1. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Metabolic Modeling of Biology Stephen Fong Bioinformatics and Bioengineering Summer Institute Monday, June 16, 2008

2. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Overview Monday Applications of Modeling in Biology Tuesday How do we use Genome-scale Models? Running simulations

3. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Seminar Questions?

4. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Scenario Human genome sequenced at the end of 2001 3.2 billion bases –Only 0.1% difference between individuals (3.2 million discrete bases) What causes one person to be more susceptible to disease (cancer) than another person?

5. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Central Biological Problem Cause and effect relationships are central to most biological problems. Why is it hard to elucidate these relationships?

6. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Cellular components A + B C DNARNA Protein Metabolite Genomics Transcriptomics Proteomics Metabolomics Fluxomics

7. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Biological cause-effect DNA is the basic biological cause Problem is that biology is similar to the telephone game How can we track down where the changes are introduced?

8. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Setting up Experiments Define your question (What are you specifically studying?) Know your system (What are the important parameters?) Know the accuracy of your testing (What do I need to make conclusions?)

9. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab What does this look like? # of genes # of conditions

10. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab An Engineer’s View Living cells are chemical factories We are concerned with 2 things: 1. The condition of the factory (cell) 2. The factory products (chemicals)

11. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Medical/Health Applications

12. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Perspective We want to keep the cell functioning properly, so how do we monitor it to keep things running smoothly?

13. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Biomarkers Identify some characteristic of a cell that uniquely specifies its functional state Know the outcome, need to determine the real cause

14. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab In the News

15. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Cancer biomarkers Cancer antigen 125 (CA125) – associated with ovarian cancer Also found in people with pancreatic, kidney or liver disease Carcinoembryonic antigen (CEA) – associated with colorectal cancer Also found in people who smoke

16. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Options for Research 1.Tabulate data -Collect as much data as possible -Record the corresponding phenotype -Correlate results 2.Model it! -Use principles to predict effects -Verify with select data

17. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Phenomics in Humans National Center for Biotechnology Information (NCBI) is a government-run resource Online Mendelian Inheritance in Man (OMIM) compiles data on specific genes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

18. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Chemical Industry Applications

19. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Perspective We’re interested in what the cell is producing, how can we make it more efficient?

20. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Metabolism

21. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Cells as Chemical Factories Eukaryotes have specialized sub-cellular functions Prokaryotes are a mixed-bag

22. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Modeled Metabolism

23. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Constraint-based Model chemical reaction: aA + cC vivivivi eE + hH A-a B0 C-c D0 E+e F0 G0 H+h compounds vivi Representation as a column in a matrix: reactions

24. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Simulating a Gene Deletion chemical reaction: aA + cC vivivivi eE + hH A-a B0 C-c D0 E+e F0 G0 H+h compounds vivi Representation as a column in a matrix: reactions

25. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab OptKnock Algorithm Uncoupled Secretion at Max GR (wild-type) Coupled secretion at Max GR (designed strain) Fong et al., Biotech & Bioeng 2005 By-Product Secretion (mmol/g-DW hr)

26. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Systems-level metabolic engineering ComputationalExperimental Computational Model Genome-scale model Algorithmic Design OptKnock algorithm Strain Construction Gene deletion Adaptive evolution Strain Characterization By-product secretion

27. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Chemical targets Polymers and plastics Antibiotics Enzymes Fuels

28. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Constraints Example: The bouncing ball

29. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Genome-scale Extreme Pathways

30. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Scenario C 298 Metabolites 339 Reactions

31. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Introduction to Genome-scale Modeling

32. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Brainstorming: Modeling

33. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Why Develop Models? An accurate model: – Confirms our understanding of biology –Allows predictions to be made –Indicates areas where knowledge is incomplete

34. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Model: Biological Approach Plasmid partitioning

35. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Traditional Biological Model Process-specific Descriptive in nature Built for hypothesis-testing

36. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Model: Engineering/Math Approach Tegner, PNAS 100(10):5944-5949. 2003

37. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Traditional Math Modeling Process-specific Quantitatively detailed Fit to observed behavior

38. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Modeling Comparison BiologicalMathematical Pro Applicable to wide variety of processes Quantitatively predictive ConLimited predictive capability Difficult to develop for all processes

39. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Genome-scale Constraint-based Models A hybrid of biological and mathematical modeling

40. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Genome-scale modeling Conceptually the same as traditional biological approaches Differences: –Scale of model –Model is of organism instead of a process –Model is mathematical instead of illustrative

41. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Constraint-based modeling Line of Optimality (LO) Substrate uptake rate Oxygen uptake rate Constrained Solution space Unconstrained Solution space Growth rate By-production secretion Flux distributions Phenotype Phase Plane

42. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Constraint-based modeling Annotation argE ppc Phosphoenolpyruvate + H 2 O + CO 2 Oxaloacetate + Phosphate 1 Phosphoenolpyruvate H 2 O CO 2 Oxaloacetate Phosphate

43. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Linear Programming Results Cellular Growth rate Predicted flux through each reaction Transport in and out of chemicals Sensitivity of each flux

44. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Generations of constraints-based models: use of ‘omics’ data 1st generation –Hard constraints –Determine capabilities (what) 2nd generation –Regulation of expression –Determine choices (why) 3rd generation –Regulation of activity –Determine trajectories (how) Genomics –annotated sequence –legacy data Expression profiling –transcriptomics –proteomic Concentration data –metabolomics –proteomic

45. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Genome-scale Modeling Recap Built on genomic and biochemical data Scales easily for large systems, but assumes steady state Starting point for biological prediction and understanding system-wide cause and effect

46. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab The Delphic Boat www.lfk.lv

47. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Application to biology If every molecule in a cell is replaced over time, is it still the same cell? If every cell in an organism is replaced over time, is it still the same organism?

48. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab Reaction?

49. Virginia Commonwealth University Department of Chemical and Life Science Engineering Evolutionary Engineering Laboratory http://www.engineering.vcu.edu/fong-lab What does this mean? The connections/blue print that make up the boat and biological systems are important