Detection and measurement of tissue-infiltrating lymphocytes

• US 9,499,865 B2
• Filed: 11/29/2012
• Issued: 11/22/2016
• Est. Priority Date: 12/13/2011
• Status: Active Grant

• Current Assignee: Adaptive Biotechnologies Corp.
• Original Assignee: Adaptive Biotechnologies Corp.
• Inventors: Faham, Malek, Klinger, Mark
• Primary Examiner(s): Thomas, David
• Application Number:
  US13/688,414
• Publication Number:
  US 20130150252A1
• Time in Patent Office: 1,454 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/06 Quantitative determination
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism
• CPC Class Codes: G01N 33/5094 for blood cell populations red blood cells G01N33/80

Abstract

The present invention is drawn to methods for measuring numbers, levels, and/or ratios of cells, such as lymphocytes, infiltrated into a solid tissue, such as a tumor or a tissue affected by an autoimmune disease, and to methods for making patient prognoses based on such measurements. In one aspect, methods of the invention comprise sorting lymphocytes from an accessible tissue, such as peripheral blood, into functional subsets, such as cytotoxic T cells and regulatory T cells, and generating clonotype profiles of each subset. An inaccessible disease-affected tissue is sampled and one or more clonotype profiles are generated. From the latter clonotype profiles, levels lymphocytes in each of the functional subsets are determined in the disease-affected tissue by their clonotypes, which are identified from lymphocytes sorted into subsets from the accessible tissue.

Claims

1. A method for identifying lymphocytes belonging to a functional subset that have infiltrated a solid tissue comprising:

sorting a sample of lymphocytes from an accessible tissue of an individual into at least one functional subset;

generating a clonotype profile for each functional subset of lymphocytes from the accessible tissue by amplifying recombined nucleic acid molecules obtained from said at least one subset to obtain a plurality of amplicons and performing high throughput sequencing of the resulting plurality of amplicons to provide a list of clonotype sequences that identify individual lymphocytes of each functional subset;

generating at least one clonotype profile from at least one sample of the solid tissue by amplifying recombined nucleic acid molecules obtained from said at least one sample of solid tissue to obtain a plurality of amplicons and performing high throughput sequencing of the resulting plurality of amplicons to provide a list of clonotype sequences in each sample; and

identifying lymphocytes belonging to a functional subset that have infiltrated from the accessible tissue into the solid tissue by identifying a clonotype sequence from the solid tissue that is present in the list of clonotype sequences of a functional subset from the accessible tissue, wherein said step of identifying lymphocytes further includes determining numbers of lymphocytes of each of said at least one functional subset,

wherein one or more of the clonotype profiles for one or more of the functional subsets comprise at least 1000 clonotypes of at least 30 nucleotides.

2. The method of claim 1 wherein at least one of said at least one functional subsets of lymphocytes comprises cytotoxic T cells, helper T cells, regulatory T cells, Th1 T cells, Th2 T cells, Th9 T cells, Th17 T cells, and/or Tfh T cells.

3. The method of claim 2 wherein said step of identifying further includes determining levels and/or ratios of lymphocytes of each of said at least one functional subset.

4. The method of claim 3 wherein said solid tissue is a solid tumor.

5. The method of claim 4 wherein said at least one functional subset of lymphocytes comprise regulatory T cells and cytotoxic T cells.

6. The method of claim 5 wherein said step of identifying includes determining a ratio of levels of regulatory T cells to cytotoxic T cells in said solid tumor.

7. The method of claim 3 wherein said at least one functional subset of lymphocytes comprise at least one subset of antigen-specific T cells.

8. The method of claim 1 wherein said accessible tissue is peripheral blood, bone marrow, lymph fluid, synovial fluid, or spinal cord fluid of said individual.

9. The method of claim 8 wherein said accessible tissue is peripheral blood of said individual.

10. The method of claim 1 wherein said step of identifying further includes enumerating said lymphocytes in each of said functional subsets by counting their respective clonotypes.

11. The method of claim 1 wherein said sample of said solid tissue comprises multiple tissue samples taken from different locations in said solid tissue.

12. The method of claim 1 wherein said at least one functional subset of lymphocytes comprise helper T cells and cytotoxic T cells.

13. The method of claim 12 wherein said helper T cells are FoxP3+ regulatory T cells.

14. The method of claim 13 wherein said cytotoxic T cells are identified by a CD8⁺ marker and wherein said regulatory T cells are identified by markers CD4⁺, CD25^+(high), and CD127^(low).

15. The method of claim 14 wherein said solid tissue is a solid tumor.

16. The method of claim 1 wherein said at least one functional subset of lymphocytes are sorted into separate containers on the basis of at least one cell surface marker or intracellular marker.

17. The method of claim 16 wherein said step of sorting said at least one functional subset of lymphocytes is implemented with a fluorescence-activated cell sorter (FACS).

18. The method of claim 1 wherein each of said clonotypes of said clonotype profiles comprises a recombined portion of a T-cell receptor gene.

19. The method of claim 18 wherein each of said clonotypes of said clonotype profiles comprises at least a portion of a V(D)J region of a nucleic acid encoding a T-cell receptor β

chain.

20. The method of claim 19 wherein all of said clonotype profiles comprises at least 10⁶ clonotypes.

21. The method of claim 1 wherein said solid tissue is a solid tissue affected by an autoimmune disease.

22. The method of claim 21 wherein at least one of said at least one or more functional subsets of lymphocytes is selected from cytotoxic T cells, helper T cells, regulatory T cells, Th1 T cells, Th2 T cells, Th9 T cells, Th17 T cells, and/or Tfh T cells, and wherein said step of detecting further includes determining numbers, levels, and/or ratios of lymphocytes of each of said one or more functional subsets.

23. The method of claim 22 wherein said one or more functional subsets of lymphocytes comprise regulatory T cells, Th1 T cells, Th2 T cells, Th9 T cells, Th17 T cells, Tfh T cells, and/or at least one functional subset of antigen-specific T cells.

24. The method of claim 22 wherein said solid tissue is selected from the group consisting of colon tissue, small intestine tissue, skin, connective tissue, subcutaneous tissue, lung tissue, or kidney tissue.

25. The method of claim 1 wherein said solid tissue is a normal tissue, and wherein at least one of said one or more functional subsets of lymphocytes is selected from B cells, T cells, cytotoxic T cells, helper T cells, regulatory T cells, Th1 T cells, Th2 T cells, Th9 T cells, Th17 T cells, Tfh T cells, antigen-specific B cells and antigen-specific T cells, and wherein said step of detecting further includes determining numbers, levels, and/or ratios of lymphocytes of each of said one or more functional subsets.

26. The method of claim 1 further comprising sorting a sample of lymphocytes from an accessible tissue of an individual into at least 2 functional subsets.

27. The method of claim 1 further comprising sorting a sample of lymphocytes from an accessible tissue of an individual into at least 3 functional subsets.

28. The method of claim 1 further comprising sorting a sample of lymphocytes from an accessible tissue of an individual into at least 4 functional subsets.

29. The method of claim 1 further comprising sorting a sample of lymphocytes from an accessible tissue of an individual into at least 5 functional subsets.