US 8,949,032 B2 · Multicellular metabolic models and methods

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.

Claims47

Dependent claims

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).

5 more elements

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).

5 more elements

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).

5 more elements

Dependencies are inferred from the claim text.

Multicellular metabolic models and methods

Life of this patent

Multicellular metabolic models and methods

Life of this patent

Abstract

Claims47