Live workshop summary version 7

1. Live workshop summaryversion 7 By Frederic, Martijn, Hans All Yellow slides have been seen/OK’d by participants Blue slides are proposed outputs

2. Setting the stage for multiscale modelling:From defunct molecules to cancer prognosis • Heterogeneity between tumors is a key feature; more and better tools are needed to diagnose the heterogeneity between patients. Make a reference model and personalize this on the basis of patient specific data • Heterogeneity at the single gene level is much stronger than at the phenotypic level • A cancer phenotype, and its persistence is selected for. The selection product thereby depends on the surrounding tissue, hence the host, which is not even constant. • The most important function may be energy, or energy, carbon and nitrogen, the essentiality of which a cell cannot mutate against.

3. Selection of cells within a tumor also depends on spatial heterogeneity and selection pressure changes with time. Samples from a tumor are often not representative. • Tumor diversity comes from stochasticity at the levels of mutations, low-molecule numbers (transcription-translation), bistability, epigenetics. • DNA changes are more persistent, unless selected against during tumorigenesis. Some epigenetics and metabolic states (glycogen) are semi-persistent.

4. Neither from-molecule-analysis will be effective by itself, nor from-phenotype-analysis. Multiscalemodelling will need to bridge the two. • Pathology should be made more quantitative, linked up with models, and molecular information should be weighed together with the imaging data. This may require reclassification of diseases. • Therapy decisions and their effects should be followed up for later testing of our models.

5. Multiscalemodeling • Subcellular level by ODE model. Agent based (1 cell=1 agent) model for tissue level. Oxygen distribution through PDEs. Blood flow important • Take the perspective of only a few substances mediating between the scales (e.g. intracellular and extracellular). • Approach metabolism (mass transfer) distinctly from signalling. • Model granularity depends on question asked • Model reduction is important, but • fully detailed model would be more useful than experimental reality because the former can be interrogated more easily in terms of predicting effects of therapy

6. Oxygenation/ROS • Oxygen gradient depends on respiration which in turn determines oxygen and glucose levels. • Tumor cells can overcome many challenges through adaptation except the energy issue • Make models that specify the selective pressures; mutation rates do not matter, mutation fixation vis-a-vis the cells’ environment, does.

7. Tumor and bystanders • 98% of metastases can be classified in terms of origin • This may imply that the future metastatic capability can be predicted from information in the primary tumor. This could empower individualized therapy. This constitutes a program of research of modelling to predict metastatic potential. Problem: knowledge of metastases is limited due to focus on primary tumors. • Decide what to model: model functionally (e.g. motility to understand metastasis, or metabolism for tumor-cell survival), from there tumor anatomy, pathways, molecules.

8. Modeling signaling pathways • static vs dynamic (transient, sustained responses) • feedback circuitry • link to metabolic network; e.g. nutrient-binding: metabolites can bind GPCRs; insulin signaling • cell context dependency

9. Genome-scale metabolic modeling • Technical motivation: - cell lines may not describe the tumor - metabolic data (fluxes) hard to measure - transcriptomicdata readily available • Mapping between scales; gene expression <> flux scale. Somewhat predictive. • because of network functional organization (stoichiometric constraints) cells have to choose between proliferation and consolidation (ROS protection) • higher growth rate correlates with longer survival

10. Molecular dynamics • Talin two-state modelling/membrane interactions shold be possible • It is unclear at this stage whether a reduced number of conformations (showing two states) emerges.

11. How to bridge pathway level with cell level (and up)? • Transparent black-box models {Consider the intracellular networks in high detail (150 000 types of molecule) in transparent black box with a limited number of inputs and outputs (e.g. 70 of each); Input/output to and from cells is limited (<150 species?); Model the intracellular as how all molecules affect the transfer functions that lead from inputs to outputs.}. We must be able to define a limited number of parameters that can be accurately measured (e.g. concentration of metabolites homogeneous in cells) and make simplifications to be able to answer this problem. • Computational research agenda to test coarse graining strategy { Show at MD level that proteins essentially live in a small number of conformation-areas. Then model proteins as existing in small number of states., each with distinct activity. Model pathway in terms of activities. Show that the heterogeneity stemming form the above converges to limited heterogeneity of pathway: treat next level in terms of limited number of pathways. Show that this leads to limited number of cell states that are frequent. Build tissue in terms of these. Etcetera; this all computational, although in parallel experimental validation will be useful. Issue is how to transfer parameters between levels} • Robustness may (or may not), alleviate heterogeneity/stochasticity problems at higher scales. The extent to which complexity can be reduced remains to be shown . Some models may already oversimplify Life. . {Completely detailed models (Markus Covert, Cell 150, 2012) versus understandable models (Palsson); Yet biology may be so complex that models need to be complex? }

12. From intracellular networks to cell movement to patient • Systems Microscopy analysis of cell movement in various tumor cell lines with RNAi knock downs and growth factor cocktails: bridge from genes to motility • Diversity in gene-motility relation; differs between cell lines, but some correlation between some genes and patient survival • Potential: from genes to networks that correlate and then model

13. From intracellular networks to cell movement to patient • Systems Microscopy analysis of cell movement in various tumor cell lines with RNAi knock downs and growth factor cocktails: bridge from genes to motility • Diversity in gene-motility relation; differs between cell lines, but some correlation between some genes and patient survival • Potential: from genes to networks that correlate and then model

14. The evolutionary scale and game models • Model: • Cells (agent based) • - tumor • - luminal • - basal • - stromal (motile/non-motile) • Microenvironment (PDE) • - TGF-ß dynamics • - Matrix degrading enzyme (MDE) dynamics • - ECM/Membrane dynamics • Evolutionary game model; non spatial; works. Costs and benefits. Independent cells, tumor cells and stromal cells. Depending on parameters independent cells outgrow tumor plus stroma cells.

15. Cancer evolution games • CoompuCell3D platform for multi-cell, multi-scale models • Whole body to cell model exists for paracetamol (acetaminophen); idiosyncratic; also intracellular model exists • Tumor initiation: failure of homeostasis; treat cancer by making cancer cells feel well such that they start to behave again as normal cells. • Paradoxes (explananda by model): • After resection tumor more aggressive • Metastasis evolutionary unfavorable • Tumor progression makes no sense (emergent environment of tumor leads to sequential selection) • Why not just tumor stem cells, but also somatic cells? • If epithelial to mesenchymal transition is common, why are most caners epithelial in origin?

16. Information entropy models • Resolution determines information entropy • One-bit theory for chemotaxis (because switch ‘is all that matters’ (??): • One needs to know the important variables; otherwise looks like noise. Apparently uncorrelated variables may be fully correlated through a third unmeasured variable. • Cooperation, defection, common goods, punishment, game models show similarities with tumors

17. Moving towards metastasis • Multiscale approach: • Development of a MS tuning model integrating the different invasion modes. • Defining determinant factors or important ECM architecture parameters. • Observations that can constrain models and link top matrix/intracells • Protease inhibition impairs collective but not single cell migration • Altering collagen scaffold porosity at same concentration by varying temperature (37, 20, 14 and 4°C) leads to an increase of migration after reorganisation • Decision making in tumor invasion depends on ECM structure and cell morphology. • Inhibition of E-cadherin blocks collective migration (not single cell migration). • Transition from collective to amoeboid migration by reducing cell-cell junction is inversely proportional to metastasis invasion ability. • Agent–based models work • Missing form current models: How ECM is remodelled by tumor cells. • Focus on questions rather than precise representations? • Multiscale modelling needs to define connective parameters • Transparent black box strategy possible.

18. Colon cancer and metabolism • MS modeling from organ regulation to metabolism, tissue regulation and pharmacological action exists • SCFA ratios matter as explicated by model • Possibility to integrate diet and microbiome • Butyrate both metabolic and protein acetylation effect • Building of model of pan colonic cancerization • Role of stem cell population • Stem cell is a cell state • Useful to model one specific system (cell line): Yes, but perhaps a few cell lines representative together for all relevant phenomena

19. Public Health • Necessity to move to nonlinear involvemtn of systems biology with public health • from common complex disease to multiple rare diseases, concept of “diseasomes”, from risk factor to “risk pattern”, personal utility… • N=1 approach is entirely different; precludes statistical approach without models What to prepare: • 1. highly dynamic personal health information • 2. from statistical risk within groups to “individualized evidence” • 3. “Virtual individual models” • Life style changes can be perosnlized; mutations/SNPs in corresponding pathways can be added

20. Lessons learnt form micro-organisms • Dangerous ‘turbo’explosions possible • Cell populations in metabolic bistable states; cancer without mutations.

21. Integration • With complete model one can address any question • Standardized and robust methods need to be defined • SWOT analysis of models necessary • How to integrate brain processes (through measured hormone levels) • Models need to span from molecule to whole body and back! • Stop stating that things are complex: we know this: irreducible complexity; Let us try whether we can do it • Why? If only to save money: lots of money now used in biomedical research; results evaporate

22. The call for proposals this would define • Develop multiscale models that predict metastatic activity/success on the basis of excised tumor material, as well as utility of and type of personalized anti-metastatic therapy • Develop multiscale models of tumor energetics/survival inclusive of oxygen, glucose, pH gradients, that take tumor cell evolutionary success and intratumor heterogeneity into account and suggest new personalized network-based drug targets. • Perhaps set this up competitively:

23. Proposal of modelling competition • Modelling competition? Like Asilomar’s CASP; homology/threading modelling • DREAM project exists in systems biology: top down modelling; the new proposal could be for bottom-up modelling. • NIH: Simon Kasif (BU, George Church); funds experiments that test model predictions. • Specific data set plus questions plus modelling types need to be defined (because existing modelling methods are complementary rather than parallel) • Question could be applied (e.g. medical) or fundamentally scientific (e.g. Warburg effect). Question should not be too complex/complicated • But this may not be enough because we cannot define what an appropriate dataset would be. May not be multiscale. • iGEM may be a good analogy; BUT this is more difficult to model than MD is. Questions may need to be limited in complexity. May be too expensive. • Link with hospitals? But should then be professional.

24. Workshop statement to be offered for publication • The participants in the recent Lorentz workshop on the multiscale systems biology of cancer have debated and then reached the conclusion that • In order to target the tumor where it is ultimately most vulnerable, multiscale modelling of cancer should be strategically directed at: • energy, carbon and nitrogen metabolism, because these are essential requirements that the tumor cell may mollify but cannot escape by mutating • signalling and gene expression changes where they affect this metabolism • the inverse causality due to the microevolution context of the tumor in its environment : the functionality required of tumors ‘causing’ tumor phenotype, ‘causing’ tumor anatomy, ‘causing’ pathways, ‘causing’ molecular changes, ‘causing’ mutations • addressing the heterogeneity between cells in the same tumor as well as between tumors in different individuals • incorporating gene sequence, gene expression, physiological as well as life style changes into single models of individual humans and thereby constituting a rational avenue for personalized therapy of cancer • the possibility to validate the multiscale models experimentally • a comprehensive approach from molecular dynamics to epidemiology, coarse graining wherever possible using ‘transparent black boxes’, thereby retaining the linkage between molecules (drugs and mutated genes) and phenotype in the context of lifestyle and environment • a module by module approach, where each module corresponds to an important functional process in tumor development. • Definition of the modules in standardized input/output/quality terms such that modules developed by different groups/consortia  can subsequently be linked • ICT-facilitated virtual patient models as strategy to integrate all information for each individual thereby creating an avenue for personalized medicine medicine, such as in the ITFoM flagship