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

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 TEFF cells, resting TREG 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 TEFF cells, activated TREG 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.

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 TEFF cells, resting TREG 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 TEFF cells, activated TREG 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 TREG 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.

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 TEFF cells, resting TREG 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 TEFF cells, activated TREG 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 TREG 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.

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.

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 TEFF cells, resting TREG 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 TEFF cells, activated TREG 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 TREG cell population and/or TREG gene signature administration of cyclophosphamide, an anti-GITR antibody, an mTOR inhibitor, or a combination thereof.