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E X PE R IM ENT A L CE LL R ES E AR CH 319 (2013) 1240–1246

Available online at www.sciencedirect.com

journal homepage: www.elsevier.com/locate/yexcr

Review Article

Predicting the future: Towards symbiotic computational


and experimental angiogenesis research

Katie Bentleya,b,n, Martin Jonesa, Bert Cruysc,d


a
Vascular Biology Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
b
Computational Biology Laboratory, CVBR, Beth Israel deaconess Medical Center, Harvard Medical School, Boston MA 02215 USA
c
Laboratory of Angiogenesis and Neurovascular Link, Department of Oncology, Vesalius Research Center, KU Leuven, Belgium
d
Laboratory of Angiogenesis and Neurovascular Link, Vesalius Research Center, VIB, Leuven B-3000, Belgium

article information abstract

Article Chronology: Understanding the fundamental organisational principles underlying the complex and multi-
Received 24 November 2012 layered process of angiogenesis is the mutual aim of both the experimental and theoretical
Received in revised form angiogenesis communities. Surprisingly, these two fields have in the past developed in near
1 February 2013 total segregation, with neither fully benefiting from the other. However, times are changing and
Accepted 2 February 2013 here we report on the new direction that angiogenesis research is taking, where from well-
Available online 13 February 2013 integrated collaborations spring new surprises, experimental predictions and research avenues.
Keywords: We show that several successful ongoing collaborations exist in the angiogenesis field and
Computational modelling analyse what aspects of their approaches led them to achieve novel and impactful biological
Interdisciplinary insight. We conclude that there are common elements we can learn from for the future, and
Angiogenesis provide a list of guidelines to building a successful collaborative venture. Specifically, we find
Prediction that a near symbiosis of computation with experimentation reaps the most impactful results by
Simulation close cyclical feedback and communication between the two disciplines resulting in continual
refinement of models, experimental directions and our understanding. We discuss high impact
examples of predictive modelling from the wider, more established integrated scientific
domains and conclude that the angiogenesis community can do nothing but benefit from
joining this brave new, integrated world.
& 2013 Elsevier Inc. All rights reserved.

Contents

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1241
Towards predictive modelling in angiogenesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1241
Predictive biological modelling can have high impact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1242
What is the secret to achieving high impact biological insight through predictive modelling? . . . . . . . . . . . . . . . . . . . . . . 1242
Towards a unified, predictive modelling mindset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1242
Symbiotic approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1242

n
Corresponding author.
E-mail address: kbentley@bidmc.harvard.edu (K. Bentley).

0014-4827/$ - see front matter & 2013 Elsevier Inc. All rights reserved.
http://dx.doi.org/10.1016/j.yexcr.2013.02.001
EX PE R IM ENT A L CE LL R ES E AR CH 319 (2013) 1240–1246 1241

Simple focused, but extendable models. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1243


Quantitative data/image analysis greatly improves the symbiotic process . . . . . . . . . . . . . . . . . . . . . . . . . . 1244
Discussion and conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1244
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1245
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1245

Introduction Towards predictive modelling in angiogenesis

The goal of biology, be it theoretical or experimental, is to study Mathematical/computational models take a long time to build, as
complex living systems and understand their fundamental does confidence in the approach. Before full integration with
principles of organisation and generation. Biology is, however, experimentation could be achieved, models were mainly built on
inherently noisy with variables that are hard to control. More- theoretical grounds with the aim of illustrating that the process
over, in vivo information is often difficult to extract and analyse. could even be modelled [11–13]. This was an important first step
Data often comes in many disjointed forms: static images, that stimulated a surge in angiogenesis modelling, which has seen an
global rather than cellular protein analysis, whole organ level increasing incorporation of experimental data over time [14–19].
functional descriptions or single pathway in vitro biochemistry. Now we can see that the field has developed still further; a small
As a result, details can remain disconnected and important pocket of fully integrated, joint ventures are emerging where
underlying mechanistic behaviours can evade discovery. Com- modellers work side by side with experimentalists, or, indeed, indi-
putational modelling can enable us to ‘‘join the dots’’ and viduals are trained in both sides of the trade [20–25]. This heralds a
integrate our disparate knowledge of signalling pathways, move in a positive direction for the angiogenesis field, catching up, as
cell/tissue level dynamics and the ever changing cell environ- we will show, with other fields where this level of integration has
ment to attempt to fully understand how and why a biological existed for much longer. We will discuss two such examples,
process unfolds as it does. particularly notable for their predictive and iterative nature.
Angiogenesis is a prime example of a hugely complex, multi- Starting from one-compartment models for breast tumour
scale, adaptive process with intricate temporal and spatial tissue [26] and skeletal muscle [27], the Popel group generated
dynamics. Multiple subcellular, cellular and multicellular a whole-body pharmacokinetic model consisting of three differ-
mechanisms occur in tandem, constantly adapting to the ever ent compartments: normal, diseased (e.g. tumour) and vascular
changing environment to generate the new tubular structures [28]. Two vascular endothelial growth factor A (VEGF) isoforms
capable of supporting and optimising blood flow: actin (the freely diffusible VEGF-121 and the matrix bound VEGF-165),
dynamics in migrating cells, cell rearrangement, lumen forma- VEGF-receptor 1 and 2 and their co-receptors (Neuropilin-1 and
tion and ultimately plexus remodelling to name but a few [1]. 2) are integrated in the model. This allowed them to investigate
Indeed, this special issue itself captures the breadth and the distribution of free and bound VEGF, which is hard to assess
diversity of mechanisms contributing to the process. Computa- experimentally, in exercising as well as pathological conditions.
tional approaches, if applied correctly, can hugely aid the One of this model’s predictions is that the higher plasma VEGF
detangling of this complexity and fuel the discovery of the levels in cancer patients compared to healthy individuals may be
general, underlying principles. caused by a change in the vascular permeability of the cancer
However, computational modelling is not new, nor is the fact patient’s healthy tissue [28]. In the next phase, the model was
that computation can aid the understanding of biological complex- extended to study the mode of action of the anti-VEGF agent
ity. A host of excellent reviews already exists, covering this issue in bevacizumab and more specifically its accompanying counter-
a wide range of biological domains [2–5] as well as specifically intuitive increase in plasma total VEGF level in treated patients
covering the large number of theoretical angiogenesis models that [29]. The model predicted that the working mechanism of
have already been developed [6–8], most recently with an impor- bevacizumab is to deplete the tumour VEGF levels rather than
tant focus on the role of incorporating experimental data along the plasma VEGF levels. By adding tumour cells, muscle fibres
with model development [9]. However, as pointed out in Ref. [10], and by sequentially integrating newly measured experimental
still there is hesitation on how best to exploit this powerful tool data they further refined their model [30]. Upon every newly
and, indeed, whether to facilitate integration at all. added parameter, they compared the obtained model with the
Here, we aim to address this hesitation. We will show first prior one. In the next step, they investigated the influence of
that real progress can be made by combining forces, and that a several parameters on the model output. In this way, they were
common theme of ‘‘successful examples’’ of biological model- able to make predictions on the role that the (1) tumour
ling is that not only are they integrated, but clear testable microenvironment, (2) anti-VEGF binding properties, (3) density
predictions from the model, and constant feedback throughout, of VEGF receptors and co-receptors on tumour cells, (4) VEGF
have been essential design principles of the research pro- secretion rate and the secreted VEGF-isoform ratio and (5)
gramme. We conclude that simply handing over an experi- tumour lymphatics play in the therapeutic potential of an anti-
mental data set to a modeller will not likely yield the most VEGF agent. Finally, their results raise interesting questions
predictive modelling results; we must work together. High regarding the use of VEGF isoform expression and/or interstitial
impact has been achieved in other fields, and is on the horizon VEGF concentration as predictive biomarkers to tune the anti-
already for the angiogenesis field. Thus we postulate that the VEGF therapy better for a specific patient [30]. In their most
time is ripe for the field of angiogenesis to sew more predictive recent instantiation of the model, the applicability of isoform-
seeds through iterative, integrated modelling in order to suc- specific anti-VEGF agents was investigated [20]. The specific
cessfully reap new biological understanding. targeting of the VEGF-121 isoform was predicted to reduce the
1242 E XP E RI ME N T AL C E L L RE S E AR CH 319 (2013) 1240–1246

unbound VEGF in the tumour and thus could be a candidate with particular, Sawai et al. experimentally proved Levine’s prediction
therapeutic potential. of a positive feedback loop on cAMP excitability in the aggrega-
A second example is the iterative evolution of a cell-centred tion of Dictyostelium discoideum (slime mould) cells, a mechan-
model that started from a simple experimentally-based model of ism now fundamental to our understanding of slime mould [41].
tip/stalk cell selection via Notch signalling, built to understand In a similar way Shankaran et al. found the mechanism of
the basic mechanisms that regulate sprouting under normal and oscillations in the MAPK pathway by combining mathematics
pathological conditions [31]. Several new predictions were made and experiments [39]. They compared two previously published
based on the unexpected, emergent behaviours that the simula- model predictions on MAPK oscillation mechanisms and found
tions generated, in particular the regular selection of branch only one of them to match their experimental data. Hence, their
spacing was predicted to be disrupted under pathologically high model was able to point towards the most probable oscillation
VEGF conditions and to give rise to abnormal synchronous Notch cause and as such had an explanatory role.
oscillations, potentially explaining the abnormal sprouting that The applicability and dependability of predictive models is
occurs in high VEGF pathologies such as cancer. This model was further exemplified by their increasing use in governmental
then extended to simulate cell migration and anastomosis, with decisions in such important areas as disease control policies
close inclusion of in vivo zebrafish sprouting data during model and drug discovery [44–47]. During the 2001 foot-and-mouth
development, giving rise to a new set of predictions concerning disease outbreak in the UK, different predictive models were
(1) the mechanism of anastomosis, (2) the instability of tip/stalk developed in near real-time to estimate the impact of confining
fate selection as the branching network structure changes under strategies on the evolution of the epidemic [47]. Ferguson et al.
loop formation, (3) as junctions become irregular and (4) the devised a simple deterministic model, consisting of ordinary
robustness of pathological oscillations due to the positive feed- differential equations, that accurately predicted the policy’s
back of cell migration, leading to potential therapeutic insights effects on the spatial evolution on the disease and as such guided
[32]. Later, extended versions of this model predicted that (1) the governmental control policy.
loss of the deacetylase Sirt1, which affects the timing of Notch
regulated gene expression, would lead to a sparser vessel net- What is the secret to achieving high impact biological
work due to low-level oscillations in Notch. This not only exactly insight through predictive modelling?
matched the phenotype found in Sirt1 mutant mouse retinas but
also provided the first mechanistic explanation and consideration Considering these examples of validated, predictive modelling
of temporal influences on the emergence of this phenotypic across the variety of fields discussed, we can begin to identify
manifestation [33] and (2) VEGFR3/VEGF-C signalling may common features that led to their success.
directly affect filopodia dynamics and the cells ability to move
in a persistent manner, with preliminary validation in the Towards a unified, predictive modelling mindset
zebrafish intersegmental vessels [34]. A recent unexpected Modelling should not be viewed as simply a method for
experimental observation was made that cells are in fact highly corroborating experimental results. Although obviously this is
dynamic in the sprout, constantly shuffling and rearranging their an important step in the development and calibration of a
positions. The model was then overhauled to include and predictive model, it has too often been the end result of
investigate this new behaviour. These model refinements in light angiogenesis models and arguably over time has led to a loss
of new data then created a surge in new insights and predictions. of confidence in in silico approaches’ potential for driving
Principally, Notch signalling may be involved in regulating cell research forward.
rearrangement behaviour [22,35]. However, it takes two to tango. A concerted effort and
commitment will be needed on both sides to move the angio-
genesis field towards achieving the kind of integrated success
Predictive biological modelling can have high impact seen in the wider biology field. Modellers need to have a more
unified direction and only develop and publish models that give
There is a surprisingly high level of hesitation in the angiogenesis rise to new predictions, but equally experimentalists need to
field to trust modelling. Perhaps one way to encourage integra- commit to actually test and explore the model predictions.
tion is proof by example. Modelling is integral and fundamental
to many other disciplines and has led to great advances in Symbiotic approach
science. The best and most longstanding example of this is the From the angiogenesis examples given, it is clear that constant,
role that modelling plays in physics, where it is ubiquitous (in open communication channels between the two disciplines is
fact, the distinction between theoretical and experimental phy- key. Though it has often been noted that models must be
sics is frequently blurred). One of the most significant results in integrated with experimentation, simply providing a modeller
physics in recent years has been the discovery of the famous with an experimental dataset will not yield the best results. The
Higgs boson. Its possible mass range was predicted by the realism and, therefore, predictive capacity of a model will
theoretical ‘‘Standard Model’’. The Large Hadron Collider at CERN increase as the level of integration and communication with
was built and in 2012 the elusive particle was finally discovered experimentalists increases. Indeed, if we push this idea to its
[36,37]. This stands as a huge testament to what can be achieved limit, the ideal scenario for developing a highly predictive model
when theoreticians and experimentalists combine forces, food is to totally immerse the modeller within the experimental
for thought for the angiogenesis community. environment and vice versa. Indeed, the importance of the
Already in the wider world of biological modelling there are experimentalist also taking the time to understand the model-
countless examples of excellent integrated research [38–43]. In ler’s perspective and toolsets should not be underestimated;
EX PE R IM ENT A L CE LL R ES E AR CH 319 (2013) 1240–1246 1243

crucial and unique contributions to a models’ design subtleties, accurate predictions meaning experimental design itself can be
leading to greater predictive power, can possibly only be devised overhauled in new directions, requiring development of new
by the theoretically-inquisitive experimentalist. From the given tools and techniques, but with great new insight that may never
examples a two-way education process in the other’s discipline have occurred otherwise.
during research was a key component to their success. Returning to the example of integration of theory and experi-
We will dub this Holy Grail of integration the ‘‘symbiotic’’ mentation in physics, we can learn that other factors may also
approach; see Fig. 1. Symbiosis was originally defined as ‘‘The contribute to the success of the field. Theoreticians and experi-
living together of unlike organisms’’—by Heinrich Anton de Bary mentalists traditionally inhabit the same spaces, both literally in
in 1879. It is defined as a process continually in flux where the terms of academic buildings, and also in the sense of generally
feedback from one to the other provides a mutual benefit and sharing the same journals and conference circuits. This extension
creates a larger system greater than the sum of its parts. This of the symbiotic approach to the workplace and dissemination of
then is perhaps the perfect analogy. A crucial component to the results is largely missing from modern biology and it would
examples given is the cycles of iterative refinement with close appear that it could only enhance the science if such a metho-
integration between modelling and experimentation. Indeed, this dology were employed more widely. The examples in angiogen-
is the essence of the generalised scientific process, to continually esis of successfully predictive models indeed employed this
refine and investigate, building and evolving our model view of spatially symbiotic arrangement, though together we must tackle
the world. It should never be expected that a theory or model is reducing the publication/conference segregation that currently
built that is totally right at the outset; science is a process of exists.
refinement. It is then simply a natural next step, in the
technological age, to implement this process with the rigour
and temporal simulation capacity of the computer. Simple focused, but extendable models
Feedback is a crucial aspect that maintains, but also can be The models exemplifying success here all exploited a simple and
exploited by, a successful symbiosis. As well as the obvious extendable design principle; a clear biological question and
benefit of including new data in iterations in the model, experi- desire to be predictive on that specific question has kept the
mental design itself is also an important aspect of the scientific model free of excessive elements and parameters that can
process. Without some guidance as to the most potentially confuse/detract from question in hand. Too often, undirected,
fruitful avenues to pursue, we can be left searching around in a overly complex models are created with too many features
vast parameter space that may contain many dead ends. The modelled at once to be able to control variables and make
symbiotic approach can generate unlikely and potentially concise predictions on single components or mechanisms’
dynamics. Thus, if we actually follow the first principle, to have
clear questions and predictions in mind, then designing the
simplest model to achieve this aim should naturally enhance
the model’s predictive capacity.
It is clear that simpler qualitative models can still be informa-
tive in the initial absence of quantitative data. Models are, by
definition, simplifications of the system being studied. Even
extreme simplifications can be instructive and are frequently
used in physics for example, with approximations such as
spherical symmetry, point particles and so on. Such models
may not provide robust quantitative data, but the qualitative
behaviours and sensitivity analysis on them can be a vital
starting point for building more realistic models and directing
new quantitative experiments to find those values that can
subsequently be included to produce robust numerical data
and testable predictions.
Thinking in a bottom–up manner naturally leads to emergent
and extendable models and is evident from many of the examples
above [31,32,38,40,41]. Bottom-Up or generative models are
approaches that use simple building blocks representing the
lowest level elements in the model only, such as molecular
Fig. 1 – Symbiotic approach: the model and our interactions. These elements are then allowed to interact by a
understanding, evolves through iterative cycles where stated set of rules, usually in a spatially coherent way, to then
continual feedback drives both model refinement and directs generate emergent behaviours at a higher level above, only evident
optimised experimental design. Fundamental to this to the observer of the simulation and not governed by rules
approach is the open, continual communication and themselves, e.g. cellular context behaviours defined by molecular
education between the disciplines throughout, represented by interactions below. These models are well characterised to gen-
the flow of ideas through a dashed ‘‘membrane’’ between the erate dynamics that are far more complex than their simple set of
disciplines. This is enhanced, where possible, by existing and underlying rules might suggest and the dynamics they produce
working in the same physical location and publishing in are often ‘emergent’, i.e., impossible to predict ab initio. See Fig. 2
shared journals and conferences. for a schematic.
1244 E XP E RI ME N T AL C E L L RE S E AR CH 319 (2013) 1240–1246

Fig. 2 – Schematic of the Bottom–Up, emergent modelling approach. (A) Assumptions of the model, built on experimental data
and understanding, are written in as rules that govern the interactions of the lowest level components in the model. The
simulation of these rules of local interaction of small components over time gives rise to higher level dynamics of the system as a
whole, observable but not directly programmed in. These emergent behaviours can then either be used against existing data
to validate the assumptions at the level below, or as new predictions. Model refinement and extensions are easily incorporated as
new or revised interaction rules/components. (B) Biological representations of the different levels are depicted, respectively
from bottom to top: intracellular components, a few interacting cells and an established vascular network. Fluorescence
microscopy images supplied by Eleonora Lapi (CRUK London, CNIO Madrid) and electron microscopy image supplied by Lucy
Collinson (CRUK London).

Further advantages of the Bottom–Up approach are that firstly


it is generally far easier to extend the model by simply adding Discussion and conclusions
additional interactions or components, as and when experimen-
tal data reveal new phenomena. Secondly, the framework is We have provided a short overview of the potential computa-
much more closely aligned with our current understanding of tional modelling holds for angiogenesis by considering what has
how complex cellular behaviours arise, from the interaction of made collaborations impactful in other fields, and made the few
many simple components, and hence is more palatable to that have so far emerged in the computational angiogenesis
experimentalists, breaking down the communication barriers field successful. Model predictions can be invaluable for finding
and aiding the flow of information needed. This type of model- new and unexpected understanding as Scianna et al. conclude
ling could represent a ‘‘Rosetta Stone’’ and will engender a with regard to their model’s predictions: ‘‘Even though it is
common language that will allow more effective communication possible to form a post hoc explanation of each solution’s
and a tightening of the integration between model and effectiveness, it is unlikely that these solutions would have
experiment. been manually discovered’’. The list of common elements that
led to the novel insight we have discussed are summarised
Quantitative data/image analysis greatly improves the symbiotic below:
process
It is often said that a model is as good as the experimental data 1) Unify computational angiogenesis towards predictive model-
that contributes to its development. The closer we can get to ling on specific scientific questions.
reliable quantitative information to feed into the model the a. Commitment from modellers to make predictions.
better. In order to incorporate new experimental findings back b. Commitment from experimentalists to test predictions.
into models effectively, it is worth exploiting computation to 2) Move towards a symbiotic research approach.
build quantitative analysis tools to extract meaningful and a. Communication: open constant, two way communication
rigorous numerical information from the experiments, leading channels between modeller and experimentalist.
to a greater synergy between the model and experiment b. Feedback: exploit the two way feedback for iterative
[22,38,39]. Indeed, given the complex morphological nature of model refinement and optimised experimental design.
the angiogenesis process there is a real need for development of 3) Design simple, focused but extendable models.
tailored computational image analysis to link our mechanistic a. Avoid over complexity and parameterisation in the model:
understanding to quantitative read-outs on network growth and less is more.
function. Already work has begun in this area, ripe to build on in b. Exploit Bottom–Up, generative approaches for their intui-
the future [48–53]. tive, emergent and extendable qualities.
EX PE R IM ENT A L CE LL R ES E AR CH 319 (2013) 1240–1246 1245

4) Develop automated quantitative data/image analysis methods. just as plans for all the high-rise building are required to undergo
a. Greatly enlarge the quantitative datasets that can feed into structural dynamics analysis to confirm earthquake resistance.’’
the model. This statement became reality when the FDA approved the cardiac
a. Gain novel insight by improving the resolution and models of Noble, Hunter and colleagues [3,46] for drug testing.
accuracy of observation. Thus if we may be so bold as to predict the future, a brave new
world is ahead if both the theoretical and experimental branches
of the angiogenesis community truly embrace, anastomose if you
will, and let the creativity and ideas flow.
When considering all these factors, the one that perhaps gets
the least praise, but deserves the most credit, for generating novel
insights is the integral, mutual education that occurs during a Acknowledgments
successful, symbiotic collaboration. A serious, continual commu-
nication effort on both sides drives one to rethink and more fully BC is funded by the Institution of Research and Innovation (IWT).
understand their position, potentially of much greater and lasting MJ is funded by a Cancer Research UK fellowship. KB is funded by
value than the simple exchange of raw data that might be Cancer Research UK and the Leducq Foundation ARTEMIS Trans-
misguidedly construed as ‘‘integration’’. After all, scientific insight atlantic Network Grant. Thanks to Dr Bill Hanage, Harvard School
comes as much from the mind as from the microscope. The of Public Health, for insight on predictive modelling in the
interested reader is directed to an excellent illustration and epidemiology field.
discussion of this aspect of the process by Drubin et al. [54].
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