Multicellular metabolic models and methods

• US 8,949,032 B2
• Filed: 07/21/2005
• Issued: 02/03/2015
• Est. Priority Date: 03/29/2002
• Status: Active Grant

• Current Assignee: Genomatica Incorporated
• Original Assignee: Genomatica Incorporated
• Inventors: Famili, Imandokht, Schilling, Christophe H.
• Primary Examiner(s): SIMS, JASON M
• Application Number:
  US11/188,136
• Publication Number:
  US 20060147899A1
• Time in Patent Office: 3,484 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G01N 2500/10 involving cells
• CPC Class Codes: G01N 33/5008 for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16C 20/30 Prediction of properties of chemical compounds, compositions or mixtures

Abstract

The invention provides a computer readable medium or media, having: (a) a first data structure relating a plurality of reactants to a plurality of reactions from a first cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (b) a second data structure relating a plurality of reactants to a plurality of reactions from a second cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (c) a third data structure relating a plurality of intra-system reactants to a plurality of intra-system reactions between said first and second cells, each of said intra-system reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (d) a constraint set for said plurality of reactions for said first, second and third data structures, and (e) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said first and second data structures, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells. The first, second and third data structures also can include a plurality of data structures. Additionally provided is a method for predicting a physiological function of a multicellular organism. The method includes: (a) providing a first data structure relating a plurality of reactants to a plurality of reactions from a first cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (b) providing a second data structure relating a plurality of reactants to a plurality of reactions from a second cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (c) providing a third data structure relating a plurality of intra-system reactants to a plurality of intra-system reactions between said first and second cells, each of said intra-system reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (d) providing a constraint set for said plurality of reactions for said first, second and third data structures; (e) providing an objective function, and (f) determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said first and second data structures, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells.

Claims

1. A computer readable medium or media having stored thereon computer-implemented instructions causing a processor to generate an output describing a physiological function of a first cell and a second cell that interact with one another via an intercellular space by performing steps comprising:

(a) providing a first stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of first reactions within a first naturally occurring biochemical network within the first cell, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the first stoichiometric matrix relates said substrate and said product;

(b) providing a second stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of second reactions within a second naturally occurring biochemical network within the second cell, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the second stoichiometric matrix relates said substrate and said product;

(c) providing a third stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of intercellular reactions relating to an interaction between said first and second cells via a third naturally occurring biochemical network within the intercellular space, each of said intercellular reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the third stoichiometric matrix relates said substrate and said product;

(d) providing a constraint set for said plurality of reactions for said first, second, and third stoichiometric matrices, the constraint set specifying an upper or lower boundary of flux through each of the reactions described in the first, second, and third stoichiometric matrices;

(e) defining an objective function to be a linear combination of fluxes through the reactions described in the first, second, and third stoichiometric matrices that relates to a physiological function of said first and second cells;

(f) determining at least one flux distribution for said plurality of first, second, and intercellular reactions across said first cell, said second cell, and said intercellular space by (i) identifying a plurality of flux vectors that each satisfies the first, second, and third stoichiometric matrices and satisfies the constraint set and (ii) identifying at least one linear combination of the identified flux vectors that minimizes or maximizes the objective function, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells; and

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

2. The computer readable medium or media of claim 1, further comprising instructions causing the processor to provide one or more fourth stoichiometric matrices, each fourth stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of reactions within one or more third cells within a multicellular organism, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the one or more fourth stoichiometric matrices relates said substrate and said product.

3. The computer readable medium or media of claim 2, wherein said one or more fourth stoichiometric matrices comprises a plurality of stoichiometric matrices.

4. The computer readable medium or media of claim 3, wherein said plurality of stoichiometric matrices comprise a stoichiometric matrix for a plurality of different cells.

5. The computer readable medium or media of claim 2, wherein said plurality of stoichiometric matrices comprise a stoichiometric matrix for a plurality of different cell types.

6. The computer readable medium or media of claim 4 or 5, wherein said one or more third cells comprise at least 4 cells, 5 cells, 6 cells, 7 cells, 8 cells, 9 cells, 10 cells, 100cells, 1000 cells, 5000 cells, 10,000 cells or more.

7. The computer readable medium or media of claim 1, wherein said first and second cells comprise eukaryotic cells.

8. The computer readable medium or media of claim 1, wherein said first and second cells comprise prokaryotic cells.

9. The computer readable medium or media of claim 7, wherein said first and second eukaryotic cells comprise cells of the same tissue or organ.

10. The computer readable medium or media of claim 7, wherein said first and second eukaryotic cells comprise cells of different tissues or organs.

11. The computer readable medium or media of claim 1, wherein at least one of said reactions is annotated to indicate an associated gene.

12. The computer readable medium or media of claim 11, further comprising a gene database having information characterizing said associated gene.

13. The computer readable medium or media of claim 1, wherein at least one reaction within said plurality of first reactions, said plurality of second reactions, or said plurality of intercellular reactions is a regulated reaction.

14. The computer readable medium or media of claim 13, wherein said constraint set includes a variable constraint for said regulated reaction.

15. The computer readable medium or media of claim 1, wherein said plurality of intercellular reactions comprise one or more reactions performed in the hematopoietic system, urine, connective tissue, contractile system, lymphatic system, respiratory system or renal system.

16. The computer readable medium or media of claim 15, wherein said intercellular reactions comprise a reactant or reactions selected from the group consisting of a bicarbonate buffer system, an ammonia buffer system, a hormone, a signaling molecule, a vitamin, a mineral or a combination thereof.

17. The computer readable medium or media of claim 1, wherein said first or second cell is selected from a mammary gland cell, hepatocyte, white fat cell, brown fat cell, liver lipocyte, red skeletal muscle cell, white skeletal muscle cell, intermediate skeletal muscle cell, smooth muscle cell, red blood cell, adipocyte, monocyte, reticulocyte, fibroblast, neuronal cell epithelial cell or a cell set forth in Table 5.

18. The computer readable medium or media of claim 1, wherein said physiological function is selected from metabolite yield, ATP yield, biomass demand, growth, triacylglycerol storage, muscle contraction, milk secretion and oxygen transport capacity.

19. The computer readable medium or media of claim 1, wherein at least one reactant within said plurality of first reactions, said plurality of second reactions, or said plurality of intercellular reactions or at least one reaction within said plurality of first reactions, said plurality of second reactions, or said plurality of intercellular reactions is annotated with an assignment to a subsystem or compartment.

20. The computer readable medium or media of claim 19, wherein a first substrate or product in said plurality of reactions is assigned to a first compartment and a second substrate or product in said plurality of reactions is assigned to a second compartment.

21. The computer readable medium or media of claim 12, wherein a plurality of reactions is annotated to indicate a plurality of associated genes and wherein said gene database comprises information characterizing said plurality of associated genes.

22. A computer readable medium or media having stored thereon computer-implemented instructions causing a processor to generate an output describing a physiological function of a plurality of first cells and a plurality of second cells that interact with one another via an intercellular space by performing steps comprising:

(a) providing a plurality of first stoichiometric matrices having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of first reactions within a plurality of first naturally occurring biochemical networks within the plurality of first cells within a multicellular organism, each of said first reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the stoichiometric matrix relates said substrate and said product;

(b) providing a plurality of second stoichiometric matrices having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of second reactions within a plurality of second naturally occurring biochemical networks within the plurality of second cells within said multicellular organism, each of said second reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the stoichiometric matrix relates said substrate and said product;

(c) providing a plurality of third stoichiometric matrices having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of intercellular reactions relating to interactions between the plurality of first and second cells within said multicellular organism via a plurality of third naturally occurring biochemical networks within the intercellular space, each of said intercellular reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the stoichiometric matrix relates said substrate and said product;

(d) providing a constraint set for said plurality of reactions for said pluralities of first, second and third stoichiometric matrices, the constraint set specifying an upper or lower boundary of flux through each of the reactions described in the pluralities of first, second, and third stoichiometric matrices;

(e) defining an objective function to be a linear combination of fluxes through the reactions described in the pluralities of first, second, and third stoichiometric matrices that relates to a physiological function of said multicellular organism;

(f) determining at least one flux distribution for said pluralities of first, second, and intercellular reactions across said plurality of first cells, said plurality of second cells and said plurality of intercellular spaces by (i) identifying a plurality of flux vectors that each satisfies the pluralities of first, second, and third stoichiometric matrices and satisfies the constraint set and (ii) identifying at least one linear combination of the identified flux vectors within said multicellular organism that minimizes or maximizes the objective function, wherein said at least one flux distribution is predictive of a physiological function of said multicellular organism; and

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

23. The computer readable medium or media of claim 22, further comprising a plurality of fourth stoichiometric matrices, each of said plurality of fourth stoichiometric matrices having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of reactions within a plurality of third cells within a multicellular organism, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the plurality of fourth stoichiometric matrices relates said substrate and said product.

24. The computer readable medium or media of claim 23, wherein said plurality of first through fourth stoichiometric matrices comprise stoichiometric matrices for a plurality of different cells.

25. The computer readable medium or media of claim 23, wherein said plurality of first through fourth stoichiometric matrices comprise stoichiometric matrices for a plurality of different cell types.

26. The computer readable medium or media of claim 24 or 25, wherein said one or more third cells comprise at least 4 cells, 5 cells, 6 cells, 7 cells, 8 cells, 9 cells, 10 cells, 100 cells, 1000 cells, 5000 cells, 10,000 cells or more.

27. A computer implemented method for predicting a physiological function of a first cell and second cell that interact with one another via an intercellular space in a multicellular organism, comprising:

(a) providing on a computer a first stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of first reactions within a first naturally occurring biochemical network within the first cell, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the first stoichiometric matrix relates said substrate and said product;

(b) providing on a computer a second stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of second reactions within a second naturally occurring biochemical network within the second cell, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the second stoichiometric matrix relates said substrate and said product;

(c) providing on a computer a third stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of intercellular reactions relating to an interaction between said first and second cells via a third naturally occurring biochemical network within the intercellular space, each of said intercellular reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the third stoichiometric matrix relates said substrate and said product;

(d) providing a constraint set for said plurality of reactions for said first, second and third stoichiometric matrices, the constraint set specifying an upper or lower boundary of flux through each of the reactions described in the first, second, and third stoichiometric matrices;

(e) defining an objective function to be a linear combination of fluxes through the reactions described in the first, second, and third stoichiometric matrices that relates to a physiological function of said first and second cells;

(f) determining at least one flux distribution for said plurality of first, second, and intercellular reactions across said first cell, said second cell and said intercellular space by (i) identifying a plurality of flux vectors that each satisfies the first, second, and third stoichiometric matrices and satisfies the constraint set and (ii) identifying at least one linear combination of the identified flux vectors that minimizes or maximizes the objective function, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells; and

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

28. The method of claim 27, further comprising one or more fourth stoichiometric matrices, each fourth stoichiometric matrix having rows and columns of elements that correspond to stoichiometric coefficients of a plurality of reactions within one or more third cells within a multicellular organism, each of said reactions comprising a reactant identified as a substrate of the reaction and a reactant identified as a product of the reaction, wherein a stoichiometric coefficient of the one or more fourth stoichiometric matrices relates said substrate and said product.

29. The method of claim 28, wherein said one or more fourth stoichiometric matrices comprises a plurality of stoichiometric matrices.

30. The method of claim 29, wherein said plurality of stoichiometric matrices comprise a stoichiometric matrix for a plurality of different cells.

31. The method of claim 29, wherein said plurality of stoichiometric matrices comprise a stoichiometric matrix for a plurality of different cell types.

32. The method of claim 30 or 31, wherein said one or more third cells comprise at least 4 cells, 5 cells, 6 cells, 7 cells, 8 cells, 9 cells, 10 cells, 100 cells, 1000 cells, 5000 cells, 10,000 cells or more.

33. The method of claim 27, wherein said first and second cells comprise eukaryotic cells.

34. The method of claim 27, wherein said first and second cells comprise prokaryotic cells.

35. The method of claim 33, wherein said first and second eukaryotic cells comprise cells of the same tissue or organ.

36. The method of claim 33, wherein said first and second eukaryotic cells comprise cells of different tissues or organs.

37. The method of claim 27, wherein at least one of said reactions is annotated to indicate an associated gene.

38. The method of claim 27, further comprising a gene database having information characterizing said associated gene.

39. The method of claim 27, wherein at least one of said reactions is a regulated reaction.

40. The method of claim 39, wherein said constraint set includes a variable constraint for said regulated reaction.

41. The method of claim 27, wherein said at least one intercellular reaction comprises one or more reactions performed in the hematopoietic system, urine, connective tissue, contractile system, lymphatic system, respiratory system or renal system.

42. The method of claim 41, wherein said intercellular reactions comprise a reactant or reactions selected from the group consisting of a bicarbonate buffer system, an ammonia buffer system, a hormone, a signaling molecule, a vitamin, a mineral or a combination thereof.

43. The method of claim 27, wherein said first or second cell is selected from a mammary gland cell, hepatocyte, white fat cell, brown fat cell, liver lipocyte, red skeletal muscle cell, white skeletal muscle cell, intermediate skeletal muscle cell, smooth muscle cell, red blood cell, adipocyte, monocyte, reticulocyte, fibroblast, neuronal cell epithelial cell or a cell set forth in Table 5.

44. The method of claim 27, wherein said physiological function is selected from metabolite yield, ATP yield, biomass demand, growth, triacylglycerol storage, muscle contraction, milk secretion and oxygen transport capacity.

45. The method of claim 27, wherein at least one reactant within said plurality of first reactions, said plurality of second reactions, or said plurality of intercellular reactions or at least one reaction within said plurality of first reactions, said plurality of second reactions, or said plurality of intercellular reactions is annotated with an assignment to a subsystem or compartment.

46. The method of claim 45, wherein a first substrate or product in said plurality of reactions is assigned to a first compartment and a second substrate or product in said plurality of reactions is assigned to a second compartment.

47. The method of claim 38, wherein a plurality of reactions is annotated to indicate a plurality of associated genes and wherein said gene database comprises information characterizing said plurality of associated genes.