Identifying epigenetic and transcriptional targets to prevent and reverse T cell exhaustion
The present invention provides methods of preventing, reversing or increasing T cell exhaustion in a patient having a disease. The present invention also provides methods for treating a disease in a patient having the disease. The present invention also provides an engineered T cell comprising a high priority epigenetic pathway that has been targeted, and uses thereof.
1 . A method of making an improved cell therapy composition, comprising the steps of:
(a) obtaining a sample comprising lymphocytes from a subject;
(b) reducing or eliminating expression of one or more genes required for the induction and/or maintenance of exhausted CD8+ T lymphocytes (T EX ) in the lymphocytes; and
(c) engineering the lymphocytes to target a therapeutically relevant antigen;
wherein the one or more genes required for the induction and/or maintenance of T EX is a transcription factor or a gene involved in epigenetic modification of DNA; and
wherein the transcription factor is TOX.
2 . The method of claim 1 , wherein the sample comprising T cells from the subject comprises blood, ascites, pleural effusion, lymph, mucus, broncho-alveolar lavage, or tissue.
3 . The method of claim 2 , wherein the sample comprising T cells from the subject comprises CD8+ T cells, tumor-associated lymphocytes, or tumor-infiltrating lymphocytes (TILs).
4 . The method of claim 1 , wherein expression of the one or more genes required for the induction and/or maintenance of T EX in the lymphocytes is reduced.
5 . The method of claim 1 , wherein expression of the one or more genes required for the induction and/or maintenance of T EX in the lymphocytes is eliminated.
6 . The method of claim 4 , wherein expression of the one or more genes required for the induction and/or maintenance of T EX in the lymphocytes is reduced by a method selected from the group consisting of RNA interference, clustered interspersed short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system, meganucleases, transcription activator-like effector nucleases (TALENs), Zinc-finger nucleases (ZFNs), antisense, ribozymes and CRISPR inhibition system comprising dead Cas9.
7 . The method of claim 5 , wherein expression of the one or more genes required for the induction and/or maintenance of T EX in the lymphocytes is eliminated by a method selected from the group consisting of RNA interference, clustered interspersed short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system, meganucleases, transcription activator-like effector nucleases (TALENs), Zinc-finger nucleases (ZFNs), antisense, ribozymes and CRISPR inhibition system comprising dead Cas9.
8 . The method of claim 1 , wherein the engineering the lymphocytes to target a therapeutically relevant antigen comprises introduction of a recombinant T cell receptor capable of binding a desired antigen/MHC or neo-antigen/MHC combination or introduction of a chimeric antigen receptor capable of binding a desired therapeutically relevant antigen.
9 . A method of reducing or preventing T cell exhaustion in a lymphocyte obtained from a subject, comprising the steps of:
reducing or eliminating expression of one or more genes required for the induction and/or maintenance of exhausted CD8+ T lymphocytes (T EX ) in the lymphocyte;
wherein the gene required for induction and/or maintenance of exhausted CD8+ T lymphocytes is TOX; and
wherein the lymphocyte is a CD8+ T cell.