Functional drivers of resistance to anti-CD19 CAR-T cell therapy in diffuse large B cell lymphoma

Chimeric antigen receptor T-cell therapy targeting CD19 (CAR-19) promotes impressive durable remissions for relapsed or refractory (rel/ref) large B-cell lymphoma (LBCL) patients with historically poor prognoses. Despite this, over half of patients still fail to respond or eventually progress. Studies to reveal mechanisms of resistance have examined host clinical parameters, CAR-19 product composition, and tumor microenvironment (TME) alterations, while a relative paucity of studies has analyzed contributions by genomic alterations in tumor cells. Factors associated with outcome include increased tumor volume, specific characteristics of infused CAR-T products, infiltration by myeloid cells in tumor microenvironments, and markers of complexity in LBCL genomes. Functional laboratory studies of resistance are largely absent in the current literature, illustrating a need for experiments in genetically accurate immunocompetent systems to confirm candidate alterations' roles in resistance and inform future improvements. In this review, we highlight key studies that have elucidated biomarkers of resistance in hosts, CAR products, TMEs, and comparatively understudied tumor-intrinsic mediators encoded by tumor genomes. We conclude with an experimental framework suitable for CAR-19 resistance biomarker identification and laboratory functional validation.

Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma

CD19-directed chimeric antigen receptor (CAR-19) T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. Although host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients with relapsed disease retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 patients with CAR-19-treated large B-cell lymphoma. We found that the pretreatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients for whom CAR T-cell therapy failed. Pretreatment reduced expression or monoallelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are related to multiple mechanisms. Our study showed that tumor-intrinsic genomic alterations are key among the complex interplay of factors that underlie CAR-19 efficacy and resistance for large B-cell lymphomas.

Abstract 3976: Recurrent BCL10 mutations drive BTK inhibitor resistance in BN2-subtype diffuse large B-cell lymphomas by constitutively activating NF-kB and the MALT1 protease

Diffuse large B cell lymphoma (DLBCL), the most common lymphoma diagnosis, is a heterogeneous group of sub-entities with differing biology and prognosis. Frontline R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone), used regardless of subtype, cures 60-70%. Patients failed by this combination have poor prognosis. Extensive efforts to improve on R-CHOP in the frontline have failed, but recent post-hoc analysis of one negative trial suggested younger patients with specific DLBCL biologic subtypes may benefit from addition of a Bruton’s Tyrosine Kinase inhibitor (BTKi). These results could inform prospective studies in a small subset of DLBCL cases, but the rest lack biomarker-driven frontline optimizations. Newer classification systems define the BN2 (LymphGen) or Cluster 1 (Chapuy consensus clusters) subtype, characterized by BCL6 translocations and/or NOTCH2 truncations. BN2 cases specifically saw no benefit from adding BTKi to R-CHOP regardless of patient age. BCL10, encoding a key protein promoting NF-kB activation through formation of a signaling complex with CARD11 and MALT1, is recurrently mutated in DLBCL (~5%), clustering strongly in BN2 (30-40%). We hypothesize that activation of NF-kB downstream of BTK due to BCL10 gain of function promotes BTKi resistant lymphomagenesis. Recurrent BCL10 mutations include the R58Q missense mutation in the oncogenic N-terminal CARD domain and frequent truncations of the regulatory C-terminal S/T-rich domain. Overexpression of BCL10 with either mutation type in DLBCL cells promoted strong activation of NF-kB assessed by immunoblotting and EGFP NF-kB reporters. Truncated BCL10 also increased MALT1 protease activity, measured by increased substrate cleavage. BCL10 mutations drove resistance to BTKis as hypothesized, but there was no difference in sensitivity to MALT1 inhibition, revealing that downstream targets overcome drug resistance by BCL10 mutant-mediated activation. Combining MALT1i with BTKi synergistically killed cells, identifying a promising therapeutic strategy for BN2 cases. Delving into the mechanism of BCL10-mutant lymphomagenesis, gene ontology analysis of transcriptome data showed cross-activation of ERK1/2 signaling, confirmed by immunoblotting, and strong induction of cytokine production and related signaling. To fuel future studies, we have established a cre-inducible conditional BCL10-truncation mouse model at the ROSA26 locus in C57BL/6J mice. After crossing into the Mb1-Cre background, these animals showed expansion of the B-cell compartment by three months of age and remain under observation for onset of lymphoma. We therefore define mechanisms and therapeutic consequences of recurrent BCL10 mutations in DLBCL and provide new drug combinations aimed at overcoming them.

Citation Format: Caroline A. Coughlin, Preet Kumar, Evan R. Roberts, Horacio Gonzalez Lopez, Marianna Lekakis, Lingxio Li, Daniel Bilbao, Jonathan H. Schatz. Recurrent BCL10 mutations drive BTK inhibitor resistance in BN2-subtype diffuse large B-cell lymphomas by constitutively activating NF-kB and the MALT1 protease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3976.

Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome

Tactical disruption of protein synthesis is an attractive therapeutic strategy, with the first-in-class eIF4A-targeting compound zotatifin in clinical evaluation for cancer and COVID-19. The full cellular impact and mechanisms of these potent molecules are undefined at a proteomic level. Here, we report mass spectrometry analysis of translational reprogramming by rocaglates, cap-dependent initiation disruptors that include zotatifin. We find effects to be far more complex than simple “translational inhibition” as currently defined. Translatome analysis by TMT-pSILAC (tandem mass tag-pulse stable isotope labeling with amino acids in cell culture mass spectrometry) reveals myriad upregulated proteins that drive hitherto unrecognized cytotoxic mechanisms, including GEF-H1-mediated anti-survival RHOA/JNK activation. Surprisingly, these responses are not replicated by eIF4A silencing, indicating a broader translational adaptation than currently understood. Translation machinery analysis by MATRIX (mass spectrometry analysis of active translation factors using ribosome density fractionation and isotopic labeling experiments) identifies rocaglate-specific dependence on specific translation factors including eEF1ε1 that drive translatome remodeling. Our proteome-level interrogation reveals that the complete cellular response to these historical “translation inhibitors” is mediated by comprehensive translational landscape remodeling.

Tactical protein synthesis inhibition is actively pursued as a cancer therapy that bypasses signaling redundancies limiting current strategies. Ho et al. show that rocaglates, first identified as inhibitors of eIF4A activity, globally reprogram cellular translation at both protein synthesis machinery and translatome levels, inducing cytotoxicity through anti-survival GEF-H1/RHOA/JNK signaling.

Abstract 1031: Translatome and protein synthesis machinery remodeling by rocaglates drives antitumor activity

Rocaglates are under active development for cancer therapy, with the first-in-class member zotatifin recently entering Phase I/II clinical trial for advanced solid tumor malignancies (NCT04092673). Initiation of this trial was based purely on rocaglates' inhibitory activity against translation initiation factor and RNA helicase eIF4A. Rapid development of these compounds towards clinical use urgently requires a complete understanding of their mechanisms. Critically, however, the full effects of rocaglates on protein synthesis are unknown, especially with regards to up-regulated proteins and rocaglate-activated translation factors that mediate their potent anticancer activity. Past rocaglate studies focused exclusively on mechanisms and targets of translational inhibition, relying exclusively on indirect RNA-based approaches that do not reliably capture proteome-level changes, a caveat proven in cancer cells responding to drugs. Formal proteomic investigations of rocaglate effects are non-existent in the literature. We addressed these vital knowledge gaps in this study. An original proteome-level analysis using metabolic pulse-labeling and TMT-mass spectrometry revealed extensive rocaglate-induced changes in protein output (translatome), including myriad rocaglate-up-regulated proteins that drive cytotoxicity through currently uncharacterized mechanisms. Specifically, we find in vitro and in vivo that rocaglates, including zotatifin, induce GEF-H1, activating anti-survival RHOA/JNK signaling. Intriguingly, these responses occur regardless of eIF4A expression. Beyond translatome remodeling, mass spectrometry-based MATRIX interrogation of the protein synthesis machinery revealed widespread rocaglate-dependent changes. As a prime example, rocaglate-augmented eEF1ϵ1 activity mediates initiator methionine-tRNAiMet delivery to drive synthesis of rocaglate-inducible proteins and phenotypes. Overall, this study transforms the current definition of rocaglates from one-dimensional eIF4A inhibitors to translation remodelers that globally reprogram protein output and the translation machinery. As human patients begin treatment with these compounds, our discovery of rocaglate-inducible proteins and rocaglate-activated translation factors that drive drug-specific responses highlights an entirely uncharacterized yet critical aspect of rocaglate potency. These timely findings emphasize systemic translational modeling as a newer concept for cancer therapy, and advocate for a systematic overhaul in our understanding of drugs traditionally defined as translation inhibitors.

Citation Format: Jyun David Ho, Jr, Tyler A. Cunningham, Caroline A. Coughlin, Artavazd Arumov, Evan R. Roberts, Daniel Bilbao, Jonathan R. Krieger, Stephen Lee, Jonathan H. Schatz. Translatome and protein synthesis machinery remodeling by rocaglates drives antitumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1031.

Abstract PO-55: Single-center experience of chimeric antigen receptor T-cell (CAR-T) immunotherapy in relapsed/refractory large B-cell lymphoma identifies association of acute toxicities with inferior disease outcomes

Chimeric antigen receptor T (CAR-T) cells are an emerging approach for the treatment of hematologic and solid tumor malignancies. Axicabtagene ciloleucel (axi-cel) and tisagenlecleucel were the first FDA-approved CAR-T therapies targeting CD19 for patients with relapsed/refractory (r/r) large B-cell lymphoma. Pivotal studies showed complete response (CR) rates of 58% and 40%, respectively, and we sought to investigate if the data are similar to our single-center results. We carried out a retrospective analysis of patients diagnosed with r/r diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, or mantle cell lymphoma who were treated with axi-cel or tisagenlecleucel at Sylvester Comprehensive Cancer Center in Miami, FL between January 2016 and October 2019. Primary objectives were to identify clinical characteristics associated with improved overall and progression-free survival (OS and PFS). Secondary analyses included incidence of post-CAR-T toxicities, including cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS). Our analysis included 44 patients: 32 received FDA-approved commercial product and 12 received axi-cel through clinical trials. Median age at time of CAR-T therapy was 62 years, and 70% of patients were male. Median number of prior treatments was 4, and 14 patients had undergone prior hematopoietic stem cell transplantation (12 autologous, 2 allogeneic). By day-30 post-treatment PET scan, 25 patients (57%) achieved CR or partial response (PR), while 16 (36%) had progressive (PD) or stable disease (SD). The remaining 3 patients decompensated rapidly post-infusion. Overall, patients with a CR or PR at 30 days had significantly improved OS and PFS compared to patients with PD or SD (OS p = 0.009, PFS p < 0.001). Univariate analyses showed patients requiring aggressive supportive measures in the post-infusion period had decreased OS compared to those who did not: requirement for ICU care (p = 0.018), vasopressor use (p = 0.01), and steroid treatment (p = 0.018) were all associated with inferior survival. There was no survival difference in DLBCL patients classified as double expressor or double hit; however, patients with germinal center B-cell (GCB) DLBCL trended strongly towards improved OS (p = 0.073) compared to non-GCB patients. CRS affected 35 patients (80%), while 24 patients (55%) experienced ICANS. Incidence of toxicities did not vary significantly in patients who received CAR-T commercially or in clinical trials. Patients who did not experience CRS had improved OS (p=0.061), and of patients who had CRS or ICANS, SD/PD patients had significantly worse PFS (p= <0.001, p= 0.024). This single-center retrospective analysis of patients receiving CAR-T therapy for r/r large B-cell lymphoma showed that incidence and management of toxicities and factors such as tumor subtype associate with treatment response. Further investigations into these factors may provide more insight into optimal management of patients undergoing CAR-T therapy.

Citation Format: Fahmin Basher, Caroline A. Coughlin, Deukwoo Kwon, Lazaros Lekakis, Jonathan Schatz. Single-center experience of chimeric antigen receptor T-cell (CAR-T) immunotherapy in relapsed/refractory large B-cell lymphoma identifies association of acute toxicities with inferior disease outcomes [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-55.