An integrated computational model of human outer retinal bioenergetics and effects of ageing

Lead Research Organisation: University College London
Department Name: Institute of Ophthalmology

Abstract

The biology of ageing is of growing importance as the elderly population grows. This project seeks to further understanding of how the back of the eye ages. The 'system' to be investigated is the layer of light sensitive cells (rods and cones) in the outer retina, the remarkably dense, supporting vascular bed (choriocapillaris) that lies beneath it and the connective tissue layer known as Bruch's membrane that sits between the choriocapillaris and the rods and cones.

Rods and cones require large amounts of energy to function normally and the very highly vascular choriocapillaris provides the necessary oxygen. This needs to be precisely controlled as too low an oxygen supply impairs rod and cone function and potentially leads to cell death. Conversely, too high a concentration of oxygen can also be toxic.

From published data, we know that with increasing age rod numbers drop, Bruch's membrane gets thicker and the choriocapillaris degrades in a way that reduces blood flow. It is possible that in healthy ageing these changes interact in a way maintains the health of rods and cones (photoreceptors).

It is not possible to make the direct measurements necessary to explore this phenomenon in more detail in patients or healthy volunteers, particularly as the anatomy of the back of the human eye varies markedly from one area to another. Also, it is very difficult to explore how changes in blood pressure and other factors might impact on photoreceptor health. Even direct measurements of choriocapillaris blood flow are challenging as a layer of pigmented cells lies just in front of it.

For these reasons we have developed a computer simulation of choriocapillaris blood flow and already identified some unexpected properties of this vascular bed. By drawing together published data and additional morphological data from post-mortem eyes donated for research purposes we intend to extend this model to describe how oxygen is delivered from the choriocapillaris to the outer retina and how much oxygen the outer retina (photoreceptors) need.

Having established the model we will be able to use it to determine how the integrated system of blood vessels, Bruch's membrane and photoreceptors behaves in healthy ageing. We predict that oxygen supply and demand will be closely matched and that, paradoxically, reduction of blood flow is beneficial as it keeps photoreceptors at an optimal concentration of oxygen. It is possible that similar combinations of age-related changes are a feature of healthy ageing at other sites, a phenomenon for which we have coined the term 'graceful ageing'.

Technical Summary

The proposed study seeks to explore the factors that determine photoreceptor oxygen tension and in particular to further understanding of how ageing of the choriocapillaris, Bruch's membrane and photoreceptor populations may combine in healthy ageing to maintain optimal oxygen concentrations at the photoreceptor inner segments.

The methodology will centre on computational models informed by anatomical and physiological datasets. The starting point will be a recently developed, novel model of human choriocapillaris blood flow. This will be coupled with a 3-dimensional model of mass transfer that will use a validated finite element code (ACEsim). In this way we will be able to model oxygen delivery to photoreceptor inner segments. In order to estimate outer retinal oxygen demand we will modify estimates of murine rod energy requirements for human rods, conventional cones and the specialised cones that are found in the fovea. By generating maps of photoreceptor density from donor eyes of differing ages we will then be able to estimate outer retinal oxygen demand. Combining this with the oxygen supply model it will be possible to estimate inner segment oxygen tension and determine whether it is likely to be optimal or adversely low (hypoxia) or high (likely to generate damaging reactive oxygen species).

The final model will allow us to explore how varying various parameters (age, choroidal blood flow, completeness of choriocapillaris network, Bruch's membrane thickness, age-related photoreceptor cell loss) are likely to alter inner segment pO2.

The model not only has relevant to ageing. It will also inform studies of drug delivery to the outer retina and pathogenesis of conditions such as age-related macular degeneration and diabetic retinopathy.

Planned Impact

The impact of this study falls into several different areas:

1) The biopharmaceutical industry will benefit from the modelling of choroidal blood flow and exchange between the choroid and outer retina for assessing delivery of therapeutics.

2) Insights into healthy ageing will help define 'unhealthy' ageing and in particular inform understanding of the pathogenesis of age-related blinding conditions. Such understanding will in turn lead to the development of new therapies.

3) The approach to be taken in this proposal is likely to deliver impact in other age-related disorders. The applicants believe that part of the relative failure to achieve therapeutic success in age-related degenerative conditions is that the interplay between different components of the system under investigation has not been taken into account. In the eye, this has led to approaches that target either the microcirculation, or Bruch's membrane or retinal pigment epithelium or photoreceptors. We consider it critical to model the system in an integrated manner, as proposed here.

Publications

10 25 50
 
Description Advances have been made in several areas. 1) We have developed a computational model of 'whole outer retinal bioegenetics' and compared energy demands of the outer retina with nutrient supply. Key findings are that oxygen and glucose can diffuse to the inner segment of rods and cones (light detecting cells) at sufficient rate to contribute significantly to outer retina energy demands but glucose alone is insufficient and other carbon sources are required. Amino acids (notably proline and glutamine) are important additional sources and the remainder is predicted to be made up from short and long chain fatty acids. However the concentration gradient for these metabolites is low and it seems that intermediate metabolism in the retinal pigment epithelium, a cell monolayer between the circulation and the photoreceptors, is required. Since the project started experimental data from other labs strongly support this idea as do our metabolic modelling studies (below). The development of the integrated model required the creation of submodels, most notably one that describes the kinetics of transport of metabolites such as glucose that has to cross basolateral and apical membranes of the retinal pigment epithelium and the plasma membrane of the photoreceptor inner segment to be effective. The model includes terms describing diffusion across Bruch's membrane and the inter photoreceptor matrix 2) We have developed a novel model of retinal pigment epithelium - photoreceptor inner segment metabolism which embraces a remarkably comprehensive database of human metabolism and allows for complex coupling of metabolites between retinal pigment epithelium and inner segments. The need for this complexity became apparent from initial modelling attempts and recently published data. Importantly, without being 'trained', some of the counter-intuitive behaviour observed in living systems emerges from the model. For instance, we have shown that if photoreceptor energy requirements are optimised but retinal pigment epithelium energy demands are included, glucose simply passes through the retinal pigment epithelium to the photoreceptor and the retinal pigment epithelium itself is fuelled by lactic acid passing in the opposite direction. The model also predicts complex coupling of metabolic intermediaries between the two cell types almost as though they behave as a single complex unit. A single cell version of the model also demonstrates the Crabtree effect purely on the basis of 'passive' network properties. 3) We have looked at spatial distribution of rods and cones and the impact that this has on outer retinal bioenergetics and aging. A novel prediction is that the large size of cone inner segments (versus the small size of rod inner segments) leads to critical spatial competition for nutrient supply that compromises rod metabolism in the macula, the part of the retina that is responsible for central vision. 4) We have shown that there is tight coupling between energy demand of the outer retina and capacity for nutrient supply by the choriocapillaris with aging. This important finding suggests that vessel degeneration and photoreceptor cell death are linked as we age such that supply and demand keep in step. It will be important to understand the mechanism of this. 5) Although the focus of this application has been outer retina, the models and principles and tools developed have much more general applicability in understanding bioenergetics and aging. For instance, 1) the coupled retinal pigment epithelium - photoreceptor metabolism model can be used to study coupling between any 2 cell types 2) the principle of competition between cells is an important general principle and 3) how supply and demand are linked in aging is an issue relevant to many organs and tissues and it will be important to understand whether this is driven by vascular factors, cells within the tissue or a combination of the two.
Exploitation Route The whole retina bioenergetics / transport model and the metabolic model are being written up for publication. The manuscripts are being prepared using R markdown to allow for every detail and assumption to be tested / challenged and this will also make it straightforward for investigators to refine the models or repurpose them for the study of different tissues. We will make datasets available to the research community to facilitate reanalysis / utilisation in different studies.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description The findings have been used to support the commercial development of a novel therapeutic for outer retinal degenerations in the USA. The details are subject to a confidentiality agreement.
First Year Of Impact 2017
Sector Healthcare
Impact Types Economic

 
Description Moorfields Eye Charity Springboard Award
Amount £102,255 (GBP)
Funding ID GR001345 
Organisation Moorfields Eye Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 06/2022 
End 12/2023
 
Description Royal Society International Exchanges
Amount £3,000 (GBP)
Funding ID IE161589 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2017 
End 06/2017
 
Description Santen PhD Studentship
Amount £288,000 (GBP)
Funding ID UCL Ref 32914 
Organisation Santen Pharmaceutical Co., Ltd 
Sector Private
Country Japan
Start 03/2018 
End 02/2021
 
Title In silico model of retinal pigment epithelial cell metabolism 
Description Linked to the integrated outer retina - retinal pigment epithelium (RPE) - choroidal circulation model is a stand-alone RPE model. As with the main model this is currently being refined on the basis of single cell RNAseq data. It has a stand-alone role in its utility particularly as a tool in understanding in vitro data relating to bioenergetics, metabolomics and transport. 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2018 
Provided To Others? No  
Impact No significant impact as yet but we have established collaborative links that we benefit from the model once it is fully validated. 
 
Title Metabolic modelling of the outer retina 
Description There are two interlinked models that we have now generated. One describes the supply and demand of nutrients at a tissue level and in particular identifies the constraints around nutrient availability to the retinal pigment epithelium and photoreceptor inner segments. This includes a model for carrier facilitated diffusion of nutrients across both aspects of the retinal pigment epithelium (RPE) and the inner segment plasma membrane as well as diffusion from the circulation to the RPE and from the RPE to photoreceptor across the inter photoreceptor matrix. The model embraces topographical differences from central to peripheral retina and aging changes in the choriocapillaris, Bruch's membrane and photoreceptors. The second model (built on the Recon3D database) captures detailed cellular and intercellular metabolism and includes separate compartments for blood, retinal pigment epithelial cells, inter photoreceptor matrix and photoreceptor inner segments. We have extended the curation of the model against published data relevant to, in particular, the distribution of transporters between compartments. Although primarily designed with human in vivo metabolism in mind the tools can also be used for elucidating mechanism using data from cultured cells. The model uses a multi compartment flux balance approach and is informed by gene expression data for retinal pigment epithelium and photoreceptors. It is currently being reworked using data from single cell RNAseq studies (as opposed to tissue level data we have used to date) prior to publication. 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2019 
Provided To Others? No  
Impact The development of this tool has supported some work in an EU consortium and is providing the basis for several grant applications. 
 
Title Computational model of outer retinal bioenergetics and metabolism 
Description There are two interlinked models that we have now generated. One describes the supply and demand of nutrients at a tissue level and in particular identifies the constraints around nutrient availability to the retinal pigment epithelium and photoreceptor inner segments. This includes a model for carrier facilitated diffusion of nutrients (glucose and amino acids) across both aspects of the retinal pigment epithelium (RPE) and the inner segment plasma membrane as well as diffusion from the circulation to the RPE across Bruch's membrane and from the RPE to photoreceptor across the inter photoreceptor matrix. The model embraces topographical differences from central to peripheral retina and aging changes in the choriocapillaris, Bruch's membrane and photoreceptors. A novel feature is the incorporation of photoreceptor coverage as a mechanism to model spatial competition between cones, which have large inner segments, and rods with their small inner segments. The second model (built on the Recon3D database) captures detailed cellular and intercellular metabolism and includes separate compartments for blood, retinal pigment epithelial cells, inter photoreceptor matrix and photoreceptor inner segments. We have extended the curation of the model against published data relevant to, in particular, the distribution of transporters between compartments. Although primarily designed with human in vivo metabolism in mind the tools can also be used for elucidating mechanism using data from cultured cells. The model uses a multi compartment flux balance approach and exploits the COBRA Toolbox. It is informed by gene expression data for retinal pigment epithelium and photoreceptors. It is currently being reworked using data from single cell RNAseq studies (as opposed to tissue level data we have used to date) prior to publication. The model predicts optimal photoreceptor ATP production as a function of nutrient availability at the choriocapillaris. It also predicts the detailed intermediate metabolite fluxes including transport fluxes in both directions between the retinal pigment epithelium and photoreceptor inner segment. What has proved especially informative is to visualise how these fluxes change as levels of metabolite change in the circulation. The magnitude and direction of correlation is visualised on ReconMap. 
Type Of Material Computer model/algorithm 
Year Produced 2020 
Provided To Others? No  
Impact Results from the models have been presented at an international meeting in Miami earlier this year and have lent evidence supporting two commercial initiatives. 
 
Title Energy metabolism toolbox 
Description Set of functions and scripts linked to iScience publication for modelling of energy-coupled metabolism in mouse embryonic fibroblasts although the code is of more generic utility. 
Type Of Material Computer model/algorithm 
Year Produced 2023 
Provided To Others? Yes  
Impact The key utility is using a metabolic model to predict rates of energy requiring processes such as protein synthesis by adopting a whole-cell approach. 
URL https://github.com/pluthert/MEF-metabolism
 
Description Systems Biology Ireland 
Organisation University College Dublin
Department Systems Biology Ireland
Country Ireland 
Sector Academic/University 
PI Contribution We have brought the modelling expertise and understanding of the outer retina and aging.
Collaborator Contribution Dr Kiel has brought understanding of signalling and protein - protein interaction networks and thermodynamics which are informing the next iteration of the metabolic model.
Impact This publication concerns downstream binding partners of Ras. It isn't recorded elsewhere as it emerged obliquely from collaboration of the present award. doi: 10.1080/21541248.2020.1724596
Start Year 2016
 
Description Article in professional magazine for retina specialists 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The magazine article described some of our findings in relation to the heterogeneity of blood flow at the back of the eye and hence heterogeneity of delivery of nutrients to the eye and the potential challenge that this presents to photoreceptors in ageing and disease
Year(s) Of Engagement Activity 2017
 
Description Invited talk Ophthalmology Conference in Miami Florida 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The presentation was part of an update to retinal specialists from across the USA
Year(s) Of Engagement Activity 2018
 
Description Ophthalmology conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation to ophthalmologists in Miami explaining how the modelling of choroidal blood flow has generated counter-intuititve insights into the importance of choroidal circulation in ageing.
Year(s) Of Engagement Activity 2017
 
Description Presentation at International Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The meeting was primarily about retinal degeneration but I was asked to speak as our modelling work suggests that as the retina ages the choroidal circulation becomes increasingly critical in terms of meeting the requirements of the rods and cones in the outer retina. Conversations after were from imaging specialists (who are demonstrating age-related changes in choroidal circulation) as well as industry representatives looking to generate therapies that enhance choroidal circulation.
Year(s) Of Engagement Activity 2019
URL https://umiamihealth.org/bascom-palmer-eye-institute/healthcare-professionals/continuing-medical-edu...