Immunocompetence assessment by adaptive immune receptor diversity and clonality characterization

• US 10,221,461 B2
• Filed: 06/29/2017
• Issued: 03/05/2019
• Est. Priority Date: 10/01/2012
• Status: Active Grant

• Current Assignee: Adaptive Biotechnologies Corp., Memorial Sloan-Kettering Cancer Center
• Original Assignee: Adaptive Biotechnologies Corp., Memorial Sloan-Kettering Cancer Center
• Inventors: Robins, Harlan S., Rubinstein, Julie, Emerson, Ryan, Yuan, Jianda
• Primary Examiner(s): Goddard, Laura B
• Application Number:
  US15/637,871
• Publication Number:
  US 20180030543A1
• Time in Patent Office: 614 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• 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

Abstract

Disclosed are methods for determining the immunological status of the adaptive immune system of a subject by identifying and quantifying rearranged DNA (and/or subsequently transcribed RNA) sequences encoding T cell receptor (TCR) and/or immunoglobulin (IG) polypeptides, in a lymphoid DNA-containing sample from the subject TCR and/or IG sequence diversity and sequence distribution permit immunocompetence and immune repertoire assessment and reflect the degree of T cell or B cell clonality and clerical expansion in the sample. Methods for stratifying patient populations on the basis of immunocompetence including likelihood of responding to immunotherapy are also described.

Claims

1. A method for treating cancer comprising administering an effective amount of one or more immunotherapy agents to a subject in need thereof that has been identified as having a tumor comprising infiltrating lymphocytes with a high clonality rating,

wherein the clonality rating is determined by identifying and quantifying the number of unique rearranged adaptive immune receptor (AIR) sequences obtained from a sample comprising the tumor comprising infiltrating lymphocytes from the subject, and

wherein the clonality rating is characterized as a high clonality rating if the combined frequency of occurrence of the observed rearranged AIR sequences is no more than 10% of the total number of rearranged AIR sequences present in the sample.

2. The method of claim 1, wherein the one or more immunotherapy agents is one or more of an immunotherapeutic antibody, a cytokine, a hematopoietic cell transplant, an immunosuppressive agent, or a vaccine.

3. The method of claim 1, wherein the one or more immunotherapy agents is one or more inhibitors of a negative regulator of an immune response.

4. The method of claim 3, wherein the negative regulator of the immune response is one or more of CTLA4/CD152, LAG3/CD223, and PD-1/CD279.

5. The method of claim 4, wherein the one or more inhibitors of the negative regulator of the immune response is an anti-CTLA-4 antibody or an anti PD-1 antibody.

6. The method of claim 1, wherein the one or more immunotherapy agents target a potentiator of an immune response.

7. The method of claim 6, wherein the potentiator of the immune response is 41BB/CD137.

8. The method of claim 1, wherein the Shannon entropy score is normalized to the range [0-1] by dividing by the logarithm of the number of unique adaptive immune receptors.

9. The method of claim 8, wherein a high clonality rating is indicative of specific clonal expansion.

10. The method of claim 1, wherein the tumor is a melanoma, a carcinoma or a sarcoma.

11. The method of claim 1, wherein the cancer is melanoma, small cell lung cancer, non-small cell lung cancer, renal cell carcinoma, pancreatic cancer, breast cancer, ovarian cancer or prostate cancer.

12. The method of claim 1, wherein the frequency of each unique rearranged adaptive immune receptor obtained from the sample comprising the tumor comprising infiltrating lymphocytes from the subject is determined by amplifying nucleic acid sequences from the sample comprising the tumor comprising infiltrating lymphocytes in a multiplex polymerase chain reaction (PCR) assay, using a plurality of AIR V-segment oligonucleotide primers and either a plurality of J segment oligonucleotide primers or a plurality of AIR C segment oligonucleotide primers to obtained a plurality of amplified rearranged DNA molecules.

13. The method of claim 12, further comprising sequencing the plurality of amplified rearranged DNA molecules.

14. The method of claim 12, wherein the plurality of rearranged DNA molecules is sufficient to quantify the full diversity of the adaptive immune receptors in said sample.

15. The method of claim 1, wherein the clonality rating is characterized as a high clonality rating if the sample comprises a low AIR sequence diversity.

16. The method of claim 1, wherein the unique rearranged AIR sequences identified and quantified are at a number that is needed to account for up to at least 50% of the total number of observed AIR sequences in the sample.