Human metabolic models and methods

• US 8,229,673 B2
• Filed: 03/27/2003
• Issued: 07/24/2012
• Est. Priority Date: 03/29/2002
• Status: Expired due to Fees

• Current Assignee: Genomatica Incorporated
• Original Assignee: Genomatica Incorporated
• Inventors: Palsson, Bornhard O., Famili, Imandokht, Covert, Markus W., Schilling, Christophe H.
• Primary Examiner(s): SIMS, JASON M
• Application Number:
  US10/402,854
• Publication Number:
  US 20040029149A1
• Time in Patent Office: 3,407 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 5/10 Boolean models
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

The invention provides in silico models for determining the physiological function of human cells, including human skeletal muscle cells. The models include a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, a constraint set for the plurality of Homo sapiens reactions, and commands for determining a distribution of flux through the reactions that is predictive of a Homo sapiens physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated Homo sapiens reaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silico Homo sapiens model and methods for determining a Homo sapiens physiological function using a model of the invention.

Claims

1. A computer readable medium or media having stored thereon computer-implemented instructions suitably programmed to cause a processor to perform the computer executable steps of:

(a) providing a stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of Homo sapiens reactions between a plurality of Homo sapiens reactants,

wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, the stoichiometric coefficient relating said substrate and said product,

wherein at least one of said Homo sapiens reactions is annotated to indicate an associated gene encoding a macromolecule that performs said reaction and wherein a plurality of chemically and electrochemically balanced Homo sapiens reactions are assigned to a plurality of different membranous compartments;

(b) providing a gene database comprising information characterizing said associated gene;

(c) providing a constraint set for said plurality of Homo sapiens reactions, the constraint set representing an upper or lower boundary condition of flux through each of the Homo sapiens reactions described in the stoichiometric matrix;

(d) defining an objective function to be a linear combination of fluxes through the Homo sapiens reactions described in the stoichiometric matrix that optimizes cell growth, reproduction, apoptosis, energy production, production of a particular compound, or a mechanical property;

(e) determining at least one steady state flux distribution for said plurality of chemically and electrochemically balanced Homo sapiens reactions across said plurality of different membranous compartments by (i) identifying a plurality of flux vectors that each satisfy a steady state condition for the stoichiometric matrix and satisfy the constraint set and (ii) identifying at least one linear combination of the flux vectors that minimizes or maximizes the objective function, wherein said at least one steady state flux distribution is predictive of a Homo sapiens physiological function at steady state; and

(f) providing output to a user of said at least one steady state flux distribution determined in step (e).

2. The computer readable medium or media of claim 1, wherein said plurality of Homo sapiens reactions comprises at least one reaction from a peripheral metabolic pathway.

3. The computer readable medium or media of claim 2, wherein said peripheral metabolic pathway is selected from the group consisting of amino acid biosynthesis, amino acid degradation, purine biosynthesis, pyrimidine biosynthesis, lipid biosynthesis, fatty acid metabolism, cofactor biosynthesis and transport processes.

4. The computer readable medium or media of claim 1, wherein said Homo sapiens physiological function is selected from the group consisting of growth, energy production, redox equivalent production, biomass production, production of biomass precursors, production of a protein, production of an amino acid, production of a purine, production of a pyrimidine, production of a lipid, production of a fatty acid, production of a cofactor, transport of a metabolite, and consumption of carbon, nitrogen, sulfur, phosphate, hydrogen or oxygen.

5. The computer readable medium or media of claim 1, wherein said Homo sapiens physiological function is selected from the group consisting of degradation of a protein, degradation of an amino acid, degradation of a purine, degradation of a pyrimidine, degradation of a lipid, degradation of a fatty acid and degradation of a cofactor.

6. The computer readable medium or media of claim 1, wherein a first substrate or product in said plurality of Homo sapiens reactions is assigned to a first compartment and a second substrate or product in said plurality of Homo sapiens reactions is assigned to a second compartment.

7. The computer readable medium or media of claim 1, wherein a plurality of said Homo sapiens reactions is annotated to indicate a plurality of associated genes and wherein said gene database comprises information characterizing said plurality of associated genes.

8. The computer readable medium or media of claim 1, wherein at least one of said Homo sapiens reactions is a regulated reaction and wherein said constraint set includes a variable boundary condition for said regulated reaction.

9. The computer readable medium or media of claim 8, wherein said variable boundary condition is dependent upon an outcome of at least one reaction in said stoichiometric matrix.

10. The computer readable medium or media of claim 8, wherein said variable boundary condition is dependent upon an outcome of a regulatory event.

11. The computer readable medium or media of claim 8, wherein said variable boundary condition is dependent upon time.

12. The computer readable medium or media of claim 8, wherein said variable boundary condition is dependent upon the presence of a biochemical reaction network participant.

13. The computer readable medium or media of claim 12, wherein said participant is selected from the group consisting of a substrate, product, reaction, protein, macromolecule, enzyme and gene.

14. The computer readable medium or media of claim 8, wherein a plurality of said reactions are regulated reactions and said constraint set comprises variable boundary conditions for said regulated reactions.

15. The computer readable medium or media of claim 1, wherein the stoichiometric matrix includes rows and columns of elements that correspond to stoichiometric coefficients of a plurality of Homo sapiens reactions between a plurality of Homo sapiens skeletal muscle cell reactants, and

wherein said at least one flux distribution is predictive of Homo sapiens skeletal muscle cell energy production.

16. A method for predicting a Homo sapiens physiological function, the method comprising:

(a) providing a stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of Homo sapiens reactions between a plurality of Homo sapiens reactants,

wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, the stoichiometric coefficient relating said substrate and said product,

wherein at least one of said Homo sapiens reactions is annotated to indicate an associated gene encoding a macromolecule that performs said reaction and wherein a plurality of chemically and electrochemically balanced Homo sapiens reactions are assigned to a plurality of different membranous compartments;

(b) providing a gene database comprising information characterizing said associated gene;

(c) providing a constraint set for said plurality of Homo sapiens reactions, the constraint set representing an upper or lower boundary condition of flux through each of the Homo sapiens reactions described in the stoichiometric matrix;

(d) defining an objective function to be a linear combination of fluxes through the Homo sapiens reactions described in the stoichiometric matrix that optimizes cell growth, reproduction, apoptosis, energy production, production of a particular compound, or a mechanical property;

(e) determining at least one steady state flux distribution for said plurality of chemically and electrochemically balanced Homo sapiens reactions across said plurality of different membranous compartments by (i) identifying a plurality of flux vectors that each satisfy a steady state condition for the stoichiometric matrix and satisfy the constrain set and (ii) identifying at least one linear combination of the flux vectors that minimizes or maximizes said objective function, wherein said at least one steady state flux distribution is predictive of a Homo sapiens physiological function; and

(f) providing output to a user of said at least one steady state flux distribution determined ins step (e).

17. The method of claim 16, wherein said plurality of Homo sapiens reactions comprises at least one reaction from a peripheral metabolic pathway.

18. The method of claim 17, wherein said peripheral metabolic pathway is selected from the group consisting of amino acid biosynthesis, amino acid degradation, purine biosynthesis, pyrimidine biosynthesis, lipid biosynthesis, fatty acid metabolism, cofactor biosynthesis and transport processes.

19. The method of claim 16, wherein said Homo sapiens physiological function is selected from the group consisting of growth, energy production, redox equivalent production, biomass production, production of biomass precursors, production of a protein, production of an amino acid, production of a purine, production of a pyrimidine, production of a lipid, production of a fatty acid, production of a cofactor, transport of a metabolite, and consumption of carbon, nitrogen, sulfur, phosphate, hydrogen or oxygen.

20. The method of claim 16, wherein said Homo sapiens physiological function is selected from the group consisting of glycolysis, the TCA cycle, pentose phosphate pathway, respiration, biosynthesis of an amino acid, degradation of an amino acid, biosynthesis of a purine, biosynthesis of a pyrimidine, biosynthesis of a lipid, metabolism of a fatty acid, biosynthesis of a cofactor, transport of a metabolite and metabolism of a carbon source, nitrogen source, oxygen source, phosphate source, hydrogen source or sulfur source.

21. The method of claim 16, further comprising:

(g) providing a modified stoichiometric matrix, wherein said modified stoichiometric matrix comprises at least one row of elements corresponding to stoichiometric coefficients of at least one added reaction, compared to the stoichiometric matrix of step (a), and

(h) determining at least one modified steady state flux distribution by (i) identifying a modified plurality of flux vectors that satisfy the steady state condition for the modified stoichiometric matrix and (ii) identifying at least one linear combination of the modified flux vectors that minimizes or maximizes said objective function, thereby predicting a modified Homo sapiens physiological function.

22. The method of claim 21, further comprising identifying at least one participant in said at least one added reaction.

23. The method of claim 22, wherein said identifying at least one participant comprises associating a Homo sapiens protein with said at least one reaction.

24. The method of claim 23, further comprising identifying at least one gene that encodes said protein.

25. The method of claim 22, further comprising identifying at least one compound that alters the activity or amount of said at least one participant, thereby identifying a candidate drug or agent that alters a Homo sapiens physiological function.

26. The method of claim 16, further comprising:

(e) providing a modified data structure, wherein said modified data structure lacks at least one reaction compared to the data structure of part (a), and

(f) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said modified data structure, thereby predicting a Homo sapiens physiological function.

27. The method of claim 26, further comprising identifying at least one participant in said at least one reaction.

28. The method of claim 27, wherein said identifying at least one participant comprises associating a Homo sapiens protein with said at least one reaction.

29. The method of claim 28, further comprising identifying at least one gene that encodes said protein that performs said at least one reaction.

30. The method of claim 27, further comprising identifying at least one compound that alters the activity or amount of said at least one participant, thereby identifying a candidate drug or agent that alters a Homo sapiens physiological function.

31. The method of claim 16, further comprising:

(g) providing a modified constraint set, wherein said modified constraint set comprises a changed upper or lower boundary condition of flux through at least one reaction compared to the upper or lower boundary condition of flux through that reaction in step (c), and

(h) determining at least one modified steady state flux distribution by (i) identifying a modified plurality of flux vectors that satisfy the steady state condition for the stoichiometric matrix and satisfy the modified constraint set and (ii) identifying at least one linear combination of the modified flux vectors that minimizes or maximizes said objective function, thereby predicting a modified Homo sapiens physiological function.

32. The method of claim 31, further comprising identifying at least one participant in said at least one reaction.

33. The method of claim 32, wherein said identifying at least one participant comprises associating a Homo sapiens protein with said at least one reaction.

34. The method of claim 33, further comprising identifying at least one gene that encodes said protein.

35. The method of claim 32, further comprising identifying at least one compound that alters the activity or amount of said at least one participant, thereby identifying a candidate drug or agent that alters a Homo sapiens physiological function.

36. The method of claim 16, wherein the gene database relates one or more reactions in said data structure with one or more genes or proteins in Homo sapiens.

37. The method of claim 16, wherein at least one of said Homo sapiens reactions is a regulated reaction and wherein said constraint set includes a variable boundary condition for said regulated reaction.

38. The method of claim 37, wherein said variable boundary condition changes in response to an outcome of at least one reaction in said stoichiometric matrix.

39. The method of claim 37, wherein said variable boundary condition changes in response to an outcome of a regulatory event.

40. The method of claim 37, wherein said variable boundary condition changes in response to time.

41. The method of claim 37, wherein said variable boundary condition changes in response to the presence of a biochemical reaction network participant.

42. The method of claim 41, wherein said participant is selected from the group consisting of a substrate, product, reaction, enzyme, protein, macromolecule and gene.

43. The method of claim 37, wherein a plurality of said reactions are regulated reactions and said constraint set comprises variable boundary conditions for said regulated reactions.

44. The method of claim 16, wherein the stoichiometric matrix includes rows and columns of elements that correspond to stoichiometric coefficients of a plurality of Homo sapiens reactions between a plurality of Homo sapiens skeletal muscle cell reactants wherein said at least one steady state flux distribution is predictive of Homo sapiens skeletal muscle cell energy production.