Mechanisms of resistance to CAR T cell therapies

Sustained efficacy of chimeric antigen receptor T-cell therapy in central nervous system lymphoma: a systematic review and meta-analysis of individual data

Background: Central nervous system lymphoma (CNSL) is considered an aggressive lymphoma with a poor prognosis. Studies investigating CNSL have shown that chimeric antigen receptor (CAR) T-cell therapy has demonstrated an effective response in limited sample sizes. Therefore, we conducted this systematic review and meta-analysis to clarify the sustained efficacy and factors associated with the sustained efficacy of CAR T-cell therapy in the treatment of CNSL. Methods: We searched studies from PubMed, Embase, Medline, and the Cochrane Center Register of Controlled Trials up to July 2023. Studies that included individual data on the duration of response (DoR) after receiving CAR T-cell therapy were enrolled. Pooled response rates were calculated using fixed-effects or random-effects models. Subgroup analysis was performed to analyze the heterogeneity, and a Cox regression model was performed to identify the factors associated with sustained efficacy. Results: In total, 12 studies including 69 patients were identified and included in this meta-analysis. The pooled relapse rate was 45% [95% CI 35, 56]. Subgroup analyses of relapse rates revealed that CAR T-cells using the CD28/4-1BB domain (CD28/4-1BB vs. CD28 vs. 4-1BB, p = 0.0151), parenchymal or leptomeningeal involvement (parenchymal or leptomeningeal vs. both parenchymal and leptomeningeal, p < 0.0001), and combined treatment with CAR T-cell therapy [Autologous stem cell transplantation (ASCT) plus CAR T-cell therapy vs. CAR T cells with maintenance therapy vs. CAR T-cell therapy alone, p = 0.003] were associated with lower relapse rates in patients. Time-to-event endpoints were assessed using reconstructed individual patient survival data to explore key modulators of DoR. Partial response status at CAR-T infusion and the use of ASCT plus CAR T-cell therapy were associated with longer DoR at the multivariate level, with hazard ratios of 0.25 and 0.26, respectively. Conclusion: CAR T-cell therapy shows promising and sustained efficacy in CNSL patients. However, further prospective large-scale studies are needed to assess these effect modifiers to optimize patient selection and improve the sustained efficacy of CAR T-cell therapy in the treatment of CNSL. Systematic review registration: https://clinicaltrials.gov/, identifier PROSPERO CRD42023451856.

CD19 occupancy with tafasitamab increases therapeutic index of CART19 cell therapy and diminishes severity of CRS

ABSTRACT

In the development of various strategies of anti-CD19 immunotherapy for the treatment of B-cell malignancies, it remains unclear whether CD19 monoclonal antibody therapy impairs subsequent CD19-targeted chimeric antigen receptor T-cell (CART19) therapy. We evaluated the potential interference between the CD19-targeting monoclonal antibody tafasitamab and CART19 treatment in preclinical models. Concomitant treatment with tafasitamab and CART19 showed major CD19 binding competition, which led to CART19 functional impairment. However, when CD19+ cell lines were pretreated with tafasitamab overnight and the unbound antibody was subsequently removed from the culture, CART19 function was not affected. In preclinical in vivo models, tafasitamab pretreatment demonstrated reduced incidence and severity of cytokine release syndrome and exhibited superior antitumor effects and overall survival compared with CART19 alone. This was associated with transient CD19 occupancy with tafasitamab, which in turn resulted in the inhibition of CART19 overactivation, leading to diminished CAR T apoptosis and pyroptosis of tumor cells.

Synthetic manipulation of the cancer-immunity cycle: CAR-T cell therapy

Synthetic immunity to cancer has been pioneered by the application of chimeric antigen receptor (CAR) engineering into autologous T cells. CAR T cell therapy is highly amenable to molecular engineering to bypass barriers of the cancer immunity cycle, such as endogenous antigen presentation, immune priming, and natural checkpoints that constrain immune responses. Here, we review CAR T cell design and the mechanisms that drive sustained CAR T cell effector activity and anti-tumor function. We discuss engineering approaches aimed at improving anti-tumor function through a variety of mechanistic interventions for both hematologic and solid tumors. The ability to engineer T cells in such a variety of ways, including by modifying their trafficking, antigen recognition, costimulation, and addition of synthetic genes, circuits, knockouts and base edits to finely tune complex functions, is arguably the most powerful way to manipulate the cancer immunity cycle in patients.

Chimeric antigen receptor T-cell therapy for adult B-cell acute lymphoblastic leukemia: state-of-the-(C)ART and the road ahead

Autologous anti-CD19 chimeric antigen receptor (CAR) T-cell therapy has recently been added to the armamentarium in the battle against B-cell acute lymphoblastic leukemia (B-ALL). In this review, we discuss the trials that led to US Food and Drug Administration approval of CAR T-cell therapies in patients with B-ALL. We evaluate the evolving role of allogeneic hematopoietic stem cell transplant in the CAR T-cell era and discuss lessons learned from the first steps with CAR T-cell therapy in ALL. Upcoming innovations in CAR technology, including combined and alternative targets and off-the-shelf allogeneic CAR T-cell strategies are presented. Finally, we envision the role that CAR T cells could take in the management of adult patients with B-ALL in the near future.

Advances in adoptive cellular therapy for colorectal cancer: a narrative review

Background and Objective

In recent years, adoptive cell therapy (ACT) has shown great potential in antitumor treatment. To significantly improve the clinical efficacy of ACT against solid tumors, we may need to carefully study the latest developments in ACT. As one of the most common malignancies, colorectal cancer (CRC) is a major risk to human health and has become a significant burden on global healthcare systems. This article reviews the recent advances in the treatment of CRC with ACT.

Methods

We searched PubMed for articles related to ACT for CRC published as of August 31, 2022, and retrieved relevant clinical trial information on the National Institutes of Health ClinicalTrials.gov website. Based on search results, comprehensive and systematic review is made.

Key Content and Findings

This article provides an overview of the research progress of ACT for CRC, including chimeric antigen receptor (CAR) T-cell therapy, T-cell receptor (TCR)-engineered T-cell therapy, and tumor-infiltrating lymphocyte (TIL) therapy. Common tumor-associated antigens (TAAs) in clinical trials of CAR-T cell therapy for CRC are described.

Conclusions

Despite many obstacles, ACT shows great promise in treating CRC. Therefore, more basic experimental studies and clinical trials are warranted to further clarify the effectiveness and safety of ACT.

Multi-antigen-targeted T-cell therapy to treat patients with relapsed/refractory breast cancer

Purpose

Adoptively transferred, ex vivo expanded multi-antigen-targeted T cells (multiTAA-T) represent a new, potentially effective, and nontoxic therapeutic approach for patients with breast cancer (BC). In this first-in-human trial, we investigated the safety and clinical effects of administering multiTAA T cells targeting the tumor-expressed antigens, Survivin, NY-ESO-1, MAGE-A4, SSX2, and PRAME, to patients with relapsed/refractory/metastatic BC.

Materials and methods

MultiTAA T-cell products were generated from the peripheral blood of heavily pre-treated patients with metastatic or locally recurrent unresectable BC of all subtypes and infused at a fixed dose level of 2 × 107/m2. Patients received two infusions of cells 4 weeks apart and safety and clinical activity were determined. Cells were administered in an outpatient setting and without prior lymphodepleting chemotherapy.

Results

All patients had estrogen receptor/progesterone receptor positive BC, with one patient also having human epidermal growth factor receptor 2-positive. There were no treatment-related toxicities and the infusions were well tolerated. Of the 10 heavily pre-treated patients enrolled and infused with multiTAA T cells, nine had disease progression while one patient with 10 lines of prior therapies experienced prolonged (5 months) disease stabilization that was associated with the in vivo expansion and persistence of T cells directed against the targeted antigens. Furthermore, antigen spreading and the endogenous activation of T cells directed against a spectrum of non-targeted tumor antigens were observed in 7/10 patients post-multiTAA infusion.

Conclusion

MultiTAA T cells were well tolerated and induced disease stabilization in a patient with refractory BC. This was associated with in vivo T-cell expansion, persistence, and antigen spreading. Future directions of this approach may include additional strategies to enhance the therapeutic benefit of multiTAA T cells in patients with BC.

Axicabtagene ciloleucel for the treatment of relapsed or refractory follicular lymphoma

INTRODUCTION

Axicabtagene ciloleucel is an autologous anti-CD19 chimeric antigen receptor (CAR) T-cell therapy that was recently approved for relapsed or refractory follicular lymphoma following progression on two or more lines of therapy including an anti-CD20 monoclonal antibody with an alkylating agent, providing a therapeutic breakthrough in a subset of indolent non-Hodgkin lymphoma associated with poor clinical outcomes.

AREAS COVERED

In this article, we outline the drug profile of axicabtagene ciloleucel in comparison to currently approved agents and other CAR T-cell and T-cell redirecting therapies under investigation for the treatment of relapsed or refractory follicular lymphoma. We also review the efficacy, safety and pharmacokinetic data from the ZUMA-5 phase II trial, which forms the basis of the recent approval of axicabtagene ciloleucel.

EXPERT OPINION

Axicabtagene ciloleucel is the first cellular therapy approved for relapsed or refractory follicular lymphoma, demonstrating high rates of durable responses and a manageable toxicity profile in heavily pre-treated patients.

Antigen glycosylation regulates efficacy of CAR T cells targeting CD19

While chimeric antigen receptor (CAR) T cells targeting CD19 can cure a subset of patients with B cell malignancies, most patients treated will not achieve durable remission. Identification of the mechanisms leading to failure is essential to broadening the efficacy of this promising platform. Several studies have demonstrated that disruption of CD19 genes and transcripts can lead to disease relapse after initial response; however, few other tumor-intrinsic drivers of CAR T cell failure have been reported. Here we identify expression of the Golgi-resident intramembrane protease Signal peptide peptidase-like 3 (SPPL3) in malignant B cells as a potent regulator of resistance to CAR therapy. Loss of SPPL3 results in hyperglycosylation of CD19, an alteration that directly inhibits CAR T cell effector function and suppresses anti-tumor cytotoxicity. Alternatively, over-expression of SPPL3 drives loss of CD19 protein, also enabling resistance. In this pre-clinical model these findings identify post-translational modification of CD19 as a mechanism of antigen escape from CAR T cell therapy.

Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL

A notable number of acute lymphoblastic leukemia (ALL) patients develop CD19-positive relapse within 1 year after receiving chimeric antigen receptor (CAR) T cell therapy. It remains unclear if the long-term response is associated with the characteristics of CAR T cells in infusion products, hindering the identification of biomarkers to predict therapeutic outcomes. Here, we present 101,326 single-cell transcriptomes and surface protein landscape from the infusion products of 12 ALL patients. We observed substantial heterogeneity in the antigen-specific activation states, among which a deficiency of T helper 2 function was associated with CD19-positive relapse compared with durable responders (remission, >54 months). Proteomic data revealed that the frequency of early memory T cells, rather than activation or coinhibitory signatures, could distinguish the relapse. These findings were corroborated by independent functional profiling of 49 patients, and an integrative model was developed to predict the response. Our data unveil the molecular mechanisms that may inform strategies to boost specific T cell function to maintain long-term remission.

Identification of NOXA as a pivotal regulator of resistance to CAR T-cell therapy in B-cell malignancies

Despite the remarkable success of chimeric antigen receptor (CAR) T-cell therapy for treating hematologic malignancies, resistance and recurrence still occur, while the markers or mechanisms underlying this resistance remain poorly understood. Here, via an unbiased genome-wide CRISPR/Cas9 screening, we identified loss of NOXA, a B-cell lymphoma 2 (BCL2) family protein in B-cell malignancies, as a pivotal regulator of resistance to CAR T-cell therapy by impairing apoptosis of tumor cells both in vitro and in vivo. Notably, low NOXA expression in tumor samples was correlated with worse survival in a tandem CD19/20 CAR T clinical trial in relapsed/refractory B-cell lymphoma. In contrast, pharmacological augmentation of NOXA expression by histone deacetylase (HDAC) inhibitors dramatically sensitized cancer cells to CAR T cell-mediated clearance in vitro and in vivo. Our work revealed the essentiality of NOXA in resistance to CAR T-cell therapy and suggested NOXA as a predictive marker for response and survival in patients receiving CAR T-cell transfusions. Pharmacological targeting of NOXA might provide an innovative therapeutic strategy to enhance CAR T-cell therapy.

Tumor-derived extracellular vesicles induce invalid cytokine release and exhaustion of CD19 CAR-T Cells

Although CD19 chimeric antigen receptor-T (CAR-T) cells therapy has achieved unparalleled success in B cell malignancies. The dysfunction of CAR-T cells due to exhaustion is considered as a key factor for treatment failure, and the mechanisms of exhaustion remain elusive. Extracellular vesicles (EVs), important media for communication between tumor and immune cells, may contribute to CAR-T cell exhaustion. Here, we demonstrated that CD19⁺ tumor cells derived EVs (NALM6-EVs) can carry CD19 antigen and activate CD19 CAR-T cells. The transient activation induced a supraphysiologic inflammatory state with increased release of multiple cytokines. Besides, the sustained activation led CD19 CAR-T cells to enter an exhausted state with upregulated inhibitory receptors, decreased expansion ability, exaggerated effector cell differentiation and impaired antitumor activity. Transcriptomic profiling validated these findings and identified dynamic changes in CD8⁺ effector T, CD8⁺ exhausted T, CD8⁺RRM2⁺ T and T helper cell subpopulations during activation to exhaustion, as well as changes in many cytokines, inflammatory and immune-related pathways. Our findings identify a credible mechanism of CAR-T cell exhaustion that driven by tumor-derived EVs and provide a novel possible trigger for early cytokine release syndrome.

Resistance of B-Cell Lymphomas to CAR T-Cell Therapy Is Associated With Genomic Tumor Changes Which Can Result in Transdifferentiation

Despite the impressive efficacy of chimeric antigen receptor (CAR) T-cell therapy (CART) in B-cell non-Hodgkin lymphomas, durable responses are uncommon. The histopathologic and molecular features associated with treatment failure are still largely unknown. Therefore, we have analyzed 19 sequential tumor samples from 9 patients, prior anti-CD19 CART (pre-CART) and at relapse (post-CART), using immunohistochemistry, fluorescence in situ hybridization, array comparative genomic hybridization, next-generation DNA and RNA sequencing, and genome-scale DNA methylation. The initial diagnosis was diffuse large B-cell lymphoma (n=6), double-hit high-grade B-cell lymphoma (n=1), and Burkitt lymphoma (n=2). Histopathologic features were mostly retained at relapse in 7/9 patients, except the frequent loss of 1 or several B-cell markers. The remaining 2 cases (1 diffuse large B-cell lymphoma and 1 Burkitt lymphoma) displayed a dramatic phenotypic shift in post-CART tumors, with the drastic downfall of B-cell markers and emergence of T-cell or histiocytic markers, despite the persistence of identical clonal immunoglobulin gene rearrangements. The post-CART tumor with aberrant T-cell phenotype showed reduced mRNA expression of most B-cell genes with increased methylation of their promoter. Fluorescence in situ hybridization and comparative genomic hybridization showed global stability of chromosomal alterations in all paired samples, including 17p/TP53 deletions. New pathogenic variants acquired in post-CART samples included mutations triggering the PI3K pathway (PIK3R1, PIK3R2, PIK3C2G) or associated with tumor aggressiveness (KRAS, INPP4B, SF3B1, SYNE1, TBL1XR1). These results indicate that CART-resistant B-cell non-Hodgkin lymphomas display genetic remodeling, which may result in profound dysregulation of B-cell differentiation. Acquired mutations in the PI3K and KRAS pathways suggest that some targeted therapies could be useful to overcome CART resistance.

Advances in Universal CAR-T Cell Therapy

Chimeric antigen receptor T (CAR-T) cell therapy achieved extraordinary achievements results in antitumor treatments, especially against hematological malignancies, where it leads to remarkable, long-term antineoplastic effects with higher target specificity. Nevertheless, some limitations persist in autologous CAR-T cell therapy, such as high costs, long manufacturing periods, and restricted cell sources. The development of a universal CAR-T (UCAR-T) cell therapy is an attractive breakthrough point that may overcome most of these drawbacks. Here, we review the progress and challenges in CAR-T cell therapy, especially focusing on comprehensive comparison in UCAR-T cell therapy to original CAR-T cell therapy. Furthermore, we summarize the developments and concerns about the safety and efficiency of UCAR-T cell therapy. Finally, we address other immune cells, which might be promising candidates as a complement for UCAR-T cells. Through a detailed overview, we describe the current landscape and explore the prospect of UCAR-T cell therapy.

CAR-T in B-Cell Lymphomas: The Past, Present, and Future

Aggressive B-cell lymphomas including diffuse large B-cell lymphoma make up the majority of non-Hodgkin's lymphoma globally. While more than half of these patients can be cured with modern chemoimmunotherapy regimens, the outcomes of relapsed or refractory disease continue to be very poor. Despite significant developments in targeted cancer therapies and immuno-oncology, the attainability of a cure remained an elusive goal outside of incorporating high doses of chemotherapy followed by hematopoietic stem cell transplantation, for patients who have chemosensitive disease. The development of chimeric antigen receptor T-cell therapy changed that paradigm and introduced a new field of therapeutic possibilities for these patients. In this review, we will discuss the current state of this therapeutic modality in B-cell lymphomas and provide opinions on where future efforts need to focus in order to further improve their clinical utility.

Determinants of CD19-positive vs CD19-negative relapse after tisagenlecleucel for B-cell acute lymphoblastic leukemia

Tisagenlecleucel therapy has shown promising efficacy for relapsed/refractory (R/R) B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However, relapses occur in 30-50% of patients. Determinants for CD19^pos versus CD19^neg relapses are poorly characterized. We report on 51 patients with R/R BCP-ALL (median age 17 years) infused with tisagenlecleucel after lymphodepletion. Complete remission rate at D28 was 96%. Prior blinatumomab increased the risk of early failure at D28. The 18-month cumulative incidence of relapse (CIR), event-free survival (EFS), and overall survival (OS) were 51%, 44%, and 74%, respectively, at a median follow-up of 15.5 months. Factors associated with a high tumor burden (occurrence of cytokine release syndrome) and prior blinatumomab were associated with an increased CIR, and a shorter EFS and OS. Pre-lymphodepletion high disease burden (MRD ≥ 10^-2, SHR 10.4, p = 0.03) and detectable MRD at D28 (SHR 7.2, p = 0.006) correlated with an increased risk of CD19^neg relapse. Low disease burden (SHR 5.3, p = 0.03) and loss of B-cell aplasia (BCA) (SHR 21.7, p = 0.004) predicted an increased risk of CD19^pos relapses. These data highlight the impact of prior therapy on patient outcome. Finally, detectable MRD at D28 and loss of BCA both define patients at high risk of relapse for whom additional interventions are needed.

Selecting the Optimal CAR-T for the Treatment of B-Cell Malignancies

PURPOSE OF REVIEW

Chimeric antigen receptor T-cell (CAR-T) therapy is a form of adoptive cellular therapy that has revolutionized the treatment landscape in hematologic malignancies, especially B-cell lymphomas. In this review, we will discuss some of the landmark data behind these therapies and then lay out our approach to utilizing this new therapy.

RECENT FINDINGS

CD19-directed CAR-Ts are the most common type currently used in treatment of relapsed B-cell lymphoid neoplasms. There are currently three FDA-approved products: axicabtagene ciluecel and tisagenlecleucel for the treatment of relapsed/refractory large B-cell lymphoma and pediatric B-cell acute lymphocytic leukemia (tisagenlecleucel only) and brexucabtagene autoleucel for the treatment of relapsed/refractory mantle cell lymphoma. These therapies are associated with distinctive acute toxicities such as cytokine release syndrome and neurotoxicity and chronic toxicities such as cytopenias and hypogammaglobulinemia. CAR-T therapy provides significant potential in the treatment of relapsed B-cell lymphomas despite current limitations. Several novel CAR cell designs are currently being studied in clinical trials which include tandem CAR-Ts, allogeneic CAR-Ts, and CAR-NK cells.

High-Dimensional Immune Monitoring for Chimeric Antigen Receptor T Cell Therapies

PURPOSE OF REVIEW

High-dimensional flow cytometry experiments have become a method of choice for high-throughput integration and characterization of cell populations. Here, we present a summary of state-of-the-art R-based pipelines used for differential analyses of cytometry data, largely based on chimeric antigen receptor (CAR) T cell therapies. These pipelines are based on publicly available R libraries, put together in a systematic and functional fashion, therefore free of cost.

RECENT FINDINGS

In recent years, existing tools tailored to analyze complex high-dimensional data such as single-cell RNA sequencing (scRNAseq) have been successfully ported to cytometry studies due to the similar nature of flow cytometry and scRNAseq platforms. Existing environments like Cytobank (Kotecha et al., 2010), FlowJo (FlowJo™ Software) and FCS Express (https://denovosoftware.com) already offer a variety of these ported tools, but they either come at a premium or are fairly complicated to manage by an inexperienced user. To mitigate these limitations, experienced cytometrists and bioinformaticians usually incorporate these functions into an RShiny (https://shiny.rstudio.com) application that ultimately offers a user-friendly, intuitive environment that can be used to analyze flow cytometry data. Computational tools and Shiny-based tools are the perfect answer to the ever-growing dimensionality and complexity of flow cytometry data, by offering a dynamic, yet user-friendly exploratory space, tailored to bridge the space between the lab experimental world and the computational, machine learning space.

Function and evolution of the prototypic CD28ζ and 4-1BBζ chimeric antigen receptors

T cells engineered to express chimeric antigen receptors (CARs) specific for CD19 have yielded remarkable clinical outcomes in patients with refractory B-cell malignancies. The first CARs to be approved by the US Food and Drug Administration and the European Medicines Agency are CD19 CARs that comprise either CD28/CD3ζ or 4-1BB/CD3ζ dual-signalling domains. While their efficacy and safety profiles in patients with B-cell malignancies are comparable overall, the functional properties these two CAR designs impart upon engineered T cells differ significantly. Remarkably, alternative costimulatory domains have not, to date, superseded these foundational designs. Rather, recent CAR advances have focused on perfecting the original CD28- and 4-1BB-based CD19 CARs by calibrating strength of activation, pre-empting T-cell exhaustion and increasing the functional persistence of CAR T cells. This article reviews the essential biological properties of these first-in-class prototypes and their recent evolution.

•

CD19 chimeric antigen receptor (CAR) therapy has shown remarkable success against B-cell malignancies.

•

The prototypic CD19 CARs comprise either CD28/CD3ζ or 4-1BB/CD3ζ signalling domains.

•

Both CD19 CARs yield similar efficacy but impart distinct T-cell functionalities.

•

Novel CAR designs aim to enhance the persistence or effector potency of T cells.

•

Genome editing averts variegated CAR expression and sustains T-cell function.

Evaluation of the clinicopathologic features of diffuse large B cell lymphoma after CD19-targeted CAR T-cell therapy emphasizing the potential diagnostic pitfalls

Clinicopathologic data of 16 cases of DLBCL, NOS after CD19-targeted CAR T-cell therapy were retrospectively reviewed. Statistical analyses were performed to investigate the diagnostic agreement and indicate the relationship of the given types or their alterations (Group I versus Group II) to the prognosis. A total of 5 distinct histologic patterns were summarized. The CAR T cells were somewhat atypical, most of which were CD8 positive in the most cases (86.7%, 13/15), with a relatively high Ki-67 (60-90%). The rearrangement of BCR was demonstrated in all cases. The diagnostic test showed that the diagnostic accuracy in cases of types III (7%) and V (7%) was typically low; the diagnostic agreement in cases of type IV (for B, T, or nonlymphoma) and V (for T, or nonlymphoma) was consistently unsatisfactory. The rates of complete response (CR), partial response (PR), and progressive disease (PD) were 18.8% (3/16), 31.3% (5/16), 50% (8/16), respectively. In the follow-up, 25% (4/16) of cases experienced a recurrence and 31.3% (5/16) had died, of which 3 cases succumbed to the side effects. Group II had better disease-free survival (DFS, P=0.009). This study first described the pathologic features of DLBCL after CD19-targeted CAR T-cell therapy. Familiarity with these histologic features and combinations of medical history and genetic analyses facilitate avoiding misdiagnoses. Multiple biopsies are potentially helpful to estimate the treatment effects or prognosis, and stable alterations to any type of III to V, but not a single given one, may indicate a good prognosis.