Sterol biosynthesis in infection and immunity.

1. Sterol biosynthesis in infection and immunity. Jane Hillston

2. Outline • Biological context • Modelling in SBGN and Bio-PEPA • Preliminary results • Future prospects

3. Host interaction pathways

4. Viruses associated with sterol pathway perturbation • Hepatitis C • Measles • HIV • West Nile • Dengue • Rotavirus • Polio Our model:- Cytomegalovirus (mCMV) infection of macrophages

5. Interacting pathways • The interaction between viral infection and the biosynthesis of cholesterol and its metabolites is not yet fully understood. • In particular the extent that it is due to direct or host-mediated (innate immune) mechanisms. • Drug treatment with statins, commonly used to suppress the sterol pathway. • The Ghazal lab have been conducting macrophage and in vivo experiments to investigate this relationship further, supported by computational models.

6. M Blanc et al (2010), under review

7. Pathway activity • 45 Entities • 26 Reactions • 47 Parameters M Blanc et al (2010), under review

8. Coordinate control • The experiments show that the effect of both the IFN and the viral infection is modification across the sterol pathway. • Statins, potent inhibitors of the sterol pathway, act quite differently. • Computational models were developed to investigate this further.

9. Modelling Workflow SBGN EdinburghPathwayEditor Bio-PEPA Eclipse-Plugin Bio-PEPA Work Bench SBGNtext2BioPEPA Logic Based Analyses PRISMetc. tools formodel checking Differential Equations CVODES, Dizzy, MatLabcompute expected means Stochastic Simulations StochKit, Dizzy compute expected variabilities L. Loewe et al. TCSB 2010

10. Modelling with SBGN • SBGN is a standardised graphical notation for capturing bio-chemical processes. • It offers different forms of diagram at different levels of abstraction. • The process diagrams, SBGN-PD, represent the dynamic behaviour of pathways. • However SBGN-PD does not capture any quantified information about the modelled process.

11. SBGN Process Diagrams are based on the Process Flow Abstraction

12. SBGN Process Diagrams are based on the Process Flow Abstraction

14. SBGN-PD in EPE with Quantitative Extensions

15. Bio-PEPA • Bio-PEPA • is a stochastic process algebra • compositional structure allows interacting models • represents the model independently from solvers • supports a large variety of mathematical techniques • active development constantly expands the repertoire of analysis techniques Ciocchetta & Hillston, TCS 2009

16. Bio-PEPA Syntax Core • The key is the definition of 'sequential components', where each component defines a chemical species. • Each sequential component lists all reactions that a species can be involved in.species = (reaction, stoichiometry) OP species + (react... OP paper OP code Role of species Meaning

17. Mapping SBGNtext to Bio-PEPA • Entity Pool Nodes => sequential species components • Processes => actions • Propensity functions => kinetic laws of actions • Quantitative properties => parameters in kinetic laws • Arc types => operator in sequential species component

18. Mapping SBGN-PD to Bio-PEPA (ii)

19. Dosing with statins • Given the widespread use of statins there is remarkably little quantitative knowledge about the sterol pathway. • Only 21/47 parameters were known. • Our initial study considered the dose of statin based on different assumptions about the abundance of a key enzyme in the pathway.

20. Sterol pathway inhibited with statin

21. Response of cholesterol flux to statin dose L Loewe et al, TCSB 2010

22. Temporal dynamics • Shutting down cholesterol production by competitive inhibition leads to accumulation of the metabolite HMG-CoA. • Inhibition of the pathway relies on excess of statin with respect to HMG-CoA. • So prolonged suppression of the pathway requires higher dosage of statin.

23. Statin loses inhibitory power over time L. Loewe et al, TCSB 2010

24. Coordinate control studies • These preliminary studies established the validity of the model. • We are now using the model to investigate the mechanisms of coordinated control which appear to be in operation in the cell under viral infection.

25. Coordinate control – no inhibition

26. Coordinate control – high statin dose

27. Coordinate control – multiple small inhibitions

28. Multi-scale systems • Cholesterol biosynthesis is implicated in many diseases: in the US 35.7 million are at high risk due to cholesterol levels (American Heart Association) • Chronic heart disease • Inflammation • Arterosclerosis • Fully understanding these will require many contributing models to be brought together to understand the overall process

29. Biological impact of statins at multi-organ level M Blanc et al (2010), under review

30. On-going work • In the short term we plan to further investigate the mechanisms of coordinate control. • Future work will continue to use the cycle of modelling and experimentation to expand our understanding of the system, working towards a multi-scale model.

31. Acknowledgements • Mattieu Blanc • Steven Watterson • Kevin A Robertson • GuanghouShui • Paul Lacaze • MizanurKhondoker • Paul Dickinson • Garwin Sing • Sara Rodriguez-Martin • Wayne Hsieh • Maria Luisa Guerriero • Stuart Moodie • Maire C O’Sullivan • Holly Gibbs • Thorsten Forster • Birgit Strobl • Mattias Mueller • Daniel M Wall • Rudolph Riemersma • Markus R Wenk • Ana Angulo • Stephen Gilmore • Laurence Loewe • Peter Ghazal Wellcome Trust