Biomarkers predictive of therapeutic responsiveness to chimeric antigen receptor therapy and uses thereof

Abstract

Cancer biomarkers and methods of using them are disclosed.

1 . A method of evaluating a subject, having a cancer, comprising:
 acquiring a value of responder or relapser status to a therapy comprising a CAR-expressing cell population for the subject, wherein said value of responder or relapser status comprises a measure of one, two, three, four, five, six, seven, or more of the following:   (i) the level or activity of CD27 and/or CD45RO− immune effector cells in a sample;   (ii) the level or activity of one, two, three, or more of resting T EFF  cells, resting T REG  cells, younger T cells, or early memory T cells, or a combination thereof, in a sample;   (iii) the level or activity of one, two, three, or more of activated T EFF  cells, activated T REG  cells, older T cells, or late memory T cells, or a combination thereof, in a sample;   (iv) the level or activity of an immune cell exhaustion marker in a sample;   (v) the level or activity of one, two, three, four, five, ten, twenty or more of the biomarkers listed in Table 1A, Table 1B, Table 7A, Table 7B, Table 8, Table 9, Table 10, Table 14, Table 16, Table 17, Table 18, Table 20,  FIG. 2B , PD-1, LAG-3, TIM-3, CD57, CD27, CD122, CD62L, KLRG1, or a CD19 CAR-expressing cell gene set signature;   (vi) a cytokine level or activity in a CAR-expressing cell product sample, wherein the cytokine is chosen from one, two, three, four, five or more of the cytokines listed in Table 16;   (vii) a transduction efficiency of a CAR-expressing cell in a manufactured CAR-expressing cell product sample; or   (viii) a quantity of CD27+PD-1− cells in a sample,   
       wherein said value is indicative of the subject's responsiveness or relapsing status to the CAR-expressing cell therapy, thereby evaluating the subject. 
     
     
         2 - 3 . (canceled) 
     
     
         4 . A method for treating a subject having a cancer, comprising:
 administering to the subject a therapeutically effective dose of a CAR-expressing cell therapy, if the subject is identified as being responsive to a therapy comprising a CAR-expressing cell population, wherein said identifying comprises a measure of one, two, three, four, five, six, seven, or more of the following:   (i) the level or activity of CD27 and/or CD45RO− immune effector cells in a sample;   (ii) the level or activity of one, two, three, or more of resting T EFF  cells, resting T REG  cells, younger T cells, or early memory T cells, or a combination thereof, in a sample;   (iii) the level or activity of one, two, three, or more of activated T EFF  cells, activated T REG  cells, older T cells, or late memory T cells, or a combination thereof, in a sample;   (iv) the level or activity of an immune cell exhaustion marker in a sample;   (v) the level or activity of one, two, three, four, five, ten, twenty or more of the biomarkers listed in Table 1A, Table 1B, Table 7A, Table 7B, Table 8, Table 9, Table 10, Table 14, Table 16, Table 17, Table 18, Table 20,  FIG. 2B , PD-1, LAG-3, TIM-3, CD57, CD27, CD122, CD62L, KLRG1, or a CD19 CAR-expressing cell gene set signature;   (vi) a cytokine level or activity in a CAR-expressing cell product sample, wherein the cytokine is chosen from one, two, three, four, five or more of the cytokines listed in Table 16; or   (vii) a transduction efficiency of a CAR-expressing cell in a manufactured CAR-expressing cell product sample; or   (viii) a quantity of CD27+PD-1− cells in a sample,   
       thereby treating the subject. 
     
     
         5 . The method of  claim 4   wherein responsive to said value, performing one, two, three, four, five, six, seven, or more of:
 identifying the subject as a complete responder, partial responder or non-responder, or a relapser or a non-relapser; 
 administering a CAR-expressing cell therapy; 
 administering an altered dosing of a CAR-expressing cell therapy; 
 altering the schedule or time course of a CAR-expressing cell therapy; 
 administering an additional agent in combination with a CAR-expressing cell therapy; 
 administering to a non-responder or partial responder a therapy that increases the number of younger T cells or naïve T cells in the subject prior to treatment with a CAR-expressing cell therapy; 
 modifying a manufacturing process of a CAR-expressing cell therapy; 
 administering an alternative therapy; or 
   if the subject is, or is identified as, a non-responder or a relapser, decreasing the T REG  cell population and/or T REG  gene signature.   
     
     
         6 . The method of  claim 4 , wherein the CAR-expressing cell therapy comprises a plurality of CAR-expressing immune effector cells. 
     
     
         7 . The method of  claim 4 , wherein the CAR-expressing cell therapy is a CAR19 therapy. 
     
     
         8 . The method of  claim 4 , wherein the measure of one or more of (i)-(viii) is obtained from:
 (a) an apheresis sample acquired from the subject, wherein optionally the apheresis sample; or   (b) a manufactured CAR-expressing cell product sample.   
     
     
         9 . (canceled) 
     
     
         10 . The method of  claim 4 , wherein the subject is evaluated prior to, during, or after receiving the CAR-expressing cell therapy. 
     
     
         11 . The method of  claim 4 , wherein the cancer is a hematological cancer. 
     
     
         12 . The method of  claim 4 , wherein the hematological cancer is an ALL or a CLL. 
     
     
         13 . The method of  claim 4 , wherein the subject is a human patient. 
     
     
         14 . The method of  claim 4 , further comprises identifying the subject as a responder, a non-responder, a relapser or a non-relapser, based on a measure of one or more of (i)-(viii). 
     
     
         15 . The method of  claim 4 , wherein the measure of one or more of (i)-(viii) evaluates a profile for one or more of gene expression, flow cytometry or protein expression. 
     
     
         16 . The method of  claim 4 , wherein the level or activity of a CD8+ T cell is evaluated using a profile or signature indicative of the percentage of CD8+ T cell in the sample. 
     
     
         17 . The method of  claim 4 , wherein the level or activity of CD27+CD45RO− immune effector cells is evaluated using a profile or signature indicative of the percentage of CD27+CD45RO− immune effector cells in the sample. 
     
     
         18 . The method of  claim 4 , wherein the level or activity is evaluated using a profile or gene signature according to one, two, three, four, five, ten, twenty, fifty, sixty, seventy, one hundred or more of a biomarker or gene set listed in Tables 1A, 1B, 3, 4, 5, 6, 7A, 7B, or  FIG. 2B . 
     
     
         19 . The method of  claim 4 , wherein the biomarker is a secreted or a cell surface biomarker listed in Table 8. 
     
     
         20 . The method of  claim 4 , wherein a responder has, or is identified as having, a greater level or activity of one, two, or more of GZMK, PPF1BP2, or naïve T cells as compared to a non-responder. 
     
     
         21 . The method of  claim 4 , wherein a non-responder has, or is identified as having, a greater level or activity of one, two, three, four, five, six, seven, or more of IL22, IL-2RA, IL-21, IRF8, IL8, CCL17, CCL22, effector T cells, or regulatory T cells, as compared to a responder. 
     
     
         22 . The method of  claim 4 , wherein a complete responder has, or is identified as having:
 (a) a greater percentage of CD8+ T cells compared to a reference value;   (b) a greater percentage of CD27+CD45RO− immune effector cells compared to a reference value;   (c) a greater percentage of CD4+ T cells compared to a reference value; or   (d) a greater percentage of one, two, three, or more of resting TEFF cells, resting TREG cells, younger T cells, or early memory T cells, or a combination thereof, compared to a reference value.   
     
     
         23 - 25 . (canceled) 
     
     
         26 . The method of  claim 4 , wherein a non-responder has, or is identified as having:
 (a) a greater percentage of one, two, three, or more of activated TEFF cells, activated TREG cells, older T cells, or late memory T cells, or a combination thereof, compared to a reference value, e.g., a responder number of activated TEFF cells, activated TREG cells, older T cells, or late memory T cells; or   (b) a greater percentage of PD-1 or LAG-3 expressing immune effector cells compared to the percentage of PD-1 or LAG-3 expressing immune effector cells from a responder, or a greater percentage of PD-1+/LAG-3+ cells in the CAR-expressing cell population compared to a responder to the CAR-expressing cell therapy,   an exhausted phenotype of PD1+CAR+ and co-expression of LAGS in the CAR-expressing cell population, or   a greater percentage of PD-1+/TIM-3+ cells in the CAR-expressing cell compared to the responder.   
     
     
         27 . (canceled) 
     
     
         28 . The method of  claim 4 , wherein a partial responder has, or is identified as having, a higher percentage of PD-1+/LAG-3+ cells than responders in the CAR-expressing cell population, or a higher percentage of PD-1+/TIM-3+ cells than responders in the CAR-expressing cell population. 
     
     
         29 . The method of  claim 4 , wherein the presence of CD8+CD27+CD45RO− T cells in an apheresis sample is a positive predictor of the subject response to a CAR-expressing cell therapy. 
     
     
         30 . The of  claim 4 , wherein a high percentage of PD1+CAR+ and LAG3+ or TIM3+ T cells in an apheresis sample is a poor prognostic predictor of the subject response to a CAR-expressing cell therapy. 
     
     
         31 . The method of  claim 4 , wherein a responder to a CAR19 therapy has, or is identified as having, the biomarker profile of Table 9. 
     
     
         32 . The method of  claim 4 , wherein a non-responder to a CAR19 therapy has, or is identified as having:
 (a) the biomarker comprising one or more of PD-1+ immune effector cells, TIM-3+ immune effector cells, LAG-3+ immune effector cells, KLRG1+ immune effector cells, CD27-immune effector cells, activated TEFF cells, activated TREG cells, activated TH1, activated TH2 cells, stimulated memory cells, or late T memory cells, or a combination thereof; or   (b) the biomarker profile of Table 10.   
     
     
         33 . (canceled) 
     
     
         34 . The method of  claim 4 , wherein gene expression of one, two, three, four or more of KLRG1, CD57, CD27, CD122, or CD62L is predictive of patient response to CTL019 therapy. 
     
     
         35 . The method of  claim 4 , wherein a relapser has, or is identified as having, elevated levels of one, two, three, four, five, six, seven, eight, nine, ten or more of C5orf32, CCL17, CSF1, CTSL1, EMP1, EPAS1, GCLM, GK, GPR56, HMOX1, IKBIP, IL10, IL13, IL1RN, IL4, IL5, IL9, MIR155, PANX2, PGAM4, PRKAR1B, TNFRSF11A, TNFRSF1B, TNFRSF8, VTRNA1-3, or ZNF282. 
     
     
         36 . The method of  claim 4 , wherein the responder has one, two, three or more of the following profile:
 (i) has a greater number of CD27+ immune effector cells compared to a reference value;   (ii) has a greater number of CD8+ T cells compared to a reference value;   (iii) has a lower number of cells expressing one or more checkpoint inhibitors compared to a reference value; or   (iv) has a greater number of one, two, three, or more of resting TEFF cells, resting TREG cells, younger cells, or early memory T cells, or a combination thereof, compared to a reference value.   
     
     
         37 . The method of  claim 4 , wherein the cytokine level or activity of (vi) is chosen from one, two, three, four, five, six, seven, eight, or more of cytokine CCL20/MIP3a, IL17A, IL6, GM-CSF, IFNγ, IL10, IL13, IL2, IL21, IL4, IL5, IL9 or TNFα, or a combination thereof. 
     
     
         38 . The method of  claim 4 , wherein a transduction efficiency of 15% or higher in (vii) is indicative of increased responsiveness or decreased relapse. 
     
     
         39 . The method of  claim 4 , wherein said value of responder or relapser status comprises a measure of the level or activity of one, two, three, four, five, ten, twenty or more of the biomarkers having a FDR p-value of below 0.1 or 0.01 listed in Table 1A, 1B, 17, 18, or 20. 
     
     
         40 . A method of evaluating the potency of a CAR-expressing cell product, said method comprising:
 acquiring a value for one, two, three, four, five, six, seven, eight, or more of:   (i) the level or activity of CD27 and/or CD45RO− immune effector cells in the CAR-expressing cell product;   (ii) the level or activity of one, two, three, or more of resting T EFF  cells, resting T REG  cells, younger T cells, or early memory T cells, or a combination thereof, in the CAR-expressing cell product;   (iii) the level or activity of one, two, three, or more of activated T EFF  cells, activated T REG  cells, older T cells, or late memory T cells, or a combination thereof, in the CAR-expressing cell product;   (iv) the level or activity of an immune cell exhaustion marker;   (v) the level or activity of one, two, three, four, five, ten, twenty or more of the biomarkers listed in Table 1A, Table 1B, Table 7A, Table 7B, Table 8, Table 9, Table 10, Table 14, Table 16, Table 17, Table 18, Table 20,  FIG. 2B , PD-1, LAG-3, TIM-3, CD57, CD27, CD122, CD62L, KLRG1, or a CD19 CAR-expressing cell gene set signature;   (vi) a cytokine level or activity in the CAR-expressing cell product sample wherein the cytokine is chosen from one, two, three, four, five or more of the cytokines listed in Table 16;   (vii) a transduction efficiency of CAR-expressing cells in the product;   (viii) a quantity of CD27+PD-1− cells in a sample; or   (ix) the level or activity of a T REG  cell or cell population;   
       wherein:
 (a) an increase in (i), (ii), (vi), (vii), (viii), or any combination thereof, is indicative of increased potency of the CAR-expressing cell product, and 
 wherein an increase in (iii), (iv), (ix), or any combination thereof, is indicative of decreased potency of the CAR-expressing cell product; 
 (b) the cytokine is chosen from one, two, three, four, five, six, seven, eight, or more (or all) of CCL20/MIP3a, IL17A, IL6, GM-CSF, IFNγ, IL10, IL13, IL2, IL21, IL4, IL5, IL9 or TNFα, or a combination thereof; or 
 (c) a transduction efficiency of 15% or higher is indicative of increased potency. 
 
     
     
         41 - 42 . (canceled) 
     
     
         43 . A method for optimizing manufacturing of a CAR-expressing cell product comprising:
 (1) acquiring a sample comprising CAR-expressing cell;   (2) activating the CAR-expressing cell in vitro;   (3) evaluating the potency of the potency of the activated CAR-expressing cell by determining one, two, three, four, five, six, seven, eight, or more of:   (i) the level or activity of CD27 and/or CD45RO− immune effector cells in the CAR-expressing cell product;   (ii) the level or activity of one, two, three, or more of resting T EFF  cells, resting T REG  cells, younger T cells, or early memory T cells, or a combination thereof, in the CAR-expressing cell product;   (iii) the level or activity of one, two, three, or more of activated T EFF  cells, activated T REG  cells, older T cells, or late memory T cells, or a combination thereof, in the CAR-expressing cell product;   (iv) the level or activity of an immune cell exhaustion marker in the CAR-expressing cell product;   (v) the level or activity of one, two, three, four, five, ten, twenty or more of the biomarkers listed in Table 1A, Table 1B, Table 7A, Table 7B, Table 8, Table 9, Table 10, Table 14, Table 16, Table 17, Table 18, Table 20,  FIG. 2B , PD-1, LAG-3, TIM-3, CD57, CD27, CD122, CD62L, KLRG1, or a CD19 CAR-expressing cell gene set signature;   (vi) a cytokine level or activity in a CAR-expressing cell product sample, wherein the cytokine is chosen from one, two, three, four, five or more of the cytokines listed in Table 16;   (vii) a transduction efficiency of CAR-expressing cells in the product;   (viii) a quantity of CD27+PD-1− cells in a sample; or   (ix) the level or activity of a T REG  cell or cell population,   
       wherein an increase in (i), (ii), (vi), (vii), (viii), or any combination thereof, is indicative of increased potency of the CAR-expressing cell product, and 
       wherein an increase in (iii), (iv), (ix), or any combination thereof, is indicative of decreased potency of the CAR-expressing cell product. 
       thereby optimizing manufacturing of the product. 
     
     
         44 . The method of  claim 43 , further comprising a step of enriching for cells having an increase in any of (i), (ii), (vi), (vii), (viii), or any combination thereof, or a decrease in any of (iii), (iv), (ix), or any combination thereof; or
 wherein the cytokine level or activity is chosen from one or more of cytokine CCL20/MIP3a, IL17A, IL6, GM-CSF, IFNγ, IL10, IL13, IL2, IL21, IL4, IL5, IL9 or TNFα, or a combination thereof.   
     
     
         45 . (canceled) 
     
     
         46 . The method of  claim 43 , which comprises a further step that depletes T REG  cells. 
     
     
         47 . The method of  claim 46 , wherein T REG  cells are depleted via CD25-depletion, GITR depletion, mTOR inhibition, or a combination thereof. 
     
     
         48 . The method of  claim 43 , wherein (i), (ii), (iii), (iv), (v), (vi), (vii), (viii), (ix), or any combination thereof (e.g., all) are evaluated following activation in vitro, and/or wherein the CAR-expressing cell therapy comprises CTL019. 
     
     
         49 . (canceled) 
     
     
         50 . The method of  claim 4 , wherein the subject receives a treatment prior to the initiation of a CAR-expressing cell therapy or a treatment post-CAR-expressing cell therapy. 
     
     
         51 . The method of  claim 4 , wherein the cancer is associated with CD19 expression. 
     
     
         52 . The method of  claim 4 , wherein the cancer is a hematological cancer. 
     
     
         53 . The method of  claim 4 , wherein the cancer or hematological cancer is selected from the group consisting of B-cell acute lymphocytic leukemia (B-ALL), T-cell acute lymphocytic leukemia (T-ALL), acute lymphocytic leukemia (ALL), chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), B cell promyelocytic leukemia, blastic plasmacytoid dendritic cell neoplasm, Burkitt's lymphoma, diffuse large B cell lymphoma, follicular lymphoma, hairy cell leukemia, small cell- or a large cell-follicular lymphoma, malignant lymphoproliferative conditions, MALT lymphoma, mantle cell lymphoma, marginal zone lymphoma, multiple myeloma, myelodysplasia and myelodysplastic syndrome, non-Hodgkin lymphoma, Hodgkin lymphoma, plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, and Waldenstrom macroglobulinemia. 
     
     
         54 . The method of  claim 4 , where the CD19 CAR-expressing cell gene signature comprises a value for expression of at least 5, 6, 7, 8, 9 or 10 genes comprising a CD19 CAR-expressing cell gene signature. 
     
     
         55 . A kit for providing a prognosis for success rate of a CAR-expressing cell therapy in a subject having cancer, said kit comprising:
 a set of reagents that specifically detects the level or activity of one or more genes listed in Table 1A, Table 1B, Table 7A, Table 7B, Table 8, Table 9, Table 10, Table 14, Table 17, Table 18, Table 20,  FIG. 2B , PD-1, LAG-3, TIM-3, CD57, CD27, CD122, CD62L, KLRG1, and/or a CD19 CAR-expressing cell gene set signature; and   instructions for using said kit;   wherein said instructions for use provide that if one or more of the detected expression levels is different from the subject is more likely to respond positively to a CAR-expressing cell therapy; and   wherein the set of reagent detects the expression of mRNA expressed from said set of genes; and/or   wherein the set of reagents detects the expression of polypeptides encoded by said set of genes.   
     
     
         56 - 57 . (canceled) 
     
     
         58 . A system for evaluating cancer in a subject, comprising:
 at least one processor operatively connected to a memory, the at least one processor when executing is configured to:   acquire a value of responder or relapser status that comprises a measure of one, two, three, four, five, six, seven, or more of the following:   (i) the level or activity of CD27 and/or CD45RO− immune effector cells;   (ii) the level or activity of one, two, three, or more of resting T EFF  cells, resting T REG  cells, younger T cells, or early memory T cells, or a combination thereof, in a sample;   (iii) the level or activity of one, two, three, or more of activated T EFF  cells, activated T REG  cells, older T cells, or late memory T cells, or a combination thereof, in a sample;   (iv) the level or activity of an immune cell exhaustion marker;   (v) the level or activity of one, two, three, four, five, ten, twenty or more of the biomarkers listed in Table 1A, Table 1B, Table 7A, Table 7B, Table 8, Table 9, Table 10, Table 14, Table 16, Table 17, Table 18, Table 20,  FIG. 2B , PD-1, LAG-3, TIM-3, CD57, CD27, CD122, CD62L, KLRG1, or a CD19 CAR-expressing cell gene set signature;   (vi) a cytokine level or activity in a CAR-expressing cell product sample, wherein the cytokine is chosen from one, two, three, four, five or more of the cytokines listed in Table 16;   (vii) a transduction efficiency of a CAR-expressing cell in a manufactured CAR-expressing cell product sample; or   (viii) a quantity of CD27+PD-1− cells in a sample,   
       responsive to a determination of the value of responder status, perform one, two, three, four, five, six, seven, or more of:
 identify the subject as a complete responder, partial responder, non-responder, relapser or non-relapser; 
 recommend administering a CAR-expressing cell therapy; 
 recommend a selection or alteration of a dosing of a CAR-expressing cell therapy; 
 recommend a selection or alteration of a schedule or time course of a CAR-expressing cell therapy; 
 recommend administering an additional agent in combination with a CAR-expressing cell therapy; 
 recommend administering to a non-responder or partial responder a therapy that increases the number of naïve T cells in the subject prior to treatment with a CAR-expressing cell therapy; 
 recommend modifying a manufacturing process of a CAR-expressing cell therapy; 
 recommend modifying the CAR-expressing cell product prior to infusion into the patient; 
 recommend adjusting the CAR-expressing cell infusion dose to achieve clinical efficacy; 
 recommend administering an alternative therapy; 
 recommend a selection of an alternative therapy; or 
 if the subject is, or is identified as, a non-responder or a relapser, recommend decreasing the T REG  cell population and/or T REG  gene signature administration of cyclophosphamide, an anti-GITR antibody, an mTOR inhibitor, or a combination thereof. 
 
     
     
         59 - 64 . (canceled) 
     
     
         65 . The method of  claim 4 , wherein the CAR19 therapy is CTL019. 
     
     
         66 . The method of  claim 4 , wherein the immune effector cells are in a CD4+ or a CD8+ T cell population. 
     
     
         67 . The method of  claim 4 , wherein the younger T cells are younger CD4 or CD8 cells, or gamma/delta cells. 
     
     
         68 . The method of  claim 4 , wherein the immune cell exhaustion marker is one, two or more immune checkpoint inhibitors. 
     
     
         69 . The method of  claim 68 , wherein the immune checkpoint inhibitor is PD-1, TIM-3 and/or LAG-3. 
     
     
         70 . The method of  claim 4 , wherein the biomarker is CCL20, IL-17a and/or IL-6. 
     
     
         71 . The method of  claim 4 , wherein the cytokine level or activity is a quality of cytokine repertoire. 
     
     
         72 . The method of  claim 4 , wherein the quantity of CD27+PD-1− cells in a sample is a quantity greater than or equal to 1×10 7  cells. 
     
     
         73 . The method of  claim 8 , wherein the apheresis sample or the manufactures CAR-expressing cell product is evaluated prior to infusion or re-infusion. 
     
     
         74 . The method of  claim 22 , wherein the reference value is a value of a non-responder percentage of CD8+ T cells.