Modulated immunodominance therapy

Abstract

The invention involves generating a T cell response to subdominant antigens and using the cells to therapeutically change the cellular homeostasis and nature of the immune response. In a preferred embodiment, the cells are generated outside of the patient avoiding the influence of the patient's immunologic milieu. By stimulating and growing the T cells from a patient in a tissue culture to one or more subdominant antigens and the transplanting them into the patient, if enough cells are expanded and transplanted, the transplanted cells overwhelm the endogenous dominant T cells in the response to either break or induce immune tolerance or otherwise modify the immune response to the cells or organism expressing that antigen. When the memory cells are established they are then reflective of this new immunodominance hierarchy so that the desired therapeutic effect is long lasting. In effect, the transplantation exogenously generated T cells reactive to the subdominant antigens is recapitulating priming and rebalancing the patient's immune response to target previously subdominant antigens in the cells or organism to produce a therapeutic benefit.

1 . A population of culture expanded T cells, the population comprising: a plurality of T cell subpopulations, each subpopulation responsive to an individual fragment of at least one subdominant antigen in an infection. 
     
     
         2 . The population of culture expanded T cells of  claim 1 , wherein each subpopulation is expanded against a different individual fragment derived from a full length form of the at least one subdominant antigen, wherein the subpopulations taken together are responsive to the full length form of the subdominant antigen. 
     
     
         3 . The T cell population of  claim 1 , wherein the T cell population is responsive to more than one subdominant antigen. 
     
     
         4 . The T cell population of  claim 1 , comprising: CD8+ cytotoxic T lymphocytes (CTL) CD4+ T cells, TH-1 or TH-2 polarized CD4+ T cells. 
     
     
         5 . The T cell population of  claim 1 , wherein the infection is selected from the group consisting of: a bacterial, a viral, a fungal, a parasitic and a prion infection. 
     
     
         6 . The T cell population of  claim 1 , wherein the at least one subdominant antigen comprises an antigen found in a virus selected from the group consisting of: EBV, HSV, VZV, Hepatitis B, Hepatitis C, HIV, HTLV, CMV, RSV and influenza viruses. 
     
     
         7 . The T cell population of  claim 6 , wherein the subdominant antigen is selected from the group consisting of: LMP1, LMP2, EBNA-1, HSV, HPV E6, HPV E7, HB core antigens, HB surface antigens, Hepatitis C antigens, HIV antigens, HTLV antigens, influenza antigens, RSV antigens and CMVpp65. 
     
     
         8 . The T cell population of  claim 1 , wherein the individual fragment is a nucleic acid fragment or a peptide. 
     
     
         9 . The T cell population of  claim 1 , wherein the subdominant antigen is a nucleic acid antigen or peptide antigen. 
     
     
         10 . The T cell population of  claim 1 , obtained in an ex vivo culture by a process comprising the steps of:
 contacting T cells responsive to a subdominant antigen in culture with agents that enrich antigen responsive T cell growth, the agents comprising cytokines, growth factors, hormones and immune cells;   expanding the subdominant antigen responsive T cells in culture; and   confirming expansion of the subdominant antigen responsive T cells by detecting one or more T cell activation markers.   
     
     
         11 . The T cell population of  claim 10 , wherein the T cells responsive to a subdominant antigen are present in human peripheral blood mononuclear cells (PBMC). 
     
     
         12 . The T cell population of  claim 11 , wherein the human PBMC are obtained from an individual, or from a patient having the infection. 
     
     
         13 . The T cell population of  claim 10 , wherein the cytokines are selected from the group consisting of: IL-2, IL-4, IL-6, IL-7, IL-12, IL-15, IL-21, and any combination thereof. 
     
     
         14 . The T cell population of  claim 13 , wherein the cytokines include any combination of two or more cytokines selected from the group consisting of: IL-2, IL-7, IL-15 and IL-21. 
     
     
         15 . The T cell population of  claim 14 , wherein:
 IL-2 is used at a concentration ranging between 2 Units (U)/ml and 1000 U/ml,   IL-7 is used at a concentration ranging between 1 ng/ml and 150 ng/ml,   IL-15 is used at a concentration ranging between 1 ng/ml and 150 ng/ml, or   IL-21 is used at a concentration ranging between 1 ng/ml and 150 ng/ml.   
     
     
         16 . The T cell population of  claim 10 , wherein the immune cells comprise antigen presenting cells stimulated with the at least one subdominant antigen. 
     
     
         17 . The T cell population of  claim 16 , wherein the antigen presenting cells are selected from monocytes, macrophages, dendritic cells, and EBV immortalized B cells. 
     
     
         18 . The T cell population of  claim 10 , comprising CD8+ cytotoxic T cells responsive to the at least one subdominant antigen. 
     
     
         19 . The T cell population of  claim 10 , wherein greater than 5% of T cells in the population are cytotoxic T cells, responsive to the at least one subdominant antigen in the infection. 
     
     
         20 . The T cell population of  claim 10 , comprising CD4+ T cells, TH-1 and TH-2 polarized cells. 
     
     
         21 . The T cell population of  claim 10 , wherein the T cell activation markers are selected from the group consisting of: cytotoxicity markers, IFN-gamma, TNF-alpha, antigen recognition markers, follicular helper cell markers, chemokine receptors, proliferation markers, cytokine responsive cell activation markers, tissue homing markers, memory cell markers and antigen specific receptors. 
     
     
         22 . A method of altering an immunodominance hierarchy in a patient having an infection and an immune response against a dominant antigen associated with the infection, the method comprising the steps of:
 identifying at least one subdominant antigen in a tissue sample from the patient;   contacting human PBMC with the at least one subdominant antigen;   contacting the PBMC with one or more cytokines selected from IL-2, IL-7, IL-15, and IL-21 to produce a population of subdominant antigen responsive T cells;   enriching for the population of subdominant antigen responsive T cells in culture;   verifying that the cytotoxic T cells responsive to the at least one subdominant antigen range between 0.01% to 20% of the population; and   administering to the patient having the infection, an effective amount of the T cell population;   wherein, administering to the patient the T cell population alters the immunodominance hierarchy within the patient.   
     
     
         23 . The method of  claim 22 , wherein the at least one subdominant antigen is selected from the group consisting of: viral antigens, bacterial antigens, parasitic antigens, prion infection related antigens, LMP1, LMP2, EBNA-1, HPV E6, HPV E7, HB core antigens, HB surface antigens, CMVpp65, RSV and influenza antigens. 
     
     
         24 . The method of  claim 22 , wherein the effective amount of the T cell population ranges between 10 6  and 10 12  T cells. 
     
     
         25 . A cell culture composition for production of a human T cell population in culture, the composition comprising:
 (a) a combination of at least two cytokines, selected from the group consisting of: IL-2, IL-7, IL-15 and IL-21;   (b) at least one subdominant antigen from an infection, wherein the subdominant antigen is present in a form which maximizes the number of epitopes available to contact T cells in the culture; and   (c) agents that promote subdominant antigen responsive T cell growth comprising hormones, inhibitors, carbohydrates, amino acids, human AB serum and immune cells.   
     
     
         26 . The composition of  claim 25 , wherein
 IL-2 is present at a concentration ranging between 2 Units (U)/ml and 1000 U/ml,   IL-7 is present at a concentration ranging between 1 ng/ml and 150 ng/ml,   IL-15 is present at a concentration ranging between 1 ng/ml and 150 ng/ml, or   IL-21 is present at a concentration ranging between 1 ng/ml and 150 ng/ml in the culture composition.   
     
     
         27 . The composition of  claim 25 , wherein the agents that promote subdominant antigen responsive T cell growth further comprise a proteasome antagonist, a drug or a cytokine. 
     
     
         28 . The composition of  claim 25 , wherein the at least one subdominant antigen is a nucleic acid, a protein or one or more peptides. 
     
     
         29 . A kit comprising the composition of  claim 25 .