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Abstract Introduction: Pirtobrutinib, a highly selective non-covalent BTK inhibitor, demonstrated encouraging efficacy in Richter transformation (RT) of chronic lymphocytic leukemia (CLL) in the BRUIN trial (Wierda et al, Lancet Haematology, 2024). However, a control arm was not included in this phase 1/2 trial, and how pirtobrutinib compares to usual care is unknown. To address this gap of knowledge, we sought to compare efficacy outcomes in BRUIN to that in a control cohort consisting of RT patients treated with usual care at Mayo Clinic. Methods: The study was approved by the Mayo Clinic IRB. Patient-level data from BRUIN (n=79; investigator-assessed) were obtained from the study sponsor. Patients with histologically confirmed RT (large B-cell lymphoma) who received at least one line of therapy (n=230) were identified from the Mayo Clinic CLL Database. Multivariable logistic regression was employed to calculate propensity scores for baseline covariates (ie, age at RT treatment line, number of prior lines of CLL treatment [truncated at 3], number of prior lines of RT treatment [truncated at 3], and LDH). For each Mayo patient, propensity scores for each line of RT therapy were calculated, and the line with the highest propensity score was chosen as the index RT treatment line. Using the inverse probability treatment weighting (IPTW) methodology, individual weights were computed, and standardized mean differences (SMDs) were examined for each of the unadjusted and weighted baseline covariates to ensure that balance was obtained between BRUIN cases and Mayo controls. Overall survival (OS; the primary endpoint) and progression-free survival (PFS) were analyzed using unweighted and weighted Cox proportional hazards models. Unweighted and weighted overall response rates (ORRs) and complete response (CR) rates were analyzed using logistic regression. Results: The final analysis dataset contained 79 BRUIN cases (median age 67 [range 26-95], 66% male) and 204 Mayo controls (median age 69 [range 30-89], 74% male). The BRUIN cohort had more patients with ECOG PS ≥1 (61% vs 40%, p=0.001) and elevated LDH (81% vs 63%, p=0.003) than the Mayo cohort. The proportion of patients with TP53 aberration was not statistically different in both cohorts (57% vs. 44%, p=0.15). The index line of RT treatment in the Mayo cohort included chemoimmunotherapy (n=167, 80%) and novel agent-based therapy (eg, cBTKi, venetoclax, PI3Ki, immune checkpoint inhibitor, etc; n=42, 20%). Median lines of prior CLL therapy were 2 (IQR 1-4) vs 1 (IQR 0-3) in the BRUIN and Mayo cohorts, respectively; median lines of prior RT therapy were 2 (IQR 1-2) vs 0 (IQR 0-2). The SMDs of the weighted baseline factors met pre-determined criteria (-0.25≤SMD≤0.25), indicating that balance between the two cohorts was achieved. The median follow-up was 18.3 months (range 0.7-32.9) in the BRUIN cohort and 122.8 months (range 0-280.2) in the Mayo cohort. The unweighted median OS was 12.5 months (95% CI 7.0-20.6) in the BRUIN cohort and 5.7 months (95% CI 3.9-10.7) in the Mayo cohort. The unweighted HR was 0.76 (95% CI 0.54-1.07, p=0.12). After IPTW, the weighted HR was 0.63 (95% CI 0.50-0.78, p<0.001), significantly favoring the BRUIN cohort. The unweighted median PFS was 3.6 months (95% CI 2.8-5.1) in the BRUIN cohort and 3.1 months (95% CI 2.5-4.3) in the Mayo cohort. The unweighted HR was 0.98 (95%CI 0.72-1.34, p=0.92). After IPTW, the weighted HR was 0.78 (95% CI 0.64-0.95, p=0.01), again favoring the BRUIN cohort. Response was evaluable/available in 69 patients in BRUIN and 182 patients in Mayo cohort. The unweighted ORR was 58% vs 53% in BRUIN and Mayo cohorts, respectively (OR=0.83, 95% CI 0.47-1.45, p=0.51), and the CR rate was 16% vs 36% (OR=2.94, 95% CI 1.43-5.88, p=0.003). After IPTW, the weighted OR was 0.65 (95% CI 0.45-0.93, p=0.02) for ORR, favoring the BRUIN cohort, and 1.89 (95%CI 1.23-2.86, p=0.02) for CR rate, favoring the Mayo cohort. Conclusions: This individual patient-level IPTW-based analysis demonstrated that single agent pirtobrutinib is associated with improved OS, PFS, and ORR compared to usual care in patients with RT. These results support the choice of pirtobrutinib over traditional therapies for RT. Although these results are encouraging, the durability of response to pirtobrutinib remains suboptimal. Ongoing trials and other future research will evaluate the efficacy of pirtobrutinib in combination with other treatments in this setting.

Abstract Background Chimeric antigen receptor T cell (CART) therapy has revolutionized treatment for hematologic malignancies. However, durable remission following anti-CD19 CART therapy (CART19) remains limited to 40–50% of patients, often due to tumor relapse and CART dysfunction (PMID:31501612). We previously demonstrated that tumor-derived extracellular vesicles (EVs) from patients with chronic lymphocytic leukemia (CLL) can directly impair CART function (PMID:33388419). In this study, we aimed to identify tumor-derived EV microRNA (miRNA) cargo associated with clinical CART failure in B cell malignancies and define how they mechanistically drive CART cell dysfunction. Methods To achieve these aims, we profiled tumor-derived EV miRNA cargo using small RNA sequencing (RNAseq) in two independent patient cohorts. Cohort 1 compared plasma-derived EVs from untreated CLL patients to those from healthy donor EVs to identify miRNAs enriched in CLL (n=23). Cohort 2 included patients with diffuse large B cell lymphoma (DLBCL) treated with axicabtagene ciloleucel (CART19, n=12). Here, plasma EV miRNAs were analyzed at baseline (pre-CART treatment) and 1-month post-CART treatment and compared between CART responders (complete remission at 6 months) and nonresponders (no response at 1 month). Enriched miRNAs from both cohorts were identified following miRNA count normalization and differential expression analysis using adjusted p values of ≤0.05. Functional studies were conducted by transfecting CART19-28ζ cells with synthetic miRNA mimics or scrambled controls. CART cells were also generated with stable overexpression of miRNA via lentiviral shRNA delivery. CART function was assessed via in vitro killing, proliferation, apoptosis assays, RNAseq, and in vivo tumor xenograft models. Results In Cohort 1, we identified several miRNAs including miR-125a to be significantly enriched in CLL-derived EVs relative to healthy controls. Similarly, in Cohort 2, miRNA-125a was also identified among the miRNAs enriched in nonresponders vs. responders to CART treatment; Notably, miR-125a was significantly enriched in nonresponders at baseline (pre-CART treatment) and 1-month post-CART treatment (p=0.0177, p=0.0196). To define the functional effects of miR-125a, we delivered synthetic mimics or stable shRNA constructs encoding miR-125a into CART cells. Delivery of miR-125a was confirmed by RT-qPCR (p<0.0001 for mimic vs. scramble, p=0.0069 for shRNA vs. scramble). Here, miR-125a delivery and overexpression impaired CART cytotoxicity/killing of target tumor cells (~25% reduction, p= 0.0039), decreased antigen-specific proliferation (~47% reduction, p=0.0002), and increased apoptosis following antigen stimulation (1.8-fold increase, p=0.0002) as compared to scramble controls in vitro. We next studied how miR-125a impacts CART functions in vivo. Here, tumor-bearing mice treated with miR-125a–overexpressing CART cells (CART sh125a) exhibited accelerated tumor progression (4.1-fold increase, p=0.0019) and significantly reduced survival as compared to mice treated with scramble control CART treatment (CART shScr) (20% vs 80% survival at day 35, p=0.0064), underscoring the dramatic detrimental impact of miR-125a on therapeutic efficacy. To uncover changes in CART gene expression induced by miR-125a delivery, RNAseq was also performed across stimulated CART sh125a vs. CART shScr cells. CART sh125a cells demonstrated broad transcriptional changes, with gene set enrichment of E2F targets, G2/M checkpoint, and apoptosis pathways (FDR p<0.0001, p<0.0001, and p=0.006) further validating the role of miR-125a in disrupting CART cell cycle control, proliferation, and survival. Conclusion In summary, our study identifies miR-125a as a tumor-derived EV cargo that drives CART dysfunction in two separate B cell malignancies (CLL and DLBCL). miR-125a was enriched in both CLL EVs and nonresponders to CART19 therapy at baseline prior and post CART treatment. Functional studies demonstrate that miR-125a delivery and overexpression directly impair CART cytotoxicity and proliferation, increase CART apoptosis, reduce therapeutic efficacy in tumor xenograft models, and disrupt key pathways related to CART cell cycle regulation and survival. These findings position miR-125a as both a key mechanistic driver of CART failure and a potential predictive biomarker for treatment response, while highlighting it as a possible therapeutic target to improve CART outcomes in the clinic.

Abstract Background: Monoclonal B-cell lymphocytosis (MBL), a precursor to chronic lymphocytic leukemia (CLL), is an understudied yet common premalignant condition present in ~8 million adults in the United States. Based on flow cytometry, MBL can be classified into two immunophenotypes: CLL-type (CD5, CD23, and CD20 co-expression) and non-CLL-type (CD5-negative). While the majority of the data to date pertains to CLL-type MBL, the available evidence indicates non-CLL-type MBL is also associated with an increased risk of hematologic malignancies. Clonal hematopoiesis of indeterminate potential (CHIP) is another precursor condition associated with hematologic malignancies. The relationship between non-CLL-type MBL and CHIP and their combined effect remains unknown. Herein, we report findings on these two precursor conditions in the largest screening cohort to date. Methods: Using flow cytometry, we screened for MBL in the Mayo Clinic Biobank participants who were 40 years or older with no prior history of hematologic cancers. Using whole-exome sequencing of whole-blood DNA, CHIP was screened on 291 genes related to myeloid (56 genes) or lymphoid malignancies (235 genes). Incident hematologic malignancies were detected during follow-up using International Classification of Diseases (ICD) codes in the medical record. All diagnoses were manually reviewed for confirmation. Multivariable logistic regression was used to evaluate the association between non-CLL-type MBL and CHIP. Time to incident hematologic malignancy was calculated from date of MBL screening to the earliest date of incident malignancy, withdrawal, death, last medical visit, or study end. Overall survival (OS) was calculated from date of MBL screening to date of death or last known alive. Multivariable Cox regression, adjusted for age, sex and residency, was used to investigate associations between non-CLL-type MBL and CHIP with clinical outcomes; with results reported using hazard ratios (HR) and 95% confidence intervals (CI). Results: In total, 8,802 individuals with MBL screening and CHIP data were analyzed. Non-CLL-type MBL was detected in 249 (2.8%) individuals; 121 (49%) were male, and median age was 78 years (range, 47-95). We identified 757 (8.6%) individuals with CHIP in at least one of the 291 genes tested. The most frequently mutated CHIP genes were DNMT3A, TET2, ASXL1, PPM1D, and TP53. A total of 47 (0.5%) individuals had both non-CLL-type MBL and CHIP; the four genes with the highest number of CHIP variants in these individuals were DNMT3A (n=16), TET2 (n=10), ASXL1 (n=3), and ATM (n=3). An association between non-CLL-type MBL and any CHIP (OR=1.6, 95%CI:1.2-2.3, P=0.006) was observed. When analyzing CHIP in genes related to myeloid malignancies, the association with non-CLL-type MBL was also significant (OR=1.6, 95%CI:1.1-2.3, P=0.012); however, the association was not statistically significant for genes related to lymphoid malignancies (OR=1.6, 95%CI:0.8-3.3, P=0.165). With a median follow-up of 5.4 years, 104 individuals developed incident hematologic malignancies (66 lymphoid and 38 myeloid malignancies). Non-CLL-type MBL (HR=3.5, 95%CI:1.9-6.5, P<0.001) and CHIP (HR=3.2, 95%CI:2.1-5.1, P<0.001) were each associated with increased risk of incident hematologic malignancies. Co-existence of both precursor conditions was associated with a substantially higher risk of incident hematologic malignancies (HR=10.3, 95%CI:4.0-26.2, P<0.001) compared to individuals with neither precursor condition. Among individuals with non-CLL-like MBL, any CHIP was a borderline significant predictor for incident hematologic malignancy (HR=3.6, 95%CI:1.0-12.9, P=0.049). Compared to individuals with no precursor conditions, OS was not significantly different in those with non-CLL-type MBL-only (HR=1.1, 95%CI:0.8-1.5, P=0.40), those with CHIP-only (HR=1.2, 95%CI:0.99-1.4, P=0.06), or those with both CHIP and non-CLL-type MBL (HR=1.3, 95%CI:0.8-2.1, P=0.39). Conclusions: In the largest screening cohort to date evaluating the relationship of CHIP and non-CLL-type MBL, we found that non-CLL-type MBL and CHIP are associated with each other. Individuals with non-CLL-type MBL were more likely to have CHIP variants in DNMT3A, TET2, ASXL1, and ATM. Among individuals with non-CLL-type MBL, the presence of any CHIP was associated with increased risk of developing hematologic malignancy.

Abstract Introduction: A subset of patients with chronic lymphocytic leukemia (CLL) experiences disease progression from CLL to Richter transformation (RT), characterized by the occurrence of a high-grade lymphoma. The outcomes of patients with RT are typically dismal and identifying better therapeutic strategies remains critically important for these patients. To discern the biologic underpinnings driving this transformation, we studied immune changes and genetic evolution in samples from CLL patients who developed RT. Methods: We identified 18 patients with CLL who developed RT; and performed single cell (sc) RNA-sequencing(seq) on sorted B and T cells from peripheral blood mononuclear cells (PBMCs) at the time of RT (n=18) and at the earlier time of CLL diagnosis (n=11). The median time between the CLL sample and the one closest to RT was 4.3 years (range, 0.2-7.3); and patients received a median of 1 CLL directed treatment (range, 0 – 7). A total of 749,906 cells and 36,601 genes were captured during scRNAseq and 720,580 cells and 21,892 genes were retained for downstream analysis, respectively. Analysis was performed using the immunopipe (https://github.com/pwwang/immunopipe) that wraps around Seurat (v5.1.0) and identified enriched pathways using Enrichr service. The sc-T cell receptor (TCR)-repertoire(R)-seq data was analyzed and visualized using scplotter (). The whole exome sequencing (WES) analysis with tumor B-cells from same patients of CLL & RT stages were done using the Agilent sureselect Human all exon v5 + UTR capture kit. Reads from paired end sequencing were processed with the sarek pipeline. Results: Analysis of 720,580 cells from 11 CLL and 18 RT samples showed 16 distinct cell types- 3 B and 13 T cell subtypes. We observed an increasing trend of CD8 TEM [mean 0.548 vs. 0.384, p = 0.12 (Wilcoxon test)] but a decreasing trend of CD4 TCM (mean 0.236 vs. 0.337, p = 0.08) and B-memory (mean 0.0085 vs. 0.0195, p = 0.51) subsets in RT compared to their CLL stage. When comparing transcriptional changes, we found that among the top 18 highly variable genes, the expression of FP236383.3 (lncRNA) and TCL1A was significantly higher (p<0.0001) in the B cell subsets of patients with RT vs. CLL stage. Additionally, in T cell subsets—primarily dnT, γδT, and CD8/CD4 naïve cells—the expression of FP236383.3, NKG7, GNLY, and CCL5 was significantly higher (p<0.0001), while the expression of LDHB, GZMK, and IL32 was significantly lower (p<0.0001) in RT vs. CLL stage samples. Comparison of specific gene set enrichment analysis showed significantly increased expression of GZMB in gdT (p<0.001) and decreased expression of GZMA, GZMK, TIGIT and TCF7 in dnT and CD8 Naïve cells (p<0.001) for RT vs. CLL stage. The top 10 differentially expressed pathways in RT included oxidative phosphorylation, allograft rejection, IFN-α/-γ responses, TNF-α signaling via NF-κβ, complement, Myc targets V1, mTORC1, hypoxia, and p53 signaling across various B and T cell subsets compared to the CLL stage. Initial analysis of TCR-R data showed that patients with RT stage have lower number of unique clones (p<0.5) and reduced clonal diversity (p<0.5), and a higher number of large and hyperexpanded clones compared to their CLL stage. Additionally, WES data indicated that the most frequently mutated gene is TP53 in tumor B cells of both CLL and RT stages. However, a higher percentage of RT-stage samples carry mutations in MGA, ATM, and IRF2BP2 genes compared to their CLL-stage. WES data also showed a trend toward differing frequencies of copy number amplification at 19q12 (p=0.10) and 4q13.1 (p=0.52) between RT and CLL stages. Conclusions: The main findings of our study are as follows:The transcriptional landscape showed significant changes in multiple genes and pathway enrichment related to cell growth, differentiation and immune response in RT vs. CLL stage.A decreased fraction of CD4 TCM cells and reduced TCR clonal diversity were observed in samples at the RT stage and may indicate a poor prognosis for the patients at this stage. WES data of tumor B cells also indicated possible genetic alterations in the RT vs. CLL stage. Data from in-depth analyses on understanding of the dynamics of T cell response and additional experiments on these patients are expected to provide valuable insights into tumor genetic heterogeneity, transcriptional and immune regulation in blood-based immune subsets.

Abstract Introduction: Chronic lymphocytic leukemia (CLL) is marked by impaired T cell responses that limit the efficacy of immunotherapies. CD19-directed chimeric antigen receptor T cell therapy (CART19) received FDA approval to treat CLL in 2024. However, itsefficacy in CLL patients remains low, with durable remission rate of ~20%. Ibrutinib, a Bruton tyrosine kinase inhibitor, has shown synergy with CART19 in preclinical and early clinical studies. We aimed to study the impact of ibrutinib on CART19 utilizing clinical samples from the pivotal clinical trial E1912 (NCT02048813) of ibrutinib/rituximab (IR) vs fludarabine/cyclophosphamide/rituximab (FCR). This trial led to the FDA approval of first line ibrutinib in CLL. Methods: We generated CART19 incorporating either CD28 (28ζ) or 41BB (BBζ) costimulatory domains from T cells isolated from patients with CLL treated with IR or FCR on the E1912 trial. IR samples were collected at baseline (pretreatment), 6- or 12-months during treatment, or at progression. FCR samples were collected at baseline, 15-18 months during treatment, or at progression. For animal experiments, NOD-SCID-γ-/- (NSG) mice were intravenously (i.v.) engrafted with 1×10⁶ luciferase⁺ CD19⁺ JeKo-1 cells. Upon tumor establishment (~10⁸ photons/sec by bioluminescence imaging), mice were randomized and treated i.v. with 1×10⁶ 28ζ or BBζ derived from longitudinal IR- or FCR-treated patient samples. To further assess the impact of prolonged ibrutinib exposure on CART19 function, we chronically stimulated healthy donor-derived 28ζ or BBζ in vitro for 22 days with JeKo-1 cells and 100nM ibrutinib or vehicle control and then tested CART19 functions. Finally, we performed single cell RNA sequencing (scRNAseq) of longitudinal patient T cell samples treated with IR. Results: Ex vivo T cell expansion was significantly enhanced following IR compared to FCR. BBζ generated from IR-treated patients after 6 months of ibrutinib exhibited enhanced in vitro expansion (p=0.016) and antigen-specific proliferation (p=0.038) in the presence of JeKo-1 cells. This corresponded with significantly improved antitumor efficacy and prolonged survival in vivo compared to cells generated at disease progression (p=0.017). In contrast, 28ζ showed no significant differences in efficacy across IR studied treatment timepoints. BBζ from FCR-treated patients did not show differences in tumor control based on treatment timepoints but demonstrated shorter survival compared to BBζ from IR-treated patients. 28ζ from FCR-treated patients generated at disease progression demonstrated significantly reduced tumor control and shorter survival compared to 28ζ produced at baseline (p=0.0002), indicating detrimental effects of FCR treatment on the therapeutic potential of CART products. To further investigate the impact of prolonged ibrutinib exposure, we utilized in vitro models of CART exhaustion. We found that, after repeated antigen stimulation with JeKo-1 cells, ibrutinib-treated BBζ had significantly increased antigen-specific degranulation (p=0.005), and cytokine production (IL-2, p=0.045; TNF-α, p=0.003; IFN-γ, p=0.001), compared to BBζ treated with vehicle control. In contrast, 28ζ did not show improved degranulation or cytokine production in cocultures with ibrutinib. Prolonged ibrutinib exposure led to downregulation of FOXO3, a transcription factor associated with T cell exhaustion which has been shown to cause dysfunction specifically in BBζ. These results further indicate that ibrutinib may be more beneficial to BBζ. Indeed, scRNAseq revealed that after ≥ 6 months of ibrutinib, T cells showed downregulation of inflammatory, oxidative stress, and apoptosis pathways, paralleled by modest activation of MYC and E2F targets. However, at disease progression, T cells under ibrutinib treatment displayed marked upregulation of interferon signaling, inflammation responses, and stress-related programs, indicating a shift toward immune reactivation or dysfunction.Conclusion: Our study shows that BBζ, but not 28ζ, generated 6 months during ibrutinib treatment has superior antitumor activity and persistence compared to similar later timepoints or FCR-treated counterparts. Prolonged ibrutinib exposure enhances BBζ function by modulating stress and apoptotic pathways. These findings highlight the importance of pre-CART treatment timing and support ibrutinib as a potential enhancer of CART cell fitness in CLL.

Abstract Recent studies have highlighted the important but pleiotropic role of IL-4 in response to chimeric antigen receptor T (CART) cell therapy. IL-4 was identified as a regulator of dysfunction in CD19-targeting CART cells with a CD28 costimulatory domain (CART19-28ζ) through a genome-wide CRISPR knockout screen as well as RNA and ATAC sequencing of baseline and exhausted healthy donor CART19-28ζ cells and pre-infusion CART19-28ζ cell products from responders and non-responders in the ZUMA-1 trial (Stewart et al, Nat Commun., 2024). However, interrogation of a single-cell atlas fromactivated pre-infusion CART cell products from patients with acute lymphoblastic leukemia revealed a beneficial role for IL-4 and other type 2 cytokines in the promotion of long-term response (Bai et al, Nature, 2024). In this report, we aim to further understand how IL-4 can be detrimental to CART cell therapy. To study the regulation of CART19-28ζ cells by IL-4, we performed RNA sequencing on CART19-28ζ cells that were stimulated with CD19+target cells in the presence of either 20 ng/mL hrIL-4 or diluent for 24 hours, one week, or two weeks in an in vitro model for exhaustion as previously described (Stewart et al, Nat Commun., 2024). We observed that hrIL-4 treatment drove the development of a distinct transcriptomic profile after chronic stimulation for one week (up genes = 3253 and down genes = 3645) or two weeks (up genes = 6435 and down genes = 6224) but not following 24 hours of activation (up genes = 0 and down genes = 0). Gene set enrichment analysis on the differentially expressed genes following two weeks of chronic stimulation showed that hrIL-4 treatment pushes CART cells to a more exhausted and less naïve phenotype (FDR = 0.015) and leads to a broad downregulation in cytokine signaling (FDR = 0.012). To investigate transcription factors associated with IL-4-induced CART cell dysfunction, we used BETA analysis with publicly available transcription factor binding sites for STAT6, GATA3, and EOMES and our differential expression data. EOMES (p = 0.039), but not STAT6 (p = 0.999) nor GATA3 (p = 0.999) significantly regulated the differentially expressed genes. In support of these findings, the addition of hrIL-4 also significantly upregulated EOMES expression after one (p < 0.0001) and two (p < 0.0001) weeks of chronic stimulation and downregulated the expression of TBX21 (p < 0.0001), a binding competitor of EOMES, following two weeks of chronic stimulation. To evaluate if EOMES is critical for IL-4-induced CART cell dysfunction, we treated either control or EOMES CRISPR knockdown CART cells with 20ng/mL hrIL-4 during chronic stimulation. EOMES knockdown reduced IL-4-induced CART19-28ζ cell dysfunction as seen by an increase in antigen-specific expansion (p = 0.046) and an increase in cytokine production including IL-2 (p < 0.0001), TNF-α (p = 0.006), and IFN-γ (p = 0.020). Having identified that EOMES is at least partially responsible for IL-4-induced CART cell dysfunction, we evaluated EOMES binding sites in human CART19-28ζ cells with CUT&RUN sequencing. Our analysis revealed EOMES binding at hypersensitivity site 2 (HS2) in the IL-4 locus which, in a previous study, was more accessible in both exhausted healthy donor CART19-28ζ cells and pre-infusion CART cell products from non-responders in the ZUMA-1 clinical trial (Stewart et al, Nat Commun., 2024). To determine how HS2 can impact CART cell functions, we generated CART19-28ζ cells from either wildtype (HS2+/+) or HS2-deleted (HS2-/-) murine T-cells and tested them in a syngeneic model of lymphoma generated by engrafting C57BL6 mice with luciferase+ TBL12 cells (1x106, tail vein injection on Day -3) following preconditioning (250mg/kg cyclophosphamide, intraperitoneal injection on Day -4). Following randomization of mice via tumor burden (n = 5 per group), mice were treated with either HS2+/+ or HS2-/- CART19-28ζ cells (1x106 cells, tail vein injection). In this model, HS2-/- CART cells showed enhanced expansion (p = 0.022), increased anti-tumor activity (p = 0.018), and improved overall survival (p = 0.003). Together, our study shows that IL-4 induces a distinct cellular fate in CART19-28ζ cells in the presence of chronic antigen-specific stimulation at least partially through the upregulation of EOMES. Further, the epigenetic regulation of CART cells by the IL-4 enhancer HS2 can significantly influence CART cell activity, and deletion of HS2 can improve CART cell therapy.

Abstract Background: The synergistic mechanisms of BCL-2 inhibitors and CD20-directed antibodies in the treatment of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) often lead to deep and durable responses. Although the use of venetoclax-obinutuzumab (Ven-O) in the frontline setting (1L) for CLL/SLL has led to a paradigm shift in the disease management, there are limited data on its efficacy in the relapsed/refractory (R/R) setting. In this study, we evaluated the efficacy and safety of Ven-O in both 1L and R/R CLL among patients treated outside the context of clinical trials at our institution. Methods We used the Mayo Clinic CLL Database to identify patients with CLL who were treated with Ven-O, both in 1L and R/R settings. Patients seen at Mayo Clinic Rochester between 2017 and 2025 were included. Overall survival (OS) was calculated from date of Ven-O initiation until last known alive date. Event-free survival (EFS) was calculated from date of Ven-O initiation until the next line of treatment or last known alive date. Kaplan-Meier methods estimated EFS and OS rates at 1, 3, and 5 years. Cox proportional hazards models were used to explore the association between baseline factors and EFS and OS; results are reported as hazard ratios (HR) and 95% confidence intervals (95%CI). Finally, we compared the OS to the age- and sex-matched general population of the state of Minnesota. Results A total of 154 patients (91 1L, 63 R/R) were included in the study. The median age was 68 years (69 1L, 68 R/R), and 68% were male (64% 1L, 73% R/R). Overall, TP53 disruptions (either del17p by FISH or TP53 mutation) were noted in 22 (15%) patients (9% 1L, 23% R/R). CLL FISH findings demonstrated del11q in 24 (19%) patients (19% 1L, 18% R/R), del13q in 46 (36%) patients (36% 1L, 36% R/R), and trisomy 12 in 21 (16%) patients (16% 1L, 18% R/R). IGHV genes were unmutated in 95 (68%) patients (60% 1L, 80% R/R). The CLL-IPI risk score was high in 54 (51%) patients (51% 1L, 53% R/R) and very-high in 18 (17%) patients (8% 1L, 34% R/R). A total of 121 (89%) patients completed planned treatment (1 year of venetoclax in 73 [90%] 1L and 2 years of venetoclax in 48 [87%] R/R). Median follow-up for the entire cohort was 1.8 years (2.2 1L, 1.5 R/R). Neither median EFS nor OS was reached for the overall cohort or within the 1L and R/R subgroups. The 1, 3, and 5-year EFS estimates for the overall cohort were 91% (86-96%), 85% (78-92%), and 67% (51-89%), respectively; corresponding EFS values for the 1L subgroup were 95% (91-100%), 89% (82-98%), and 67% (47-95%), respectively; and for the R/R subgroup were 85% (76-95%), 77% (65-92%), and 77% (65-92%), respectively. The 1, 3, and 5-year OS estimates were 98% (95-100%), 95% (91-99%), and 88% (76%-100%), respectively; corresponding OS values for the 1L subgroup were 99% (96-100%), 97% (94-100%), and 97% (94-100%) and for the R/R subgroup were 96% (91-100%), 91% (82-100%), and 61% (27-100%), respectively. Univariable analyses showed that TP53 disruption was associated with shorter EFS (HR 3.8, 95%CI 1.4-10.2, p=0.01), although IGHV mutation status was not associated with shorter EFS. A higher level of serum beta-2 microglobulin (HR 1.27, 95%CI 1.01-1.59, p=0.04) and R/R status (HR 4.9, 95%CI 0.9-25.8, p=0.06) were associated with a shorter OS. Interestingly, TP53 mutation status and IGHV mutation status were not associated with inferior OS. There was no difference in the observed and expected OS for both the 1L (p-0.23) and R/R (p=0.14) Ven-O treated cohorts compared to the age- and sex-matched general population of the state of Minnesota. Conclusions Our study shows that Ven-O is a well-tolerated regimen with demonstration of durable treatment responses both in the 1L and R/R groups, when used outside the context of a clinical trial. To the best of our knowledge, these data for the first time demonstrate no difference in OS of patients treated with Ven-O compared to age- and sex-matched general population, in both the 1L and R/R settings.

Abstract Introduction: Although current clinical treatment approaches targeting Bruton Tyrosine Kinase (BTK) and BCL2, either as monotherapy or in combination are highly effective in chronic lymphocytic leukemia (CLL), CLL remains incurable. Identifying novel drugs that are potent and effective in the relapsed/refractory (RR) setting remains an unmet need. Methods: Utilizing the CellTiter-Glo 2.0 Cell Viability Assay, we have developed a preclinical drug screening platform which allows conducting drug sensitivity profiling of primary peripheral blood mononuclear cells (PBMCs) collected from CLL patients to a panel of drugs, in the presence and/or absence of bone marrow stromal cells (BMSCs). This unique system mimics the in vivo stromal microenvironment in CLL and enables testing of multiple drug responses in primary patient samples, particularly when leukemic cell numbers are low. In this study, we employed this high throughput drug screening platform to profile drug sensitivity in CLL B cells after disease progression on a BTK inhibitor (BTKi) to a panel of 12 drugs, including inhibitors of BCL2 (venetoclax and LP-118 [Newave]), AXL (TP-0903), histone deacetylase (panobinostat and belinostat), p53 (eprenetapopt and idasanutlin), proteasome (carfizomib) and Type III Receptor Tyrosine Kinase (crenolanib), next generation BTKi (LP-168 [Newave]), as well as a novel anti-cancer drug transcriptional chemical inducer of proximity (TCIP1) and the natural green tea extract (GTE) product Sunphenon 90D (Taiyo International). After 24-hour drug exposure, leukemic cell viability was measured, killing curves and IC50 levels generated and calculated by nonlinear curve regression in GraphPad Prism. Results: Using the Mayo Clinic CLL Database and the Mayo Clinic CLL Tissue Bank, we identified 47 patients with RR CLL, all of whom experienced disease progressionon a BTKi (35 ibrutinib +/- CD20 antibody, 10 acalabrutinib +/- CD20 antibody, 2 other). Median age at BTKi initiation was 64 years (range, 41-82), and 36 (77%) were male. IGHV status was unmutated in 44 (94%) patients, FISH at diagnosis showed del17p in 11 (27%), del11q in 6 (15%), +12 in 5 (12%), del13q in 12 (30%), and not detected in 6 (15%) patients. TP53 mutation was seen in 13 (32%) patients at the start of BTKi therapy. Median number of lines of CLL therapy prior to start of BTKi was 2 (range, 0–8); 13 patients received BTKi as their first-line therapy. Our drug screening results showed definite responses to all tested drugs based on dose range generated killing curves and IC50 levels for 30 RR CLL patient samples, though results varied. Among 12 drugs tested, LP-118 (0.1nM), venetoclax (2.6nM), carfizomib (2.2nM), TP-0903 (116.2nM), crenolanib (1769nM), and TCIP1 (1805nM) demonstrated the highest killing effects, while the remaining generated killing but at higher doses: belinostat (6800nM), eprenetapopt (4500nM), idasanutlin (4900nM), LP-168 (7500nM) and GTE (55.6uM). We also observed that RR CLL cohort exhibited significantly increased drug resistance to most of the tested drugs in the presence of BMSCs with corresponding increases in IC50s (with vs. without BMSCs, fold-change respectively): LP-118 3.92-fold, venetoclax 1.98-fold, carfilzomib 2.58-fold, TP-0903 1.65-fold, panobinostat 204.23-fold, TCIP1 1.91-fold, crenolanib 1.31-fold, idasanutlin 1.69-fold, belinostat 6.14-fold, LP-168 1.29-fold, eprenetapopt 3.44-fold and GTE 1.08-fold (11 out of 12 with p-values <0.05 except for GTE which was not significant, Mann-Whitney U test). We found that even for three drugs with the strongest killing effect based on IC50 levels (LP-118, venetoclax, carfilzomib), their killing effects were significantly reduced in the presence of BMSC (p=0.0002, 0.0002, and <0.0001, respectively). Conclusions: Our results highlight the spectrum of currently available drugs that show promise for therapeutic use in patients with RR CLL who experience disease progression on BTKi. The killing impact was still seen, albeit diminished, even in the presence of BMSC. Our ongoing work will be to associate the drug profiles with each patient's clinical history, as well as to the comprehensive genetic and epigenetic features of the CLL B cell clone.

Abstract Introduction: Hemophagocytic lymphohistiocytosis (HLH) is a rare and life-threatening hyperinflammatory syndrome resulting from immune dysregulation. While diagnostic and therapeutic guidelines (e.g., HLH-2004) are established for pediatric HLH, adult-onset HLH remains both a diagnostic and therapeutic challenge, with limited characterization and sparse outcome data. Here, we conduct a single-institution retrospective cohort study to evaluate clinical features, causes, and prognostic markers associated with outcomes. Methods: We performed a retrospective chart review of all adult patients (≥18 years) first diagnosed with HLH across all Mayo Clinic sites between January 1, 2006 and July 1, 2025. Diagnosis was based on hematologist adjudication at time of care. Patients with prior diagnoses of HLH or HLH related to T-cell therapy (CAR-T) were excluded. Clinical and laboratory variables were extracted from electronic health records. The primary outcome was overall survival (OS), defined as time from diagnosis of HLH to death or last follow-up. OS was estimated using the Kaplan-Meier method. Multivariable analysis to identify independent predictors of mortality was performed using a Cox proportional hazards regression model, adjusting for age at diagnosis, sex, HLH etiology, and relevant clinical and laboratory parameters. Model discrimination was assessed using Harrell's concordance index (c-index). Descriptive statistics were summarized using median and interquartile range (IQR) for continuous variables and frequency with percentages for categorical variables. Results: A total of 203 patients diagnosed with HLH were included. The median age at diagnosis was 55 years (range 18-86). The cohort was predominantly male (n=130, 64%) and White (n=163, 80%). The majority of diagnoses occurred in more recent years, with 75 patients (36.9%) diagnosed between 2021–2025, 61 (30.0%) between 2016–2020, and 43 (21.2%) between 2011–2015. Prior to HLH diagnosis, 86 patients (42.4%) had a history of malignancy, 55 (27.1%) had a history of autoimmune disease, and 28 (13.8%) had a history of transplant. The most common HLH etiologies were malignancy-associated (n=99, 49%), infectious (n=51, 25%), and autoimmune (n=24, 12%), in addition to idiopathic (n=6, 3%), post-transplant lymphoproliferative disease or graft-vs-host disease (n=3, 1%), drug-induced (n=3, 1%), or primary HLH (n=1, 0.5%). The most common malignancies included T-cell (n=35, 17.2%) and diffuse large B-cell lymphoma (n=24, 11.8%). Forty-four cases (21.7%) were associated with Epstein-Barr virus (EBV), either through overt viremia or malignancies with EBV positivity on pathology report. Five patients (2.5%) had COVID-19–associated HLH and 2 (1.0%) were attributed to immune checkpoint inhibitors. Overall, 164 patients (80.8%) met the HLH-2004 diagnostic threshold of ≥5 out of 8 criteria, while 196 (96.6%) met the HLH-2024 ≥4 of 7 modified criteria. Among patients with available information, elevated ferritin was present in 197 of 198 (99.5%), fever in 185 of 202 (91.6%), cytopenias involving ≥2 lineages in 184 of 199 (92.5%), hemophagocytosis in 156 of 182 (85.7%), elevated sCD25 in 117 of 121 (96.7%), hypertriglyceridemia in 117 of 186 (62.9%), hypofibrinogenemia in 118 of 196 (60.2%), splenomegaly in 125 of 188 (66.5%), and impaired NK cell activity in 16 of 25 (64.0%). In addition, hepatomegaly was noted in 57 of 195 patients (29.2%). After a median follow-up of 58.3 months, median OS was 62 days (95% CI 40-110) from day of diagnosis. In a multivariable Cox proportional hazards model with moderate discrimination (c-index=0.75), after adjusting for age at diagnosis and sex, T-cell lymphoma–driven HLH (HR 1.78, 95% CI 1.05–3.00, p = 0.03) and elevated blood urea nitrogen (median 51.0 mg/dL, IQR 27.9–99.1; HR 2.07, 95% CI 1.37–3.13, p < 0.005) were independently associated with shorter OS Conclusions: In this cohort of adult patients with HLH, malignancy was found to be the most common trigger for HLH. T-cell malignancies in particular were strongly correlated with poor survival. Elevated blood urea nitrogen at diagnosis also identified patients at significantly higher risk of death, consistent with other critical illnesses that can present with multi-organ failure. These findings emphasize the need for adult-specific prognostic tools incorporating disease etiology and organ dysfunction markers to better stratify risk and guide clinical management in adult-onset HLH.

Abstract Introduction: Although therapies targeting Bruton Tyrosine Kinase (BTK), either as monotherapy or in combination have revolutionized the treatment in chronic lymphocytic leukemia (CLL), the disease remains incurable. Continuous treatment with these agents frequently leads to the development of resistance and disease progression, mostly associated with mutations in BTK or PLCG2. However, a significant fraction of BTKi-resistant patients does not harbor mutations in these genes, revealing that multiple distinct mechanisms of resistance can independently develop in these patient cohorts. Identifying novel molecular pathways associated with drug resistance in the relapsed/refractory (RR) setting of CLL requires more exploration. Materials and Methods: Using the Mayo Clinic CLL Database and tissue bank, we identified 30 RR patients, who had had disease progressionon a BTKi. The median lines of prior therapies were four. The median age at start of treatment was 57.9 (range, 36-78), 77% were male. Rai stage at diagnosis was 0 in 10% of patients, stage I in 37%, stage II in 20%, stage III in 6%, and stage IV in 27%. IGHV unmutated was observed in 87% of cases. Five patients subsequently evolved to Richter's Transformation (RT). A total of 64 blood samples were collected at different timepoints: baseline (before BTKi therapy), during treatment and at disease progression from BTKi (Ibrutinib/Acalabrutinib/Pirtobrutinib/Nemtabrutinib). The CD5+/CD19+ tumor population was enriched by flow sorting. We performed whole genome sequencing (WGS) in tumor/germline pairs with an average sequencing depth of 60X. Copy number variants (CNVpytor), structural variants – SV (Manta and DELLY2), single nucleotide variants (SNV) and indels (MuTect2, Strelka) were calculated. Mutational signature analysis was conducted independently on each disease timepoint with sigProfiler. De novo signatures were extracted with non-negative matrix factorization, then decomposed and mapped to known signatures from the COSMIC Human Cancer Signatures database. Results: Prior to start of BTKi treatment, the most common abnormality was del13q (65%), followed by abnormalities in TP53 (mutation and/or del17p) in 59% of patients, del8p, del11q (23% each), and mutations in SF3B1 (35%), NFKIE, NOTCH1 and MAPK signaling pathway (BRAF, KRAS, NRAS, PTPN11) in 23% of cases, each. Complex karyotype, defined as >3 copy number abnormalities was found in 59% of cases. Disease progression was observed 4.4 years (median; range 1.9-10.8 yrs) after starting BTKi therapy. At disease progression, there was an overall increase in genomic complexity. Overall, 17 cases (56%) showed mutations in BTK (p.C481S, p.C481Y, p.L528W, p.A428D) and/or PLCG2 (p.P844H). Four cases showed mutations in both genes or two or more independent mutations in BTK. Del17p and/or TP53 mutations were found in 20 (67%) cases, 9 of them with biallelic abnormalities. A third of patients (N=10) were found to have MAPK mutations, and 9 (30%) cases had mutations in the epigenetic regulators CREBBP, SETD2, SETD1A andKMT2D. Loss of heterozygosity, including 11q and 17p was found in 13% of cases. Chromothripsis was found in 23% of cases. In patients without BTK or PLCG2 mutations (N=13), TP53 abnormalities were present in 92% of cases and mutations in the MAPK pathway in 46% of these patients. Finally, we identified several SVs involving driver genes at disease progression, including inversions in RB1 (N=1), NOTCH1 (N=1) and translocations in MYC (N=1) and IGH (N=2). Analyzing the mutational signatures, baseline timepoints were dominated heavily by aging signatures (SBS5, SBS1). However, in cases that progressed after therapy, we found enrichment of mutational signatures associated with defective DNA mismatch repair (SBS44, 6%), chemotherapy treatment (SBS25, 14%), homologous and nucleotide excision repair deficiency (SBS8, 48%), and indirect effects of AID-induced somatic mutagenesis (SBS85, 7%). Additionally, the Melphalan signature (SBS99, 10%) was found in patients treated alkylating agents. Conclusions: Disease progression of CLL on BTKi confirmed the existence of multiple driver genes beyond BTK, PLCG2 andTP53, including the high prevalence of mutations in MAPK pathway and epigenetic regulators, and increased genomic complexity. Ongoing efforts are focused on integrating these findings with clinical demographics, epigenetic modifications, and preclinical drug sensitivity profiles.