Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling

The scarcity of malignant Hodgkin and Reed-Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast, liquid biopsies show promise for molecular profiling of cHL due to relatively high circulating tumour DNA (ctDNA) levels1-4. Here we show that the plasma representation of mutations exceeds the bulk tumour representation in most cases, making cHL particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumours, we demonstrate Hodgkin and Reed-Sternberg ctDNA shedding to be shaped by DNASE1L3, whose increased tumour microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R mutations that are dependent on IL-13 signalling and therapeutically targetable with IL-4Rα-blocking antibodies. Finally, using PhasED-seq5, we demonstrate the clinical value of pretreatment and on-treatment ctDNA levels for longitudinally refining cHL risk prediction and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL, as well as capturing molecularly distinct subtypes with diagnostic, prognostic and therapeutic potential.

CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity

Understanding the intricate dynamics between adoptively transferred immune cells and the brain tumor immune microenvironment (TIME) is crucial for the development of effective T cell-based immunotherapies. In this study, we investigated the influence of the TIME and chimeric antigen receptor (CAR) design on the anti-glioma activity of B7-H3-specific CAR T-cells. Using an immunocompetent glioma model, we evaluated a panel of seven fully murine B7-H3 CARs with variations in transmembrane, costimulatory, and activation domains. We then investigated changes in the TIME following CAR T-cell therapy using high-dimensional flow cytometry and single-cell RNA sequencing. Our results show that five out of six B7-H3 CARs with single costimulatory domains demonstrated robust functionality in vitro. However, these CARs had significantly varied levels of antitumor activity in vivo. To enhance therapeutic effectiveness and persistence, we incorporated 41BB and CD28 costimulation through transgenic expression of 41BBL on CD28-based CAR T-cells. This CAR design was associated with significantly improved anti-glioma efficacy in vitro but did not result in similar improvements in vivo. Analysis of the TIME revealed that CAR T-cell therapy influenced the composition of the TIME, with the recruitment and activation of distinct macrophage and endogenous T-cell subsets crucial for successful antitumor responses. Indeed, complete brain macrophage depletion using a CSF1R inhibitor abrogated CAR T-cell antitumor activity. In sum, our study highlights the critical role of CAR design and its modulation of the TIME in mediating the efficacy of adoptive immunotherapy for high-grade glioma.

SIGNIFICANCE

CAR T-cell immunotherapies hold great potential for treating brain cancers; however, they are hindered by a challenging immune environment that dampens their effectiveness. In this study, we show that the CAR design influences the makeup of the immune environment in brain tumors, underscoring the need to target specific immune components to improve CAR T-cell performance, and highlighting the significance of using models with functional immune systems to optimize this therapy.

Modular chimeric cytokine receptors with leucine zippers enhance the antitumour activity of CAR T cells via JAK/STAT signalling

The limited availability of cytokines in solid tumours hinders maintenance of the antitumour activity of chimeric antigen receptor (CAR) T cells. Cytokine receptor signalling pathways in CAR T cells can be activated by transgenic expression or injection of cytokines in the tumour, or by engineering the activation of cognate cytokine receptors. However, these strategies are constrained by toxicity arising from the activation of bystander cells, by the suboptimal biodistribution of the cytokines and by downregulation of the cognate receptor. Here we show that replacement of the extracellular domains of heterodimeric cytokine receptors in T cells with two leucine zipper motifs provides optimal Janus kinase/signal transducer and activator of transcription signalling. Such chimeric cytokine receptors, which can be generated for common γ-chain receptors, interleukin-10 and -12 receptors, enabled T cells to survive cytokine starvation without induction of autonomous cell growth, and augmented the effector function of CAR T cells in vitro in the setting of chronic antigen exposure and in human tumour xenografts in mice. As a modular design, leucine zippers can be used to generate constitutively active cytokine receptors in effector immune cells.

CAR T-cell design dependent remodeling of the brain tumor immune microenvironment identify macrophages as key players that inhibit or promote anti-tumor activity

Understanding interactions between adoptively transferred immune cells and the tumor immune microenvironment (TIME) is critical for developing successful T-cell based immunotherapies. Here we investigated the impact of the TIME and chimeric antigen receptor (CAR) design on anti-glioma activity of B7-H3-specific CAR T-cells. We show that five out of six B7-H3 CARs with varying transmembrane, co-stimulatory, and activation domains, exhibit robust functionality in vitro. However, in an immunocompetent glioma model, these CAR T-cells demonstrated significantly varied levels of anti-tumor activity. We used single-cell RNA sequencing to examine the brain TIME after CAR T-cell therapy. We show that the TIME composition was influenced by CAR T-cell treatment. We also found that successful anti-tumor responses were supported by the presence and activity of macrophages and endogenous T-cells. Together, our study demonstrates that efficacy of CAR T-cell therapy in high-grade glioma is dependent on CAR structural design and its capacity to modulate the TIME.

Common trajectories of highly effective CD19-specific CAR T cells identified by endogenous T cell receptor lineages

Current chimeric antigen receptor-modified (CAR) T cell products are evaluated in bulk, without assessing functional heterogeneity. We therefore generated a comprehensive single-cell gene expression and T cell receptor (TCR) sequencing dataset using pre- and post-infusion CD19-CAR T cells from blood and bone marrow samples of pediatric patients with B cell acute lymphoblastic leukemia (B-ALL). We identified cytotoxic post-infusion cells with identical TCRs to a subset of pre-infusion CAR T cells. These effector precursor cells exhibited a unique transcriptional profile compared to other pre-infusion cells, corresponding to an unexpected surface phenotype (TIGIT+, CD62Llo, CD27-). Upon stimulation, these cells showed functional superiority and decreased expression of the exhaustion-associated transcription factor, TOX. Collectively, these results demonstrate diverse effector potentials within pre-infusion CAR T cell products, which can be exploited for therapeutic applications. Furthermore, we provide an integrative experimental and analytical framework for elucidating the mechanisms underlying effector development in CAR T cell products.

CD19-CAR T Cells Develop Exhaustion Epigenetic Programs During a Clinical Response

The goal of this study was to determine the epigenetic landscape of CD19-CAR T cells pre and post infusion in leukemia patients as an initial step to elucidate intrinsic mechanisms that limit CAR T-cell effector functions in humans. A longitudinal analysis of CD8+ CD19-CAR T cell epigenetic changes was performed by whole-genome DNA methylation profiling of CAR T cells during manufacturing and from peripheral blood mononuclear cells (PBMCs) of 15 patients enrolled on our institutional, autologous CD19-CAR T cell therapy study (NCT03573700). CAR T cell expansion and persistence were determined by measuring vector copy numbers in the PBMCs of treated patients. We had previously established novel exhaustion DNA methylation datasets that delineate between progenitor and fully exhausted T cells. These datasets served as a guide for stratifying our post-infusion CAR T cells along the exhaustion developmental trajectory. Our data show that CD19-CAR T cells lose repressive DNA methylation at effector loci (e.g. PRF1, TBET) while gaining methylation at genes associated with memory potential (e.g. LEF1, TCF7). We confirmed these epigenetic changes are coupled to endogenous human T cell effector and memory differentiation by cross-referencing our epigenetic data with publicly available transcriptional profiles for antigen-specific effector and long-lived memory CD8 T cells from individuals vaccinated for yellow fever. Furthermore, we show that CAR T cells were unable to mount an in vivo recall response after relapse of antigen-positive disease or recovery of endogenous B cells. These observations support the conclusion that CD19-CAR T cells acquire stable epigenetic exhaustion programs that limit their protective capacity.

This work was supported by the National Institutes of Health (1R01AI114442 to BY and LRP to CCZ), the National Comprehensive Cancer Network Young Investigator Award (to CZ), Alex’s Lemonade Stand Foundation Young Investigator Grant (to CZ), Stand Up to Cancer- SU2C (to BY), the American Lebanese Syrian Associated Charities (ALSAC) to BY, and Assisi foundation to BY.

Common trajectories of highly effective CD19-specific CAR T cells identified by endogenous T cell receptor lineages

Current chimeric antigen receptor-modified (CAR) T cell therapy products are evaluated in bulk, without assessment of the possible heterogeneity in effector potential between cells. Conceivably, only a subset of the pre-infusion product differentiates into optimal effectors. We generated a comprehensive single-cell gene expression and T cell receptor (TCR) sequencing dataset using both pre- and post-infusion CD19-CAR T cells from peripheral blood and bone marrow of pediatric patients with B cell acute lymphoblastic leukemia (B-ALL). We identified potent effector post-infusion cells with identical TCRs to a subset of pre-infusion CAR T cells. Effector precursor CAR T cells exhibited a unique transcriptional profile compared to other pre-infusion cells, and the number of effector precursor cells infused correlated with peak CAR T cell expansion. Additionally, we identified an unexpected cell surface phenotype (TIGIT+, CD62Llo, CD27−), conventionally associated with inhibiting effective T cell responses, that we used to successfully enrich for subsequent effector potential. Collectively, these results demonstrate that highly diverse effector potentials are present among cells in pre-infusion cell products, which can be exploited for diagnostic and therapeutic applications. Furthermore, we provide an integrative experimental and analytical framework for elucidating the biological mechanisms underlying effector development in other CAR T cell therapy products.

This work was supported by the National Institutes of Health (NIH)/National Cancer Institute grant P30CA021765, NIH grants U01AI150747 and R01AI136514 (PGT), the American Society of Transplantation and Cellular Therapy (AT), the American Society of Hematology (AT), the Key for a Cure Foundation (PGT), the Mark Foundation ASPIRE Award (PGT), and the American Lebanese Syrian Associated Charities (SG, PGT). Part of the laboratory studies were performed by the Center for Translational Immunology and Immunotherapy (CeTI2), which is supported by SJCRH. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

CAR T cells redirected to cell surface GRP78 display robust anti-acute myeloid leukemia activity and do not target hematopoietic progenitor cells

Developing CAR T cells for acute myeloid leukemia (AML) has been hampered by a paucity of targets that are expressed on AML blasts and not on hematopoietic progenitor cells (HPCs). Here we demonstrate that GRP78 is expressed on the cell surface of primary AML blasts but not HPCs. To target GRP78, we generate T cell expressing a GRP78-specific peptide-based CAR, which show evidence of minimal fratricide post activation/transduction and antigen-dependent T cell differentiation. GRP78-CAR T cells recognize and kill GRP78-positive AML cells without toxicity to HPCs. In vivo, GRP78-CAR T cells have significant anti-AML activity. To prevent antigen-dependent T cell differentiation, we block CAR signaling and GRP78 cell surface expression post activation by using dasatinib during GRP78-CAR T cell manufacturing. This significantly improves their effector function in vitro and in vivo. Thus, targeting cell surface GRP78-positive AML with CAR T cells is feasible, and warrants further active exploration.

CD19-CAR T cells undergo exhaustion DNA methylation programming in patients with acute lymphoblastic leukemia

CD19-CAR T cell therapy has evolved into the standard of care for relapsed/refractory B cell acute lymphoblastic leukemia (ALL); however, limited persistence of the CAR T cells enables tumor relapse for many patients. To gain a deeper understanding of the molecular characteristics associated with CAR T cell differentiation, we performed longitudinal genome-wide DNA methylation profiling of CD8⁺ CD19-CAR T cells post-infusion in ALL patients. We report that CAR T cells undergo a rapid and broad erasure of repressive DNA methylation reprograms at effector-associated genes. The CAR T cell post-infusion changes are further characterized by repression of genes (e.g., TCF7 and LEF1) associated with memory potential and a DNA methylation signature (e.g., demethylation at CX3CR1, BATF, and TOX) demarcating a transition toward exhaustion-progenitor T cells. Thus, CD19-CAR T cells undergo exhaustion-associated DNA methylation programming, indicating that efforts to prevent this process may be an attractive approach to improve CAR T cell efficacy.

Zebley et al. show that CD8⁺ CD19-CAR T cells undergo genome-wide DNA methylation changes during an antitumor response in patients with B cell acute lymphoblastic leukemia (ALL). Post-infusion CAR T cell differentiation involves acquisition of DNA methylation programs associated with effector function, repression of memory potential, and transition toward exhaustion.

152 Common trajectories of highly effective anti-CD19 chimeric antigen receptor-modified T cells identified by endogenous T cell receptor lineages

Background

Chimeric antigen receptor modified (CAR) T cells have revolutionized the treatment of blood cancers, though some patients still show a poor response in either CAR expansion, effector response, or persistence.1 In this study, we determined the features of pre-infusion CAR-transduced T cells that generated optimally functional responses after infusion.

Methods

Using both the pre-infusion product and PBMCs isolated at weeks 1–4, 8, and 3-months post-infusion from 15 patients undergoing experimental anti-CD19 CAR T cell treatment for refractory or relapsed B-ALL, we generated a comprehensive single cell gene expression and T cell receptor (TCR) sequencing dataset on over 180,000 CAR T cells (figure 1).

Results

As expected, pre-infusion CAR T cells tend to highly express genes associated with proliferation, while post-infusion CARs show signs of either cytotoxic effector differentiation or dysfunctional terminal differentiation. Sequencing of the endogenous TCR, at the single cell level, allows us to track the trajectories of clonally and transcriptionally related cells (figure 2). Post-infusion cells with significant cytotoxic effector function share TCRs with a statistically defined subset of CARs in the pre-infusion sample (figure 3). Using a machine learning approach, we found that potent effector precursor CAR T cells have a specific transcriptional profile distinct from the other pre-infusion CAR T cells, including markers of early effector function such as increased EOMES, GNLY, GZMH, GZMK, KLRD1, and IFNγ. Formalizing this signature, we have developed a robust classifier that can predict with 82.8% accuracy whether a CAR T is likely to become a favorable effector based on its pre-infusion profile (figure 4). This prediction model can be used to evaluate the extent to which a patient‘s generated CAR product will be able to mount a robust response after encountering its target. Additionally, there are a number of genes, as a part of this signature, that are expressed on the cell surface and can be utilized as a method to differentiate the effector precursor pre-infusion CAR T cells from other pre-infusion CARs, including CD52, CD74, CD86, and LAG3, among others.

Abstract 152 Figure 1

Clustering of 184, 791 CAR-transduced T cells based on gene expression

Abstract 152 Figure 2

Alluvial plot depicting CAR T cell lineage tracing using the endogenous T cell receptor

Abstract 152 Figure 3

Visualization of CAR T cell clusters with arrows indicating the shared TCRs between pre-infusion and post-infusion cells

Abstract 152 Figure 4

Machine learning classifier of pre-infusion, early effector CAR T cell phenotype

Conclusions

Our findings suggest a therapeutic approach that enriches these cells prior to infusion resulting in superior per cell CAR effector activity.

Reference

Xu X, Huang S, Xiao X, Sun Q, Liang X, Chen S, et al. Challenges and Clinical Strategies of CAR T-cell Therapy for Acute Lymphoblastic Leukemia: Overview and Developments. Front Immunol 2020;11:569117.

Ethics Approval

This study was approved by St. Jude Children’s Research Hospital’s Institutional Review Board (IRB); IRB number Pro00007661. All patients consented to the use of materials for the research study.

A Chimeric GM-CSF/IL18 Receptor to Sustain CAR T-cell Function

The inability of chimeric antigen receptor (CAR) T cells to sustain their effector function after repeated exposure to tumor cells is a major obstacle to their success in patients with solid tumors. To overcome this limitation, we designed a novel chimeric cytokine receptor to create an autocrine loop that links activation-dependent GM-CSF production by CAR T cells to IL18 receptor signaling (GM18). Expression of GM18 in CAR T cells enhanced their effector function in an antigen- and activation-dependent manner. In repeat stimulation assays, which mimic chronic antigen exposure, CAR.GM18 T cells had a significantly greater ability to expand and produce cytokines in comparison with their unmodified counterparts targeting EPHA2 or HER2. In vivo, CAR.GM18 T cells induced tumor regression at cell doses at which standard CAR T cells were ineffective in two solid tumor xenograft models. Thus, our study highlights the potential of hijacking cytokines that are physiologically secreted by T cells to bolster their antitumor activity. SIGNIFICANCE: We designed a chimeric cytokine receptor (GM18) that links CAR T-cell activation to MYD88 signaling. GM18 endows CAR T cells with sustained effector function in the setting of chronic antigen exposure, resulting in potent antitumor activity in preclinical solid tumor models.This article is highlighted in the In This Issue feature, p. 1601.

De novo DNA methylation programs regulate CAR T-cell exhaustion

Chimeric antigen receptor (CAR) T-cell therapy is revolutionizing cancer immunotherapy for patients with B cell malignancies. While clinical trials have demonstrated the curative potential of this approach, a significant and well-established limitation is the heightened contraction and transient persistence that CAR T-cells experience during prolonged antigen exposure. Building upon our prior observation that deleting the de novo DNA methyltransferase 3a (Dnmt3a) prevents T cell exhaustion in the prototypical model of LCMV-induced T cell exhaustion, we assessed the role of DNMT3A programming in the dysfunction of human CAR T-cells. Deletion of DNMT3A in multiple human CAR T-cell systems resulted in a striking preservation of the CAR T-cell’s ability to proliferate and mount an effector response during chronic antigen exposure. Whole genome methylation profiling of DNMT3A KO CAR T-cells established an atlas of epigenetically regulated genes targeted during CAR T-cell dysfunction. Cross-reference of our published murine exhaustion methylation profiles with our newly identified human CAR T-cell methylation atlas revealed conservation of epigenetically regulated exhaustion-associated genes. Using a novel epigenetic-based bioinformatic tool that predicts human T-cell differentiation we further documented the preserved developmental plasticity of the DNMT3A KO CAR T-cells. Lastly, analysis of publicly available RNAseq expression data from CD19-CAR T-cell products prior to infusion into CLL patients demonstrated that DNMT3A programming is significantly coupled to clinical outcome. Collectively our results demonstrate that de novo DNA methylation programming is a key factor limiting T-cell based immunotherapy.

Dendritic cells facilitate thymic recovery and hasten immune reconstitution after hematopoietic stem cell transplantation (169.44)

The well-established role of dendritic cells in antigen presentation demonstrates their important role in development of T cells. In hematopoietic stem cell transplantation (HSCT) donor T cells are essential for engraftment, immune reconstitution, and graft vs. leukemia effect. Surprisingly, the role of Dendritic cells (DCs) in facilitating donor engraftment of hematopoietic stem cells has not been studied. Previously, we have demonstrated the importance of ex vivo expanded regulatory T cells (Tregs) in facilitating thymic engraftment after HSCT. Here we show the addition of dendritic cells given simultaneously with murine stem cells significantly improves engraftment after HSCT. Histological analysis demonstrated that thymic recovery was faster and more robust when dendritic cells were administered along with hematopoietic stem cells (HSC). Cell recovery and immune reconstitution was observed to occur more quickly in the thymus, spleen, bone marrow, and peripheral blood in experimental samples given additional DCs in HSCT. FACS analysis also confirmed immune reconstitution and donor cell engraftment was faster and increased survival was observed in experimental animals given DCs as well as stem cells. We hypothesize that the additional DCs establish themselves in the recipient thymus and assist in educating donor T cells, hastening immune reconstitution and improving cell engraftment.

Dendritic cells and Regulatory T cells facilitate donor engraftment after hematopoietic stem cell transplantation (145.35)

The role of thymic DCs in facilitating donor engraftment after hematopoietic stem cell transplantation (HSCT) has not been investigated. Here we show addition of ex-vivo generated DCs accelerates thymic engraftment as well as enhances T cell recovery after HSCT. We also show the ability of regulatory T cells (Tregs) to facilitate engraftment. Control group received 103 lin-sca-1+c-kit+ (LSK) HSC progenitors while DC and Treg groups received LSK cells along with ex-vivo generated DCs or ex vivo expanded Tregs. On day of HSCT, C57BL/6 recipients received lethal irradiation with 1000 cGy. Day 4 & 7 post HSCT, thymuses of the DC and T reg groups contained 1.5 and 2 fold, respectively, higher number of thymocytes compared to control group. Furthermore, at 4 and 7 days after HSCT, H&E slides of thymuses of showed increased cellularity with medullary lymphoid regeneration in the cohort receiving Tregs. We demonstrate that ex-vivo generated DCs efficiently migrate and home to the thymic medulla and hasten thymic recovery as demonstrated by the higher number of total thymoctyes. The addition of Tregs facilitates engraftment as demonstrated by total number of thymocytes, and lymphoid regeneration in the medullary region of the thymus. Lastly, recipients receiving Tregs were able to facilitate engraftment compared to control group as demonstrated by survival 50% and 0%, respectively (p=0.04).