro@maths.ox.ac.uk
Inke Nathke
Professor,
epithelial biology
Dundee
inke@lifesci.dundee.ac.uk
Aimee Parker
Research scientist,
immunology
IFR
Aimee.Parker@ifr.ac.uk
Carmen Pin
Research leader,
gut health
IFR
carmen.pin@ifr.ac.uk
Joe Pitt-Francis
Lecturer,
computational biology
Oxford
joe.pitt-francis@cs.ox.ac.uk
Laura Vaux
PDRA,
gut health
IFR
Laura.Vaux@ifr.ac.uk
Daniel Ward
PhD student,
engineering mathematics
Bristol
dw0293@bristol.ac.uk
Sarah Waters
Professor,
applied mathematics
Oxford
waters@maths.ox.ac.uk
Alastair Watson
Professor,
translational medicine
UEA
Alastair.Watson@uea.ac.uk
Year(s) Of Engagement Activity 2017