Compositions and methods for enhancing mucosal immunity

A method of assessing the type of immune response in an inflammatory or autoimmune disease in a subject, the method comprising:

• a. detecting the level of cytokines IL2, IL13, IL4, IL5, IL17 and IL22 in a sample from the subject;
• b. determining the level of gene expression of at least one T cell biomarker selected from the group consisting of, Cd93, Large, Cpa3, Pde8a, Pgr, Nm1, Dapk1, Cyp4f39, Noxred1, Treml2, Fam213a, Bmp8, Lrrc32, Cyp11a1, tarm1, Chat2, Chil3, Gpm6b, Bace2, Lag3, Acbd7, Ctse, Hsd17b11 and Hrh4 in a sample from the subject;
• c. comparing the level of the cytokines or the at least one T cell biomarker in the sample from the subject to a baseline level in a control subject not having an inflammatory or autoimmune disease, wherein a higher level of the cytokines or the at least one T cell biomarker in the sample as compared to the level of the cytokines or the at least one T cell biomarker in the control is indicative of a g13Th1 or g13Th2 T cell response;
• and,
• d. wherein when a g13Th1 or g13Th2 T cell response is indicated, treatment of the inflammatory or autoimmune disease is recommended.

A method of detecting a pathological T cell response in an inflammatory or autoimmune disease in a subject, the method comprising:

• a. determining the presence of a pathological g13Th1 T cell by detecting the level of cytokines IL2, IL13, IL17, IL22 and IFNg in a sample from the subject;
• b. determining the level of gene expression of at least one pathological g13Th1 T cell biomarker selected from the group consisting of:
• Cd93, Large, Cpa3, Pde8a, Pgr, Nm1, Dapk1, Cyp4f39, Noxred1, Treml2;
• c. comparing the level of the cytokines or the at least one g13Th1 T cell biomarker in the sample from the subject to a baseline level in a control subject not having an inflammatory or autoimmune disease, wherein a higher level of the cytokines or the at least one g13Th1 T cell biomarker in the sample as compared to the level of the cytokines or the at least one g13Th1 T cell biomarker in the control is indicative of a pathological T cell response;
• and,
• d. wherein when a pathological T cell response is indicated, treatment of the inflammatory or autoimmune disease is recommended.

A method of detecting a pathological T cell response in an inflammatory or autoimmune disease in a subject, the method comprising:

• a. determining the presence of a pathological g13Th2 T cell by detecting the level of cytokines IL2, IL13, IL4, IL5 and IFNg in a sample from the subject;
• b. determining the level of gene expression of at least one g13Th2 T cell biomarker selected from the group consisting of:
• Fam213a, Bmp8, Lrrc32, Cyp11a1, tarm1, Chat2, Chil3, Gpm6b, Bace2, Lag3, Acbd7, Ctse, Hsd17b11 and Hrh4;
• c. comparing the level of the cytokines or the at least one g13Th2 T cell biomarker in the sample from the subject to a baseline level in a control subject not having an inflammatory or autoimmune disease, wherein a higher level of the cytokines or the at least one g13Th2 T cell biomarker in the sample as compared to the level of the cytokines or the at least one g13Th2 T cell biomarker in the control is indicative of a pathological T cell response;
• and,
• d. wherein when a pathological T cell response is indicated, treatment of the inflammatory or autoimmune disease is recommended.

A method of detecting a protective T cell response in an inflammatory or autoimmune disease in a subject, the method comprising:

• a. determining the presence of a protective g13Th1 T cell by detecting the level of cytokines IL2, IL13, IL17, IL22 and IFNg in a sample from the subject;
• b. determining the level of gene expression of at least one g13Th1 T cell biomarker selected from the group consisting of:
• Cd93, Large, Cpa3, Pde8a, Pgr, Nm1, Dapk1, Cyp4f39, Noxred1 and Treml2;
• c. comparing the level of the cytokines or the at least one g13Th1 T cell biomarker in the sample from the subject to a baseline level in a control subject not having an inflammatory or autoimmune disease, wherein a higher level of the cytokines or the at least one g13Th1 T cell biomarker in the sample as compared to the level of the cytokines and/or to the at least one g13Th1 T cell biomarker in the control is indicative of a protective T cell response;
• and,
• d. wherein when a protective T cell response is indicated, treatment of the inflammatory or autoimmune disease is recommended.

A method of detecting a protective T cell response in an inflammatory or autoimmune disease in a subject, the method comprising:

• a. determining the presence of a protective g13Th2 T cell by detecting the level of cytokines IL2, IL13, IL4, IL5 and IFNg in a sample from the subject;
• b. determining the level of gene expression of at least one g13Th2 T cell biomarker selected from the group consisting of:
• Fam213a, Bmp8, Lrrc32, Cyp11a1, tarm1, Chat2, Chil3, Gpm6b, Bace2, Lag3, Acbd7, Ctse, Hsd17b11 and Hrh4;
• c. comparing the level of the cytokines or the at least one g13Th2 T cell biomarker in the sample from the subject to a baseline level in a control subject not having an inflammatory or autoimmune disease, wherein a higher level of the cytokines or the at least one g13Th2 T cell biomarker in the sample as compared to the level of the cytokines and/or to the at least one g13Th2 T cell biomarker in the control is indicative of a protective T cell response;
• and,
• d. wherein when a protective T cell response is indicated, treatment of the inflammatory or autoimmune disease is recommended.