Means and methods for determining T cell recognition

1. A method for determining whether a sample from an individual contains T cells that recognize a tumor-specific T cell epitope or a T cell epitope from an autoantigen or from a pathogen, comprising:

inducing, enhancing and/or maintaining expression of Bcl-6 and/or STAT5 in at least one B cell;

inducing, enhancing and/or maintaining expression of an anti-apoptotic nucleic acid in said at least one B cell;

allowing expansion of said at least one B cell into a B cell culture;

incubating B cells of said B cell culture with at least one compound comprising said tumor-specific T cell epitope or said T cell epitope from an autoantigen or from a pathogen;

incubating the resulting B cells with T cells from said sample; and

determining whether at least one T cell recognizes said tumor-specific T cell epitope or said T cell epitope from an autoantigen or from a pathogen.

2. The method according to claim 1 , comprising incubating said B cells with at least one peptide.

3. The method according to claim 1 , wherein said at least one peptide has a length of between 5 and 40 amino acids, preferably between 8 and 35 amino acids or between 9 and 31 amino acids.

4. The method according to claim 1 , wherein said B cells are incubated with at least 2, preferably with at least 5, preferably with at least 10 different peptides.

5. The method according to claim 1 , wherein said T cells comprise CD8+ cytotoxic T cells and/or CD4+ helper T cells.

6. The method according to claim 1 , wherein said at least one B cell and said T cells are from the same human individual.

7. The method according to claim 1 , herein said T cell epitope is from a modified self-antigen or from a non-self antigen or from an autoantigen.

8. The method according to claim 1 , wherein said T cell epitope is a tumor-specific T cell epitope.

9. The method according to claim 8 , wherein said tumor is a melanoma or epithelial cancer.

10. The method according to claim 1 , wherein said T cell epitope is from a pathogen.

11. The method according to claim 10 , wherein said pathogen is a virus, a bacterium or a parasite.

12. The method according to claim 1 , wherein said T cell epitope is from an autoantigen.

13. The method according to claim 1 , wherein it is determined whether at least one T cell from said sample has recognized at least one of said T cell epitopes by determining whether said at least one T cell is activated.

14. The method according to claim 13 , wherein said T cell activation is determined by measuring cytokine release.

15. The method according to claim 1 , further comprising preparing a medicament comprising T cells that recognize at least one T cell epitope of said compounds.

16. The method according to claim 1 , further comprising identifying at least one T cell epitope recognized by a T cell.

17. The method according to claim 16 , further comprising preparing an immunogenic composition, or a prophylactic agent or vaccine, comprising said at least one T cell epitope.

18. The method according to claim 16 , further comprising preparing an immunogenic composition, or a prophylactic agent or vaccine, comprising an antigen presenting cell, preferably a B cell, which displays on its surface said at least one T cell epitope.

19. The method according to claim 1 , wherein the B cells are incubated with T cells from an individual suffering from, or having suffered from, a disorder.

20. The method according to claim 19 , wherein said individual is suffering from, or has suffered from, cancer, preferably melanoma or epithelial cancer.

21. The method according to claim 19 , wherein said individual is suffering from, or has suffered from, a pathogen, preferably a virus, a bacterium or a parasite.

22. The method according to claim 19 , wherein said individual is suffering from, or has suffered from, an autoimmune disease, preferably multiple sclerosis, diabetes or coeliac disease.

23. The method according to claim 1 , wherein said T cells are from a sample from said individual, characterized in that the proportion of T cells specific for a T cell epitope that is associated with said disease, relative to the total amount of T cells, is lower than 10%, more preferably lower than 9%, more preferably lower than 8%, more preferably lower than 7%, more preferably lower than 6%, more preferably lower than 5% in said sample or in a T cell culture after in vitro expansion of said sample.

24. The method according to claim 1 , wherein said T cells are from a sample from said individual, characterized in that the proportion of T cells specific for a T cell epitope that is associated with a disorder of interest, relative to the total amount of T cells, is lower than 1.9%, more preferably lower than 1.8%, more preferably lower than 1.7%, more preferably lower than 1.6%, more preferably lower than 1.5% in said sample or in a T cell culture after in vitro expansion of said sample.

25. The method according to claim 1 , wherein said T cells are from a sample from said individual, characterized in that the proportion of T cells specific for a T cell epitope that is associated with a disorder of interest, relative to the total amount of T cells, is lower than 1.0%, more preferably lower than 0.9%, more preferably lower than 0.8%, more preferably lower than 0.7%, more preferably lower than 0.6%, more preferably lower than 0.5%, more preferably lower than 0.4%, more preferably lower than 0.3% in said sample or in a T cell culture after in vitro expansion of said sample.

26. The method according to claim 1 , wherein a sample from said individual is used, or wherein T cells of a resulting T cell culture after in vitro expansion of said sample are used, wherein the percentage of T cells specific for a T cell epitope that is associated with said disease, relative to the total number of T cells in said sample or in said resulting in vitro T cell culture, is lower than 10%, more preferably lower than 9%, more preferably lower than 8%, more preferably lower than 7%, more preferably lower than 6%, more preferably lower than 5%.

27. The method according to claim 1 , wherein a sample from said individual is used, or wherein T cells of a resulting T cell culture after in vitro expansion of said sample are used, wherein the percentage of T cells specific for a T cell epitope that is associated with a disorder of interest, relative to the total number of T cells in said sample or in said resulting in vitro T cell culture, is lower than 1.9%, more preferably lower than 1.8%, more preferably lower than 1.7%, more preferably lower than 1.6%, more preferably lower than 1.5%.

28. The method according to claim 1 , wherein a sample from said individual is used, or wherein T cells of a resulting T cell culture after in vitro expansion of said sample are used, wherein the percentage of T cells specific for a T cell epitope that is associated with a disorder of interest, relative to the total number of T cells in said sample or in said resulting in vitro T cell culture, is lower than 1.0%, more preferably lower than 0.9%, more preferably lower than 0.8%, more preferably lower than 0.7%, more preferably lower than 0.6%, more preferably lower than 0.5%, more preferably lower than 0.4%, more preferably lower than 0.3%.

29. The method according to claim 23 , wherein said disease or said disorder is selected from the group consisting of cancer, preferably melanoma or epithelial cancer, an infectious disease, preferably a viral infection, a bacterial infection or a parasite infection, and an autoimmune disease, preferably multiple sclerosis, diabetes or coeliac disease.

30. The method according to claim 1 , wherein said anti-apoptotic nucleic acid comprises a gene encoding an anti-apoptotic molecule, preferably of the BCL2 family, preferably Bcl-xL, Mcl-1, Bcl-2, A1, Bcl-w, Bcl2L10, or a functional part or homologue thereof, most preferably Bcl-xL or Mcl 1.