Table S1 and Figures S1 -S8

Tolerance to self-antigens prevents the elimination of cancer by the immune system1,2. We used synthetic chimeric antigen receptors (CARs) to overcome immunological tolerance and mediate tumor rejection in patients with chronic lymphocytic leukemia (CLL). Remission was induced in a subset of subjects, but most did not respond. Comprehensive assessment of patient-derived CAR T cells to identify mechanisms of therapeutic success and failure has not been explored. We performed genomic, phenotypic and functional evaluations to identify determinants of response. Transcriptomic profiling revealed that CAR T cells from complete-responding patients with CLL were enriched in memory-related genes, including IL-6/STAT3 signatures, whereas T cells from nonresponders upregulated programs involved in effector differentiation, glycolysis, exhaustion and apoptosis. Sustained remission was associated with an elevated frequency of CD27+CD45RO-CD8+ T cells before CAR T cell generation, and these lymphocytes possessed memory-like characteristics. Highly functional CAR T cells from patients produced STAT3-related cytokines, and serum IL-6 correlated with CAR T cell expansion. IL-6/STAT3 blockade diminished CAR T cell proliferation. Furthermore, a mechanistically relevant population of CD27+PD-1-CD8+ CAR T cells expressing high levels of the IL-6 receptor predicts therapeutic response and is responsible for tumor control. These findings uncover new features of CAR T cell biology and underscore the potential of using pretreatment biomarkers of response to advance immunotherapies.

Background Adoptive cell therapy with chimeric antigen receptor T cells (CAR-T) has become a standard treatment for patients with certain aggressive B cell malignancies and holds promise to improve the care of patients suffering from numerous other cancers in the future. However, the high manufacturing cost of CAR-T cell therapies poses a major barrier to their broader clinical application. Among the key cost drivers of CAR-T production are single-use reagents for T cell activation and clinical-grade viral vector. The presence of variable amounts of contaminating monocytes in the starting material poses an additional challenge to CAR-T manufacturing, since they can impede T cell stimulation and transduction, resulting in manufacturing failure. Methods We created K562-based artificial antigen-presenting cells (aAPC) with genetically encoded T cell stimulation and costimulation that represent an inexhaustible source for T cell activation. We additionally disrupted endogenous expression of the low-density lipoprotein receptor (LDLR) on these aAPC (aAPC-ΔLDLR) using CRISPR-Cas9 gene editing nucleases to prevent inadvertent lentiviral transduction and avoid the sink effect on viral vector during transduction. Using various T cell sources, we produced CD19-directed CAR-T cells via aAPC-ΔLDLR-based activation and tested their in vitro and in vivo antitumor potency against B cell malignancies. Results We found that lack of LDLR expression on our aAPC-ΔLDLR conferred resistance to lentiviral transduction during CAR-T production. Using aAPC-ΔLDLR, we achieved efficient expansion of CAR-T cells even from unpurified starting material like peripheral blood mononuclear cells or unmanipulated leukapheresis product, containing substantial proportions of monocytes. CD19-directed CAR-T cells that we produced via aAPC-ΔLDLR-based expansion demonstrated potent antitumor responses in preclinical models of acute lymphoblastic leukemia and B-cell lymphoma. Conclusions Our aAPC-ΔLDLR represent an attractive approach for manufacturing of lentivirally transduced T cells that may be simpler and more cost efficient than currently available methods.

Abstract The success of chimeric antigen receptor (CAR)–mediated immunotherapy in acute lymphoblastic leukemia (ALL) highlights the potential of T-cell therapies with directed cytotoxicity against specific tumor antigens. The efficacy of CAR T-cell therapy depends on the engraftment and persistence of T cells following adoptive transfer. Most protocols for T-cell engineering routinely expand T cells ex vivo for 9 to 14 days. Because the potential for engraftment and persistence is related to the state of T-cell differentiation, we hypothesized that reducing the duration of ex vivo culture would limit differentiation and enhance the efficacy of CAR T-cell therapy. We demonstrated that T cells with a CAR-targeting CD19 (CART19) exhibited less differentiation and enhanced effector function in vitro when harvested from cultures at earlier (day 3 or 5) compared with later (day 9) timepoints. We then compared the therapeutic potential of early versus late harvested CART19 in a murine xenograft model of ALL and showed that the antileukemic activity inversely correlated with ex vivo culture time: day 3 harvested cells showed robust tumor control despite using a 6-fold lower dose of CART19, whereas day 9 cells failed to control leukemia at limited cell doses. We also demonstrated the feasibility of an abbreviated culture in a large-scale current good manufacturing practice–compliant process. Limiting the interval between T-cell isolation and CAR treatment is critical for patients with rapidly progressing disease. Generating CAR T cells in less time also improves potency, which is central to the effectiveness of these therapies. Cancer Immunol Res; 6(9); 1100–9. ©2018 AACR.

The chimeric antigen receptor (CAR) technology started out as a tool to understand lymphocyte biology but rapidly developed into a T cell therapeutic agent for the treatment of cancers. Here, we describe the technological advances in the field of CARs and highlight critical components of its success. Additionally, we describe how various laboratories have worked toward developing new, safer, and more potent CARs for cancer.

Therapies directed to specific antigens expressed on multiple myeloma [MM] cells are desirable given the high likelihood of relapse in patients [pts] and the toxicities associated with current treatment options. BCMA and TACI are surface proteins of interest as they promote the survival and proliferation of mature plasma cells. Given that their gene expression by RT-PCR is higher in MM cells compared to normal plasma cells [PCs], and the association of increasing serum BCMA levels with disease progression, we sought to assess if similar patterns were seen on PCs measured by flow cytometry. We specifically examined changes in BCMA/TACI expression (frequency and intensity) with progression of MM, whether expression of BCMA and TACI are correlated, and if levels of their expression correlates with PC burden as determined by IHC.

The recent clinical success of CD19-directed chimeric antigen receptor (CAR) T cell therapy in chronic and acute leukemia has led to increased interest in broadening this technology to other hematological malignancies and solid tumors. Now, advances are being made using CAR T cell technology to target myeloma antigens such as B cell maturation antigen (BCMA), CD138, and kappa-light chain as well as CD19 on putative myeloma stem cells. To date, only a limited number of multiple myeloma patients have received CAR T cell therapy but preliminary results have been encouraging. In this review, we summarize the recently reported results of clinical trials conducted utilizing CAR T cell therapy in multiple myeloma (MM).

Autologous T cells modified to recognize novel antigen targets are a novel form of therapy for cancer. We review the various potential forms of observed and hypothetical toxicities associated with genetically modified T cells. Despite the focus on toxicities in this review, re-directed T cells represent a powerful and highly effective form of anti-cancer therapy; we remain optimistic that the common toxicities will become routinely manageable and that some theoretical toxicity will be exceedingly rare, if ever observed.

137 Background: The adoptive transfer of autologous T cells genetically modified to express a CD19-specific, 4-1BB/CD3ζ-signaling CAR (CTL019) has shown remarkable activity and induces long-term remissions in a subset of patients with relapsed/refractory chronic lymphocytic leukemia (CLL) and acute lymphoblastic leukemia (ALL). In ALL, CTL019 induces a complete response (CR) in over 90% of patients while in CLL 25% of patients obtain a CR. It is not fully understood why only certain patients respond to therapy. Methods: We employed next generation sequencing of RNA (RNAseq) to identify predictive indicators of response to CTL019. We performed RNAseq on leukapheresis and manufactured product T cells prior to re-infusion from 35 CLL and 7 pediatric ALL patients with heavily pre-treated and high-risk disease. To characterize potency, we performed RNAseq on the infusion product after stimulation with the CAR. Results: We find that durable remission in CLL is associated with gene expression signatures of early memory and T-effector cells, while T cells from non-responding patients are enriched in signatures of T-regulatory cells, terminal differentiation, and exhaustion. In following the results from CLL, we find that pediatric ALL manufactured T cells are significantly enriched for an early memory, naïve T cell state and all achieved a CR. In parallel in vitro experiments, stimulation of the infusion product further demonstrated that CTL019 cells from CRs have an increased capacity for activation upon stimulation. We tested if we could extend these observations to identify a phenotype of T cells that is predictive of response prior to CTL019 manufacturing and find that the signatures predictive of response at the pre-infusion stage are also observed at the earlier leukapheresis time point. Conclusions: These findings suggest that intrinsic T cell fitness dictates response to CAR T cells. These gene expression signatures, along with additional immunological biomarkers, may be used to identify which patients are most likely to respond to adoptive transfer strategies and suggest manufacturing modifications that might potentiate the generation of maximally efficacious infusion products. Clinical trial information: NCT01029366, NCT01747486, NCT01626495.

Abstract Adoptive T cell immunotherapy involves the isolation, ex vivo expansion and reinfusion of T cells, and is dependent on T cell engraftment and persistence for efficacy. IL-2 is the most commonly used cytokine for ex vivo T cell culture; however, there is renewed interest in IL-7 and IL-15 due to their ability to enhance the survival and proliferation of stem cell memory (Tscm) T cells. Peripheral blood (PB) contains substantial numbers of Tscm, central memory (Tcm) and effector subsets. During ex vivo culture, PB T cells differentiate into cells with a predominantly CD45RO+, CD27−, CCR7− effector phenotype. Exogenous IL-7/15 delays this transition in phenotype and preserves a greater proportion of Tscm and Tcm cells. We hypothesize that limited ex vivo T cell culture in the presence of IL-7/15 rather than IL-2 will enhance engraftment and persistence of T cells in vivo. We show that T cells can be harvested from ex vivo cultures as early as day 3 (d3) following activation. T cells expressing a chimeric antigen receptor targeting CD19 (CART-19) show potent yet specific cytotoxicity in vitro. We investigated the therapeutic potential of cells harvested at d3 versus later time points using a Nalm-6 leukemic cell xenograft mouse model. We demonstrate that d3 CART-19 cells show potent anti-leukemic activity compared to day 5 or day 9 cells. Comparing CART19 cells cultured in IL-2 or IL-7/15 for 3 or 9 days, we show that mice treated with d3 cells cultured in IL-7/15 exhibit the greatest anti-leukemic efficacy at a 10-fold lower dose compared with day 9 cells. In summary, we show that limiting T cell culture ex vivo to the minimum required for lentiviral transduction, in the presence of IL-7/15, provides the most efficacious T cells for adoptive immunotherapy.

Adoptive cell therapy employing T cells equipped with a chimeric antigen receptor (CAR) containing a single chain antibody fragment fused to T cell signaling domains 4-1BB and CD3zeta (CTL019) has shown great potency against various hematopoietic malignancies, e.g. B cell acute lymphoblastic leukemia (ALL). However, it has not shown the same response rate in other malignancies such as chronic lymphocytic leukemia (CLL). We recently demonstrated that the in vivo expansion and persistence of CAR T cells is an important predictor of response to CTL019 in CLL (PMID: 26333935) and ALL (Thudium et al., ASH 2016; Fraietta et al., ASH 2016). Furthermore, it is well known that prolonged culture of T cells negatively impacts the in vivo expansion of the adoptively transferred cells. We therefore hypothesized that minimizing the ex vivo manipulation of T cells would improve the efficacy of CAR T cells.

The adoptive transfer of autologous T cells genetically modified to express a CD19-specific, 4-1BB/CD3z-signaling CAR (CTL019) has shown remarkable activity and induce long-term remissions in a subset of patients with relapsed/refractory chronic lymphocytic leukemia (CLL). To date, little is known about predictive indicators of efficacy. This study was designed to evaluate biomarkers of clinical response to CTL019 in CLL. We studied forty-one patients with advanced, heavily pre-treated and high-risk CLL who received at least one dose of CTL019 cells. We show that in vivo expansion and persistence are key quality attributes of CTL019 cells in CLL patients who have complete responses to therapy; in 2 patients responses are sustained beyond five years and accompanied by the persistence of functional CTL019 cells. Furthermore, durable remissions were associated with transcriptomic signatures of early memory T cells, while T cells from non-responding patients were enriched in genes belonging to known pathways of terminal differentiation and exhaustion. Polychromatic flow cytometry also demonstrated a significantly higher level of T cell exhaustion markers on the infused CAR T cells and reduced CD27 expression in non-responding patients. Accordingly, the combined assessment of PD1 and CD27 expression on CD8+ CTL019 cells in the infusion product accurately predicted response to treatment. Restimulation of the infusion product through the CAR further demonstrated that CTL019 cells from complete responders secreted significantly higher levels of several cytokines, including CCL20, IL-21, IL-22, IL-17, and IL-6, suggesting that the STAT3 signaling pathway may play a role in potentiating the enhanced potency of CTL019 cells. To identify a phenotype of T cells that is predictive of response prior to CTL019 manufacturing, we initially retrospectively evaluated the proportions of naïve, stem cell memory, central memory, effector memory and effector cells at the time of leukapheresis and observed either marginally significant or no significant correlations with clinical outcome. A systematic, unbiased analysis of the same biomarker panel revealed that the frequency of CD27+CD45RO- cells in the CD8+ T cell population correlated significantly with complete and durable responses to this therapy. Analysis of the infusion products using the same flow cytometric panel showed that most (>95%) of T cells expressed CD45RO at the end of the manufacturing run; CD27 expression frequencies, however, were maintained at the same level as in the leukapheresis. Together, these findings suggest that intrinsic T cell fitness dictates both response and resistance to highly active engineered CAR T cells. Thus, enrichment of T cells with optimal differentiation potential and proliferative capacity by timing of collection or culture modification might potentiate the generation of maximally efficacious infusion products. These data and additional immunological biomarkers may be used to identify which patients are most likely to respond to adoptive transfer strategies, leading to an enhanced personalized approach to cellular therapy.

Abstract Introduction For chimeric antigen receptor T cell-based (CAR-T) and engineered T cell receptor (TCR) immunotherapies, T cell expansion methods and phenotype/s of transplanted T cells may heavily influence clinical outcomes. Much current focus is on the potential of defined CD4+/CD8+ T cell populations vs bulk, and on the potential superiority of CAR-T cells from naïve (TN) or central memory (TCM) versus effector memory (TEM) cells. Many commercial T cell activation and expansion methods utilize rigid magnetic beads bound to antibodies against CD3 and CD28 as substrates. These methods are often associated with high costs and licensing restrictions for clinical and commercial applications. Additionally, de-beading processes can be highly complex and inefficient, adding additional time, costs and risks. It has been shown that substrate rigidity influences T cell expansion and phenotype. We hypothesized that a novel phase-change substrate could modulate expanded T cell phenotype/s and address de-beading challenges. Methods An alginate-based phase-change hydrogel was synthesized and coated onto magnetic beads to form hydrogel-coated particles of approximately 10 µm diameter. This hydrogel, in the presence of chelating agents, rapidly dissolves, enabling removal magnetic bead removal. The coated particles were conjugated with streptavidin (SA) and bound to biotinylated antibodies against CD3 (OKT3) and CD28 (28.2) to form CD3/CD28 hydrogel particles (CD3/CD28-HP). Human CD3+ T cells from peripheral blood were seeded (Day 0) at 1x10E6 cells/mL in 24 well plates (n=3) in complete RPMI medium supplemented with IL-2. To each well, 25 µL of CD3/CD28-HP were added per 0.5x10E6 cells in a single stimulation. Media addition or change of culture vessel occurred each 2-3 days. Following expansion, chelating agent was added and magnetic beads removed. Flow cytometry was used to assess cell viability and expression of phenotypic markers including CD3, CD4, CD8, CD45RA and CCR7. ELISA was used to measure secretion of IL-2, IL-4, and IFNγ. Residual magnetic beads were counted via hemocytometer. Results CD3/CD28-HP promoted significant T cell expansion of 0.3, 1.4, 2.4, 4.8 and 6.6 population doublings (PD) by Days 2, 5, 6, 9, and 13 respectively (p<0.01-p<0.001 vs Day 0). Similarly, CD3/CD28-HP-induced expansion in a separate lab using a different T cell donor yielded 4.7 PD by Day 9 (p<0.001 vs Day 0). Phenotypic markers were assessed on Days 6 and 13. Expansion using CD3/CD28-HP led to significantly more CD8+ cells and significantly fewer CD4+ cells versus the starting population on both days (p<0.05-p<0.001). When compared to a commercially available magnetic CD3/CD28 bead product, CD3/CD28-HP produced a significantly larger CD8+ population on Days 6 (p<0.05)and 13 (p<0.001), and a smaller population of CD4+ T cells on Day 13 (p<0.01). CD3/CD28-HP-based expansion significantly increased the percentage of CD3/CD45RA expressing T cells compared with the magnetic bead-based product on Day 6 (p<0.05). Also, on Day 6, T cells expanded using CD3/CD28-HP showed increased CD8/CD45RA/CCR7 expression when compared to T cells expanded with the commercial magnetic bead product (p<0.05). Cytokine secretion was assessed on Days 6 and 13. Cells expanded using both expansion methods secreted IL-2, IL-4, and IFNγ, with no significant differences in secretory function observed between expansion methods. Following de-beading of expanded cells, cell recovery was 96% for the CD3/CD28-HP-expanded cells and 93% for cells expanded using commercial magnetic bead-based expansion product. Additionally, in de-beaded cells, fewer residual magnetic particles were present in the CD3/CD28-HP-expanded population than in cells expanded via the commercial magnetic bead-based expansion product. Conclusions These data demonstrate the utility of a novel phase-change hydrogel system to efficiently induce T cell proliferation, promote expansion of functional T cells expressing markers associated with CD8+, TN and TCM phenotypes, and to separate expanded cells efficiently from magnetic beads. In future studies, we will determine if T cells expanded using this method show increased stemness and persistence in in vivo models, and further explore the possibilities of this novel system for rapid expansion and recovery of specific T cell subtypes. Disclosures Jesuraj: Quad Technologies: Employment, Other: stock options. Cole:Quad Technologies: Employment, Other: Stock Options. Wells:Quad Technologies: Employment, Other: Stock Options. Qin:Quad Technologies: Employment, Other: Stock options. Kevlahan:Quad Technologies: Employment, Equity Ownership. Maus:Novartis: Patents & Royalties: related to CTL019, Research Funding. Ball:Quad Technologies: Employment, Other: Stock Options.

How the formation and activity of CD4+Foxp3+ regulatory T cells (Tregs) are shaped by TCR recognition of the diverse array of peptide:MHC complexes that can be generated from self-antigens and/or foreign Ags in vivo remains poorly understood. We show that a self-peptide with low (but not high) stimulatory potency promotes thymic Treg formation and can induce conventional CD4+ T cells in the periphery to become Tregs that express different levels of the transcription factor Helios according to anatomical location. When Tregs generated in response to this self-peptide subsequently encountered the same peptide derived instead from influenza virus in the lung-draining lymph nodes of infected mice, they proliferated, acquired a T-bet+CXCR3+ phenotype, and suppressed the antiviral effector T cell response in the lungs. However, these self-antigen–selected Tregs were unable to suppress the antiviral immune response based on recognition of the peptide as a self-antigen rather than a viral Ag. Notably, when expressed in a more immunostimulatory form, the self-peptide inhibited the formation of T-bet+CXCR3+ Tregs in response to viral Ag, and Ag-expressing B cells from these mice induced Treg division without upregulation of CXCR3. These studies show that a weakly immunostimulatory self-peptide can induce thymic and peripheral Foxp3+ Treg formation but is unable to activate self-antigen–selected Tregs to modulate an antiviral immune response. Moreover, a strongly immunostimulatory self-peptide expressed by B cells induced Tregs to proliferate without acquiring an effector phenotype that allows trafficking from the draining lymph node to the lungs and, thereby, prevented the Tregs from suppressing the antiviral immune response.

We examined the formation, participation, and functional specialization of virus-reactive Foxp3+ regulatory T cells (Tregs) in a mouse model of influenza virus infection. “Natural” Tregs generated intrathymically, based on interactions with a self-peptide, proliferated in response to a homologous viral Ag in the lungs and, to a lesser extent, in the lung-draining mediastinal lymph nodes (medLNs) of virus-infected mice. In contrast, conventional CD4+ T cells with identical TCR specificity underwent little or no conversion to become “adaptive” Tregs. The virus-reactive Tregs in the medLNs and the lungs of infected mice upregulated a variety of molecules associated with Treg activation, as well as acquired expression of molecules (T-bet, Blimp-1, and IL-10) that confer functional specialization to Tregs. Notably, however, the phenotypes of the T-bet+ Tregs obtained from these sites were distinct, because Tregs isolated from the lungs expressed significantly higher levels of T-bet, Blimp-1, and IL-10 than did Tregs from the medLNs. Adoptive transfer of Ag-reactive Tregs led to decreased proliferation of antiviral CD4+ and CD8+ effector T cells in the lungs of infected hosts, whereas depletion of Tregs had a reciprocal effect. These studies demonstrate that thymically generated Tregs can become activated by a pathogen-derived peptide and acquire discrete T-bet+ Treg phenotypes while participating in and modulating an antiviral immune response.

Abstract It is generally accepted that developing thymocytes can become Foxp3+ regulatory T cells (Tregs) through recognition of self-antigens during thymic selection. Tregs can also develop from conventional CD4+ T cells responding to exogenously administered peptides (including food antigens) in vivo, and via TGF-β signaling during activation in vitro, but the processes by which Treg induction may occur in response to self-peptides in the periphery remain unclear. We are examining this question by transferring conventional CD4+CD25-Foxp3- T cells specific for influenza virus hemagglutinin (HA) into mice that express varying amounts of the HA molecule as a self-antigen (HA Tg mice). We find that conventional CD4+ T cells can convert into Foxp3+ Tregs upon recognition of a self-antigen in the lymph nodes and spleens, and that accumulation of HA-specific Tregs is greater in mice expressing HA at lower levels than it is in mice expressing relatively higher levels of HA. Conversion occurs most efficiently at sites draining mucosal surfaces, in agreement with published studies demonstrating the existence of specialized subsets of dendritic cells at these locations that promote Treg induction. We also find that the extent of Treg induction in response to a self-antigen is essentially unaffected by acute viral infection. These studies are defining parameters that determine the ability of self-peptides to induce the formation of Foxp3+ Tregs in the periphery.