Epigenetic method for the identification of subpopulations of CD8+ T lymphocytes, in particular CD8 alpha and beta T lymphocytes

1. A method for identifying CD3+CD8+ natural killer T cells (NKT cells) in a sample derived from a human, wherein said method comprises:

i) determining the methylation status of at least one CpG position in a genomic region for CD8 beta from the human sample, said genomic region comprising SEQ ID NO: 5 and/or SEQ ID NO: 6, comprising the steps of:

a) treating the genomic region comprising SEQ ID NO: 5 and/or SEQ ID NO: 6 with bisulfite,

b) amplifying the bisulfite treated genomic region comprising SEQ ID NO: 5 with a first primer pair of SEQ ID NOs: 8 and 9 to produce a first amplicon, and/or amplifying the bisulfite treated genomic region comprising SEQ ID NO: 6 with a second primer pair of SEQ ID NOs: 10 and 11 to produce a second amplicon,

c) determining in the first amplicon the methylation status of the CpG positions 40, 63, 95, 135, 142, 169, 194, 213, 216, 232, 245, 273, 339, 345, and 393, the CpG positions being relative to SEQ ID NO: 5 and/or determining in the second amplicon the methylation status of the CpG positions 165, 196, 219, 267, 277, 307, 314, 341, and 410, the CpG positions being relative to SEQ ID NO: 6; and

ii) determining the methylation status of at least one CpG position in a genomic region for CD8 alpha from the human sample, said genomic region comprising SEQ ID NO: 7, comprising the steps of:

a) treating the genomic region comprising SEQ ID NO: 7 with bisulfite,

b) amplifying the bisulfite treated genomic region comprising SEQ ID NO: 7 with a suitable primer pair to produce a third amplicon,

c) determining in the third amplicon the methylation status of the CpG positions 67, 92, 116, 123, 133, 161, 199, 231, 255, 267, and 291, the CpG positions being relative to SEQ ID NO: 7; and

iii) identifying the immune cells as CD3+CD8+ NKT cells when the CpG positions in the first amplicon and/or second amplicon are more than 80% methylated, and the CpG positions in the third amplicon are less than 20% methylated.

2. The method according to claim 1 , further comprising quantifying the relative amount of said CD3+CD8+ NKT cells, said quantifying comprising detecting the methylation status of a control gene and comparing said methylation status of the control gene with the methylation status of said CpG positions in the first, second, and/or third amplicons.

3. The method according to claim 1 , wherein said nucleic acid based assay is performed on a DNA-chip.

4. The method according to claim 1 , wherein said sample is selected from a body fluid, tissue, organ or a blood lymphocyte or a fraction thereof.

5. The method according to claim 1 , wherein said method is performed without a step of purifying and/or enriching the immune cells in the sample derived from the human.

6. The method according to claim 1 , further comprising formulating said CD3+CD8+ NKT cells as identified for transplantation into a patient.

7. The method according to claim 1 , wherein said human suffers from or is likely to suffer from an autoimmune disease, transplant rejection, infectious disease, cancer, and/or allergy.

8. A method for monitoring the level of CD3+CD8+ NKT cells in a human, comprising performing the method according to claim 1 , and comparing said relative amount of the CD3+CD8+ NKT cells to a sample taken earlier or in parallel from the same human and/or to a control sample.

9. The method according to claim 8 , further comprising treating the human with a chemical and/or biological substance, and measuring and/or monitoring the amount of said CD3+CD8+ NKT cells in response to said chemical and/or biological substance.