Apparatus and method for computer modeling type 1 diabetes

• US 20070071681A1
• Filed: 03/15/2006
• Published: 03/29/2007
• Est. Priority Date: 03/15/2005
• Status: Abandoned Application

• Current Assignee: Entelos, Inc. (SilkRoad Inc.)
• Original Assignee: Entelos, Inc. (SilkRoad Inc.)
• Inventors: Paterson, Thomas, Polidori, David, Young, Daniel, Ramanujan, Saroja, Zheng, Yanan, Gadkar, Kapil, Kreuwel, Huub, Whiting, Chan, Shoda, Lisl Katharine Mie
• Application Number:
  US11/377,614
• Publication Number:
  US 20070071681A1
• Time in Patent Office: Days
• US Class Current: 424/9.200
• CPC Class Codes: G01N 2800/042 Disorders of carbohydrate metabolism, e.g. diabetes, glucose metabolism
• 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: G16H 50/50 for simulation or modelling of medical disorders

Abstract

The invention encompasses novel methods for developing a computer model of type 1 diabetes in a mammal. In particular, the models can include representations of biological processes associated with a pancreatic lymph node and one or more pancreatic islets. Alternatively, the models can include representations of biological processes associated with at least two conditions selected from the group consisting of autoreactive T cell production, autoreactive T cell priming, insulitis and hyperglycemia. The invention also provides methods for developing a computer model of a non-insulin replacement treatment of type 1 diabetes. The invention also encompasses computer models of type 1 diabetes, methods of simulating type 1 diabetes and computer systems for simulating type 1 diabetes and the uses thereof.

Claims

1. A method for developing a model of type 1 diabetes said method comprising:

identifying one or more biological processes associated with a pancreatic lymph node;

identifying one or more biological processes associate with one or more pancreatic islets;

mathematically representing each biological process to generate one or more representations of a biological process associated with the pancreatic lymph node and one or more representations of a biological process associated with the one or more pancreatic islets; and

combining the representations of biological processes to form a model of type 1 diabetes.

2. The method of claim 1, further comprising:

identifying one or more biological processes associated with a gut and/or gut associated lymphoid tissue; and

mathematically representing each biological process associated with the gut and/or gut associated lymphoid tissue.

3. The method of claim 1, wherein the one or more pancreatic islets comprises at least two pancreatic islets.

4. The method of claim 1, wherein at least one of the one or more biological processes associated with a pancreatic lymph node is a biological process related to a balance of effector and regulatory cell populations.

5. The method of claim 4, wherein the regulatory cell population comprises cells of lymphoid lineage.

6. The method of claim 4, wherein the regulatory cell population comprises regulatory T cells.

7. The method of claim 6, wherein the regulatory T cells of the regulatory cell population do not express intrinsic effector cell activity.

8. The method of claim 6, wherein the regulatory T cells of the regulatory cell population include both innate regulatory T cells and adaptive regulatory T cells.

9. The method of claim 6, wherein the regulatory T cells of the regulatory cell population suppress effector T cell activity via direct and indirect mechanisms.

10. The method of claim 1, wherein at least one of the one or more biological processes associated with one or more pancreatic islets is a biological process related to a balance of effector and regulatory cell populations.

11. The method of claim 10, wherein the regulatory cell population comprises cells of lymphoid lineage.

12. The method of claim 10, wherein the regulatory cell population comprises regulatory T cells.

13. The method of claim 12, wherein the regulatory T cells of the regulatory cell population do not express intrinsic effector cell activity.

14. A computer-readable medium having computer-readable instructions stored thereon that, upon execution by a processor, cause the processor to simulate type 1 diabetes, and further wherein the instructions comprise:

a) mathematically representing one or more biological processes associated with a pancreatic lymph node;

b) mathematically representing one or more biological processes associated with one or more pancreatic islets;

c) defining a set of mathematical relationships between the representations of biological processes to form a model of type 1 diabetes.

15. The computer-readable medium of claim 14, wherein the instructions further comprise mathematically representing one or more biological processes associated with a gut and/or gut associated lymphoid tissue.

16. The computer-readable medium of claim 14, wherein the instructions further comprise accepting user input specifying one or more parameters associated with one or more of the mathematical representations.

17. The computer-readable medium of claim 14, wherein the instructions further comprise accepting user input specifying one or more variables associated with one or more of the mathematical representations.

18. The computer-readable medium of claim 14, wherein the instructions further comprise applying a virtual protocol to the model of type 1 diabetes.

19. The computer-readable medium of claim 14, wherein the instructions further comprise defining one or more virtual patients.

49. A method of simulating type 1 diabetes, said method comprising executing a computer model of type 1 diabetes according to any one of claims 14, 25 and 41.

53. The method of claim 49, further comprising accepting user input specifying one or more parameters or variable associated with one or more mathematical representations prior to executing the computer model.

54. The method of claim 53, wherein the user input comprises a definition of a virtual patient.

20. A system, comprising:

a) a processor including computer-readable instructions stored thereon that, upon execution by a processor, cause the processor to simulate type 1 diabetes in a mammal, the computer readable instructions comprising;

i) mathematically representing one or more biological processes associated with a pancreatic lymph node;

ii) mathematically representing one or more biological processes associated with one or more pancreatic islets;

iii) defining a set of mathematical relationships between the representations of biological processes associated with the pancreatic lymph node and representations of biological processes associated with the one or more pancreatic islets;

iv) applying a virtual protocol to the set of mathematical relationships to generate a set of outputs;

b) a first user terminal, the first user terminal operable to receive a user input specifying one or more parameters associated with one or more mathematical representations defined by the computer readable instructions; and

c) a second user terminal, the second user terminal operable to provide the set of outputs to a second user.

21. A method for developing a model of progression of type 1 diabetes said method comprising:

identifying one or more biological processes associated with development of each of at least two conditions selected from the group consisting of autoreactive T cell production, autoreactive T cell priming;

insulitis and hyperglycemia;

mathematically representing each biological process to generate one or more representations of a biological process associated with each of the at least two conditions; and

combining the representations of biological processes to form a model of progression of type 1 diabetes.

22. The method of claim 21, wherein the at least two conditions comprise insulitis and hyperglycemia.

23. The method of claim 21, wherein the at least two conditions comprise autoreactive T cell priming.

24. The method of claim 21, wherein autoreactive T cell priming includes a biological process related to a balance of effector and regulatory cell populations.

25. A computer-readable medium having computer-readable instructions stored thereon that, upon execution by a processor, cause the processor to simulate progression of type 1 diabetes, and further wherein the instructions comprise:

a) mathematically representing one or more biological processes associated with development of each of at least two conditions selected from the group consisting of autoreactive T cell production, autoreactive T cell priming;

insulitis and hyperglycemia;

b) defining a set of mathematical relationships between the representations of biological processes to form a model of progression of type 1 diabetes.

26. The computer-readable medium of claim 25, wherein the instructions further comprise accepting user input specifying one or more parameters associated with one or more of the mathematical representations.

27. The computer-readable medium of claim 25, wherein the instructions further comprise accepting user input specifying one or more variables associated with one or more of the mathematical representations.

28. The computer-readable medium of claim 25, wherein the instructions further comprise applying a virtual protocol to the model of type 1 diabetes.

29. The computer-readable medium of claim 25, wherein the instructions further comprise defining one or more virtual patients.

30. A system, comprising:

a) a processor including computer-readable instructions stored thereon that, upon execution by a processor, cause the processor to simulate progression of type 1 diabetes in a mammal, the computer readable instructions comprising;

i) mathematically representing one or more biological processes associated with development of each of at least two conditions selected from the group consisting of autoreactive T cell production, autoreactive T cell priming;

insulitis and hyperglycemia;

ii) defining a set of mathematical relationships between the representations of biological processes associated with the at least two conditions;

iii) applying a virtual protocol to the set of mathematical relationships to generate a set of outputs;

b) a first user terminal, the first user terminal operable to receive a user input specifying one or more parameters associated with one or more mathematical representations defined by the computer readable instructions; and

c) a second user terminal, the second user terminal operable to provide the set of outputs to a second user.

31. A method for developing a model of a non-insulin replacement treatment of type 1 diabetes said method comprising:

identifying one or more biological processes associated with a β

cell population in at least one of one or more pancreatic islets;

identifying one or more biological processes associated with an effect of the non-insulin replacement treatment of type 1 diabetes;

mathematically representing each biological process to generate one or more representations of a biological process associated with the β

cell population and one or more representations of a biological process associated with an effect of the non-insulin replacement treatment of type 1 diabetes; and

combining the representations of biological processes to form a model of a non-insulin replacement treatment of type 1 diabetes.

32. The method of claim 31, further comprising the steps of:

identifying one or more biological processes associated with a pancreatic lymph node; and

mathematically representing each biological process to generate one or more representations of a biological process associated with the pancreatic lymph node.

33. The method of claim 31, wherein the one or more biological processes associated with the β

cells comprises a biological process associated with an autoimmune response against the β

cells.

34. The method of claim 31, wherein the one or more biological processes associated with increasing β

cells comprises a biological process associated with resistance of the β

cells to death.

35. The method of claim 31, wherein the one or more biological processes associated with increasing β

cells comprises a biological process associated with β

cell proliferation.

36. The method of claim 31, wherein the one or more biological processes associated with increasing β

cells comprises a biological process associated with β

cell neogenesis.

37. The method of claim 31, wherein at least one of the one or more biological processes associated with the β

cell population is a biological process related to a balance of effector and regulatory cell populations.

38. The method of claim 37, wherein the regulatory cell population comprises cells of lymphoid lineage.

39. The method of claim 37, wherein the regulatory cell population comprises regulatory T cells.

40. The method of claim 39, wherein the regulatory T cells of the regulatory cell population do not express intrinsic effector cell activity.

41. A computer-readable medium having computer-readable instructions stored thereon that, upon execution by a processor, cause the processor to a non-insulin replacement treatment of type 1 diabetes and further wherein the instructions comprise:

a) mathematically representing one or more biological processes associated with a cell population in at least one of one or more pancreatic islets;

b) mathematically representing one or more biological processes associated with an effect of the non-insulin replacement treatment of type 1 diabetes;

c) defining a set of mathematical relationships between the representations of biological processes to form a model of the non-insulin replacement treatment of type 1 diabetes.

42. The computer-readable medium of claim 41, wherein the instructions further comprise mathematically representing one or more biological processes associated with a pancreatic lymph node.

43. The computer-readable medium of claim 41, wherein the instructions further comprise mathematically representing one or more biological processes associated with a gut and/or gut associated lymphoid tissue.

44. The computer-readable medium of claim 41, wherein the instructions further comprise accepting user input specifying one or more parameters associated with one or more of the mathematical representations.

45. The computer-readable medium of claim 41, wherein the instructions further comprise accepting user input specifying one or more variables associated with one or more of the mathematical representations.

46. The computer-readable medium of claim 41, wherein the instructions further comprise applying a virtual protocol to the model of type 1 diabetes.

47. The computer-readable medium of claim 41, wherein the instructions further comprise defining one or more virtual patients.

50. The method of claim 46, further comprising applying a virtual protocol to the computer model to generate set of outputs representing a phenotype of type 1 diabetes.

51. The method of claim 50, wherein the virtual protocol comprises a therapeutic regimen, a diagnostic procedure, passage of time, or exposure to environmental toxins.

52. The method of claim 50, wherein the phenotype represents a diseased state.

48. A system, comprising:

a) a processor including computer-readable instructions stored thereon that, upon execution by a processor, cause the processor to simulate progression of type 1 diabetes in a mammal, the computer readable instructions comprising;

i) mathematically representing one or more biological processes associated with one or more pancreatic islets;

ii) mathematically representing one or more biological processes associated with a β

cell population in at least one of the one or more pancreatic islets;

iii) mathematically representing one or more biological processes associated with an effect of a non-insulin replacement treatment of type 1 diabetes;

iv) defining a set of mathematical relationships between the representations of biological processes associated with the one or more pancreatic islets and the representations of biological processes associated with the β

cell population and the representations associated with an effect of the non-insulin replacement treatment of type 1 diabetes;

v) applying a virtual protocol to the set of mathematical relationships to generate a set of outputs;

b) a first user terminal, the first user terminal operable to receive a user input specifying one or more parameters associated with one or more mathematical representations defined by the computer readable instructions; and

c) a second user terminal, the second user terminal operable to provide the set of outputs to a second user.

55. A computer-based mathematical model of a biological system comprising a representation of a tissue, wherein the tissue comprises a plurality of distinct distributed sites and the representation of the tissue comprises a plurality of representations, wherein each of the plurality of representations associated with one of the plurality of distinct distributed sites.

56. The model of claim 55, wherein the tissue is selected from the group consisting of lung, brain, liver, joints, intestine and pancreas.

57. the model of claim 55, wherein the distinct distributed sites describe spatial heterogeneity within the tissue.

58. The model of claim 55, wherein the distinct distributed sites describe temporal heterogeneity within the tissue.

59. The model of claim 55, wherein the distinct distributed sites describe distinct stages in progression of a disorder within the tissue.