1. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions Bordbar, A., Lewis, N. E., Schellenberger, J., Palsson, B. Ø. & Jamshidi, N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol. Syst. Biol. 6, 422 (2010). macrophage M. tuberculosis phagosome compartment 1

2. Tubercle bacillus About one-third of the world's population is infected! Only a 10% lifetime chance that the latent infection will progress to overt 9.27 million new cases and 1.76 million deaths in 2007 (WHO, 2009)WHO, 2009 the prevalence of TB per 100,000 people was highest in sub-Saharan Africa, and was also relatively high in Asia 2

3. Tubercle bacillus Tuberculosis typically attacks the lungs hematogenous transmission can also spread infection to more distant sites, such as peripheral lymph nodes, the kidneys, the brain, and the bones Antibiotic resistance is a growing problem in multiple drug- resistant tuberculosis (MDR-TB) infections. multiple drug- resistant tuberculosis Classic symptoms of active TB infection are a chronic cough with blood-tinged sputum, fever, night sweats, and weight loss 3

4. Key aspects of TB’s pathogenicy The environment of the Phagosome is nutrient poor, hypoxic, nitrosative and oxidative In order to survive TB accumulates mycolic and fatty acids on its cell wall. It also stops biomass accumulation fatty acids/lipids are the main carbon sources 4

5. Modeling the interaction 4 steps: 1) Construction of the MAC (I-MAT and GMME) 2) Adaptation of the TB (modified biomass rxn) 3) Integration of the 2 into TB-MAC model 4) Analysis TB-MAC model in different contexts (latent and infectious stages ) MAC:= Alveolar macrophage host model TB:= Mycobacterium tuberculosis model 5

6. Constructing the human alveolar macrophage, iAB-AMØ-1410 X 2 Biomass maintenance reaction- represents the turn over of Lipids, proteins, RNA, etc 6 Combined model +

7. ATP production- 96.1% agreement with in- vitro experiments Nitric oxide production ~ 98% accuracy High glucose oxidation leading to High rate of lactate production (like Warburg effect). Macrophage model - Results 7

8. Results: Macrophage model vs. Recon1 Majority of genes and reaction are preserved Small reduction in Reaction count but Large reduction of metabolic Functions is due to exchange constrains and removal of key reactions for Recon 1 Important Carbohydrate and central metabolism were well preserved as expected but Peripheral functions were not preserved 8

9. Infection in silico 9

10. Tweak the Biomass Reaction example (?): 10 Original Biomass reaction = ATP_COEF * ATP + 20 * NADH + 4 * Valine+ 7 * etc Where ATP_COEF=40 A) iterative sampling for each Biomass component 1) Set: biomass rxn flux >= 0.75 * max biomass flux 2) Preform Monte Carlo sampling in order to determine mean ATP flux. 3) Set new ATP_Coef and return to 1) B) Figure out the connection between flux and GE data (?) C) Based on the results of A above the function from B Find new_ATP_COEF to achieve the best fit between ATP flux and GE Data D) Final biomass function = new_ ATP_COEF * ATP + new_NADH_COEF * NADH + 7 * etc

11. Modifications of the original iNJ661 biomass objective function to produce the final infectious state TB objective function 11

12. Macrophage-TB combined model- Results: The integration radically decreases major objective function fluxes of the Macrophage: 51% reduction of the mean reaction flux span Max ATP, nitric oxide, NADH fluxes in the Macrophage: reduced by 75%,55%, 70% respectively. Bottom line: Macrophage solution space was substantially decreased without adding any additional constrains on its the internal reactions. 12

13. Integration and results of the alveolar macrophage (iAB-AMØ-1410) and Mycobacterium tuberculosis (iNJ661) reconstructions 13

14. Results: Changes in reaction activity of TB- A shift toward non carbohydrates usage -- Glycolysis is suppressed Gluconeogenesis is up regulated- Glucose is generate from non-carbohydrates Glyoxylate shunt is up regulated- Acytyl-Coa generated from fatty acids 14

15. Increased accuracy of gene deletion tests tests 15

16. Infection-specific models: latent, pulmonary, and meningeal tuberculosis Tuberculosis Macrophage Active infection Latent Infection Projection of Macrophage GE 16

17. Thanks ! 17

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19. Three infection-specific models 19