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Abstract Pseudouridine (Ψ) is the most prevalent RNA modification in human cells. Although Ψ was among the first post-transcriptional modifications discovered (1951), its biological functions remain poorly understood. More recently, Ψ was incorporated into COVID-19 mRNA vaccine, where it enhances RNA stability and reduces innate immune sensing. However, the precise roles of RNA Ψ in cancer, including leukemia, are largely unknown. Here, we identify RNA Pseudouridine Synthase D4 (RPUSD4) as a novel vulnerability in acute myeloid leukemia (AML) via directly catalyzing mitochondrial RNA (mt-RNA) Ψ formation. We further provide proof-of-concept evidence that targeting RPUSD4 suppresses leukemogenesis and stimulates anti-leukemia immunity. To investigate whether RNA Ψ dysregulation is involved in leukemia, we first compared RNA Ψ levels between primitive CD34+ cells (LSC-enriched) and CD34- bulk cells from multiple primary AML specimens. CD34+ AML cells exhibited significantly elevated RNA Ψ levels. We also examined Ψ levels across various RNA types in AML cells, identifying that mt-RNA contained much higher Ψ levels than other RNA types. These findings imply that RNA Ψ, particularly mt-RNA Ψ, may play a role in LSC biology and leukemogenesis. Further unbiased CRISPR screening revealed RPUSD4 as the most critical Ψ synthase for LSC maintenance. Large-scale transcriptomic and patient data analyses showed that RPUSD4 is highly expressed in AML specimens (P = 3.5 × 10-9), particularly within LSCs (P = 1.4 × 10-18). RPUSD4 knockout (KO) significantly suppressed AML proliferation, reduced mitochondrial OxPhos, and decreased LSC frequency in vitro and substantially delayed AML progression in vivo (MLL-r and FLT3ITD models). Of note, RPUSD4 KO-mediated anti-leukemia effects could be fully rescued by wild-type but not catalytically inactive RPUSD4 both in vitro and in vivo, demonstrating that Ψ synthase activity is essential for its function in leukemia. To profile RPUSD4-dependent Ψ sites, we applied two orthogonal technologies, direct nanopore sequencing and PRAISE sequencing (PMID: 36997645), both capable of detecting Ψ at single-base resolution. These approaches converged on a single RPUSD4-dependent Ψ at position 3,067 on mt-16S rRNA. This Ψ site is essential for maintaining rRNA stability. RPUSD4 KO induced mt-16S rRNA decay, thereby suppressing mitochondrial translation. This led to OxPhos inhibition, growth suppression, and LSC eradication in AML. Mechanistically, RPUSD4 is exclusively localized in mitochondria, where it directly interacts with the mt-RNA exonuclease PNPase. Under physiological conditions, PNPase resides within mitochondria and degrades mt-RNA to prevent accumulation of mitochondrial double-stranded RNA (mt-dsRNA). Upon RPUSD4 depletion, PNPase translocates from mitochondria to the cytosol, resulting in two major consequences: (i) mRNA decay:Cytosolic PNPase degrades mRNAs, particularly the nuclear-encoded mitochondrial mRNAs, such as DHODH(Dihydroorotate dehydrogenase). By retrogradely upregulating DHODH, RPUSD4 promotes de novo pyrimidine synthesis in AML. (ii) Aberrant mt-dsRNA accumulation: The buildup and cytoplasmic release of mt-dsRNA activates “viral mimicry” response that sensitizes AML cells to T cell cytotoxicity. Finally, to therapeutically target RPUSD4, we developed an RNA-based inhibitor, CpG-siRNARPUSD4, by conjugating a specific RPUSD4 siRNA to a Toll-like receptor (TLR9) ligand. CpG-siRNARPUSD4 is specifically internalized by TLR9+ cells, including AML cells, thereby maximizing selectivity and minimizing toxicity. Preclinical studies demonstrate that pharmacologically targeting RPUSD4 significantly prolonged survival across multiple AML models, including patient-derived xenograft (PDX) models, and rendered AML cells more susceptible to T cell–mediated cytotoxicity. Furthermore, the RPUSD4 inhibitor exhibited a promising synergistic effect with DHODH inhibitor in treating relapsed AML in vivo. For instance, in a representative relapsed PDX model, median survival times (in days) were: Ctrl – 28, RPUSD4 inhibitor – 36, DHODH inhibitor – 39, and combination – over 60. In conclusion, our findings uncover a previously unrecognized role of RPUSD4 and mt-RNA Ψ in leukemic metabolism, anti-leukemia immunity, and LSC maintenance. This study also bridges a critical knowledge gap regarding the role of RNA Ψ in leukemogenesis.

Abstract Background: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma (NHL), accounting for approximately 30% of all NHL cases. DLBCL diagnosis relies on histologic examination, immunophenotyping, molecular and fluorescence in situ hybridization (FISH) analysis to differentiate it from similar NHL subtypes with overlapping morphological features, including more high-grade lymphomas like double-hit lymphoma. Because FISH is performed in a panel of single- or dual-target test format and analyzed through microscopy and manual image analysis, assessment of multiple target biomarkers can be cumbersome and expensive. As additional biomarkers for diagnosis, subtyping, prognosis, and therapeutic decision-making become available, target panels will become larger, posing additional challenges to clinical laboratories. Patients and Methods In this study, Hi-C sequencing of FFPE samples was performed to identify all genomic rearrangements by a single sequencing analysis for an unselected DLBCL case series of 159 patients, and the results were compared to FISH for the detection of clinically important variants. Results Hi-C sequencing showed superior performance compared to FISH: standard FISH for DLBCL includes testing for MYC, BCL2, and BCL6. Between FISH and Hi-C, these biomarkers were detected 105 times, of which, FISH detected 80/105 (76%) and Hi-C detected 102/105 (97%). The cohort included 4 double-hit lymphomas by FISH but Hi-C sequencing detected five. Besides DLBCL diagnostic biomarkers (MYC, BCL2, BCL6), many additional biomarkers were detected by Hi-C sequencing including variants not tested by FISH because the clinical suspicion was ambiguous and the relevant FISH probes were not used, and those not tested because the biomarkers were not thought to be common and, hence, left out of the FISH panel. In total, Hi-C sequencing detected additional biomarkers in 42 (26%) cases, including (1) variants targeted by FISH (i.e. MYC, BCL2, BCL6) but negative, (2) classification biomarkers for other lymphomas (CCND1, MALT, IRF4), and (3) those not tested because the biomarkers are not common and not included in the FISH panel. These additional biomarkers were supportive of suspected diagnosis of DLBCL versus double-hit lymphoma (24 cases), prompted reconsideration of a different diagnosis that may have led to different treatments (6 cases, e.g. mantle cell lymphoma), or biomarkers such as PDL1, ALK, and ATM which have implications for targeted therapies and/or inclusion in clinical trials (5 cases). Conclusion The Hi-C FFPE sequencing technology has the potential to improve the workflow of pathology labs for detection of a wide range of structural variants informing precision diagnosis and treatment for lymphomas.

Abstract Introduction: Brexucabtagene autoleucel (Brexu-cel) is a CD19-targeted chimeric antigen receptor (CAR-)T cell therapy approved for treatment of relapsed/refractory (r/r) B-ALL. Brexu-cel's approval was founded on data from the ZUMA-3 trial, in which 78 patients (pts) were treated at the pivotal dose of 1x10e6 CAR-T cells/kg, resulting in a complete remission (CR) rate of 73%. Three-year follow-up from ZUMA-3 demonstrated median relapse-free and overall survival (RFS/OS) of 11.6 and 25.6 months (mos) for all treated pts. Amongst responders, the median OS was 60.4 mos for those who did not receive a subsequent allogeneic hematopoietic cell transplant (HCT) (n=43), but only 36.3 months for those who did (n=14). This has led some to conclude that HCT may not be beneficial following brexu-cel therapy for r/r B-ALL; however, it must be noted that 29 (37%) of the pts treated on ZUMA-3 received brexu-cel for post-HCT relapse. T cells collected from individuals who relapse in the post-HCT setting are largely of donor origin, making the CAR-T product comparable to a genetically modified donor lymphocyte infusion (DLI). The immunology at play in this scenario may be different from that in which CAR-T cells are of truly autologous origin. Methods: The Real-World Outcomes Collaborative for CAR-T in ALL (ROCCA) consortium database includes pt characteristics and outcomes of brexu-cel therapy given as standard-of-care across 41 US institutions. We identified pts who achieved an MRD negative (neg) CR by either flow cytometry (minimum sensitivity 10e-4) or NGS following brexu-cel for r/r Ph neg B-ALL and categorized them into three groups with regard to use of HCT: Never HCT, Pre-CAR HCT, or Post-CAR HCT. Pts who received second HCT following brexu-cel for post-HCT relapse (n=9) were excluded. Pt/disease characteristics, RFS, and OS were assessed for each group, landmarked at 73 days after brexu-cel infusion (the median time to consolidative allogeneic HCT). Results: In the ROCCA database we identified 165 pts who achieved MRD neg CR following brexu-cel, amongst whom 69 never underwent HCT, 49 were transplanted pre-CAR (ie, brexu-cel served as a genetically modified DLI), and 47 underwent post-CAR consolidative HCT while in CR. The median follow-up is 373 days. The median age was higher in the Never HCT group (49, range 19-83) in comparison with the Pre-CAR HCT (40, 24-72) and Post-CAR HCT (34, 18-70) groups. Thirty-five percent were >60yo in the Never HCT group vs 20% in the Pre-CAR HCT and 9% in the Post-CAR HCT groups. Ph-like disease was present in 38%, 29%, and 43% of the Never HCT, Pre-CAR HCT, and Post-CAR HCT groups, respectively (p=0.35). No significant differences were observed in pre-apheresis bone marrow blasts, presence of CNS disease at apheresis, prior blinatumomab or inotuzumab treatment, or use of bridging therapy across the groups, though there was a higher prevalence of non-CNS extramedullary disease in the Pre- and Post-CAR HCT groups (32, 39%) vs the Never HCT group (13%) (p=0.004). A minority of pts in all groups were deemed to be in MRD neg CR prior to apheresis (6-20%). Median RFS was 260 days in the Never HCT group and not reached in the Pre- and Post-CAR HCT groups (p=0.002), with respective 1-yr RFS of 38%, 64%, and 67%. Median OS was not reached in any group and was similar for all at 1-yr at 68-79% (p=0.13). Characteristics of those in the Never HCT group who were least likely to relapse included age >60 (OR 0.22, CI 0.07-0.73 vs age 18-39, p=0.024) and those with non-Ph-like B-ALL (OR 0.33, CI 0.12-0.94, vs Ph-like, p=0.037) in univariate analyses. Conclusions: Real-world data regarding outcomes following brexu-cel therapy allow evaluation of the role for consolidative allogeneic HCT, which remains one of the most important unresolved questions in the use of CAR-T therapy for r/r B-ALL. This analysis demonstrates that a first consolidative HCT after achieving MRD neg CR with brexu-cel is associated with a significant decrease in relapse. Additionally, use of brexu-cel for post-HCT relapse is also associated with a significantly lower risk of relapse compared with those who never received an allogeneic HCT. With the current duration of followup, OS is not significantly different across the three groups. These data suggest there is a benefit for relapse-free survival in pts receiving an allogeneic HCT at some point in the course of treatment for r/r Ph neg B-ALL.

Abstract Background Acute graft-versus-host disease (GVHD) is a major cause of non-relapse mortality (NRM) after allogeneic hematopoietic cell transplantation (HCT). High-dose steroids are standard first-line therapy for grade II–IV acute GVHD, whereas systemic treatment (tx) is generally not recommended for grade I. However, in practice many patients (pts) with grade I GVHD receive systemic steroids. A prior GITMO randomized trial (n=173) of grade I GVHD to either systemic steroid tx or “watch and wait” found that preemptive steroid tx reduced progression to grade II but not grade III/IV GVHD, increased serious infections, and resulted in similar chronic GVHD, NRM and survival (Bacigalupo, Haematologica 2017). In this study we analyzed real world evidence for early systemic steroid use and the potential impact of serum biomarkers in grade I GVHD. Methods We analyzed clinical data and serum samples from pts with grade I acute GVHD at 24 Mount Sinai Acute GVHD International Consortium (MAGIC) centers between 2014 and 2022 who were treated according to physician discretion. Pts were divided into a preemptive steroid tx group or a watch-and-wait group (systemic steroids administered only if progression to grade II–IV GVHD). Preemptive steroid use was treated as a time-dependent covariate and a frailty proportional hazards model with random effects was used to adjust for center effects to account for possible heterogeneity in clinical practices across transplant centers. Serum samples collected at the diagnosis of grade I GVHD were analyzed for ST2 and REG3α to calculate validated Ann Arbor (AA) scores (1, 2, 3). Results Grade I GVHD was diagnosed in 1143 pts; 591 (52%) received preemptive tx and 552 (48%) were treated by a watch-and-wait strategy. In the preemptive tx group, steroids were initiated at a median of 0 days and within 7 days for >90%. The median initial dose of steroids was 1 mg/kg of prednisone or its equivalent. In the watch and wait group, only 184 pts (33%) required systemic steroids for progression to grade II-IV GVHD at a median of 14 days from grade I diagnosis. Preemptive steroid tx reduced the risk of grade II–IV acute GVHD (HR, 0.71; 95% CI, 0.56–0.89; P=0.003), but not the risk of grade III/IV acute GVHD (HR, 1.03; 95% CI, 0.69–1.52; P=0.899) or chronic GVHD (HR, 1.03; 95% CI, 0.69–1.52; P=0.899), consistent with the GITMO trial. The 12-month incidence of NRM was higher for preemptive tx vs. watch and wait (13% vs 7%, P=0.002). In multivariate analysis preemptive steroid use independently predicted an increased risk of NRM (HR, 1.63; 95% CI, 1.06–2.50; P=0.026) as did several other known risk factors (older recipient age, umbilical cord blood donor, HCT-CI ≥3, and myeloablative conditioning). Greater NRM in the preemptive tx group was driven primarily by 3-fold more infectious deaths; deaths due to uncontrolled GVHD were similar for both tx groups. The risk for relapse was unexpectedly lower in the preemptive tx group (HR 0.64; 95% CI 0.47-0.88; P=0.006) and overall survival was therefore not different between groups, but risk factors for relapse such as minimal residual disease status were not available precluding further analysis of this finding. Serum was collected in 871 (76%) pts at onset of grade I GVHD for retrospective biomarker analysis. AA scores were AA1 (80%), AA2 (15%), and AA3 (5%). AA scores were highly predictive of progression to grade III/IV GVHD (AA1 vs AA2 vs AA3: 9% vs 14% vs 44%, all P<0.001) and the risk of 12-month NRM (8% vs 16% vs 39%, all P<0.001); this pattern was observed in both tx groups. The negative effect of preemptive steroid tx was most pronounced in pts with grade I/AA1 GVHD who experienced 5-fold more infectious related deaths compared to pts managed with a watch and wait approach. Conclusion Treatment of grade I GVHD with systemic steroids did not reduce the incidence of grade III/IV GVHD or deaths due to uncontrolled GVHD and instead increased the risk of NRM from infections compared to pts who were treated only after GVHD progressed. Importantly, 2/3 of the watch and wait pts never needed systemic steroid tx. These findings remained robust after adjusting for multiple confounders, including center effects, and were consistent with the GITMO trial. MAGIC biomarkers at the onset of grade I GVHD predicted outcomes and a watch and wait strategy may be best for the 80% of pts with AA1 GVHD. Better treatment options are needed for the 20% of pts with grade I and AA2/3 GVHD.

Abstract INTRODUCTION Allogeneic hematopoietic cell transplantation (alloHCT) is indicated in patients (pts) with FLT3-ITD mutated AML. The randomized BMT CTN 1506 trial (Levis et al. JCO) demonstrated that maintenance with FLT3 inhibitor gilteritinib (gilt) significantly improved relapse-free survival (RFS) among pts with detectable peri-alloHCT minimal residual disease (MRD) but was also associated with a greater degree of myelosuppression and infections. In older pts, aged >60 years, increasing post-HCT toxicity may adversely impact outcomes. On this basis, we performed a post-hoc analysis of pts aged > 60 years enrolled onto BMT CTN 1506 to examine the impact of gilteritinib maintenance in older pts. METHODS Pts ≥60 years randomized on BMT CTN 1506 (gilt=47, placebo=57; N=104) were included. The primary endpoint of this post-hoc analysis was RFS. We additionally assessed overall survival (OS), incidence of relapse, non-relapse mortality (NRM) in all pts and in pts with detectable MRD. RESULTS Baseline characteristics were balanced. Age was similar (65.2 vs 64.7 years; p = 0.12), as was prior TKI exposure, and NPM1 mutation status. Myeloablative conditioning (MAC) was used in 8 (17%) pts randomized to gilt and 18 (32%) pts randomized to placebo (p=0.08). Median f/u of survivors was 43.8 months (range:1-61 mo.). Estimated RFS and OS at 48 months were not different between groups (RFS: gilt: 57.0%, 95%CI 44.1-73.7%, placebo: 57.1%, 95%CI 45.4-71.8%; OS: gilt: 56.9%, 95%CI 42.9-46.7%, placebo: 58.4%, 95%CI 46.7-73.1%). While gilt assignment did not affect survival, several predictors of poorer survival were identified including use of reduced intensity conditioning (RIC) (HR = 3.46; p = 0.014), use of calcineurin inhibitor/MTX for graft-vs-host disease (GVHD) prophylaxis (HR = 2.29; p = 0.041), high-risk cytogenetics (HR = 2.64; p = 0.021), and MRD (+) pre-HCT (HR = 2.29; p = 0.018). Finally, relative to gilt assignment, opposing rates of relapse and NRM were observed. The incidence of relapse was lower with gilt (16%, 95%CI 6.8-28% vs 32%, 95%CI 20-45%, p=0.046) but NRM was higher (27%, 95%CI 15-41% vs 11%, 95% CI 4.3-21%, p=0.033). We next analyzed the 49 pts (gilt=22, placebo=27) with detectable peri-HCT MRD. RFS and OS again were not different (RFS: gilt: 44.4%, 95%CI 27.1-72.7%, placebo: 43.8%, 95%CI 28.4-67.5%, OS: gilt: 49.2%,95%CI, 31.3-77.4%, placebo: 55.6%, 95%CI 39.4-77.8%). The incidence of relapse trended lower in gilt pts (25%, 95%CI, 5.3-44.7% vs 45% (95%CI, 25-63%), p=0.2) while NRM trended higher (31%, 95%CI 12-52% vs 11%, 95%CI, 2.7-26%, p=0.12). Seventeen (36%) patients completed planned 2 year maintenance with gilt compared to 29 (51%) completing therapy with placebo. Median time on gilt was 13.2 months. The most common reason for discontinuation was adverse events (n=19, 40%), of which cytopenias (n=8) and infections (n=4) were most frequent. Non-relapse causes of death among gilt treated pts included infections (n=8), intracranial hemorrhage related to thrombocytopenia (n=1), second cancer (n=1), and Guillain-Barre syndrome (n=1). Most infections (n=5) were attributed to GVHD as an underlying cause. CONCLUSION Among pts aged ≥60 years, gilt maintenance did not improve RFS or OS. Gilt use was associated with reduced relapse regardless of peri-HCT MRD status demonstrating disease effect; however, higher NRM limited overall benefit. In older FLT3 mutated pts, employing strategies to mitigate HCT related toxicity, e.g. alternative GVHD prophylaxis strategies, may better accommodate use of maintenance therapy including gilt. Lower doses of gilt (particularly with azole co-use) may be worth exploring to mitigate drug AEs, improve compliance, thus further improving benefit.

Abstract A systematic approach to identifying novel therapeutic strategies is essential for expanding curative options in hematopoietic malignancies such as acute myeloid leukemia (AML). We have recently established a high-resolution genetic platform that enables de novo therapeutic development through the CRISPR-Tiling Instructed Computer-Aided (CRISPR-TICA) workflow (Nat Struct Mol Biol 2024, PMID: 38316881). Using this approach, we further identified a new therapeutic pocket and its lead compound for AML treatment (Sci Adv 2024, PMID: 38394203). Here, we present an integrative pipeline, CRISPR-TICA.ai, which combines CRISPR-based functional genomics with generative artificial intelligence (GenAI)-driven ligand modeling to perform high-throughput evaluation of the top 100 leukemia-essential genes and their therapeutic potential in AML. We first used the CRISPR screen dataset published by Novartis (Cancer Discov 2016, PMID: 27260157), which tile-scanned 68 genes in three cancer cell lines, as the initial training dataset to establish the CRISPR-TICA.ai pipeline. Structurally, ligandable protein surface pockets were identified by employing the P2Rank algorithm (J Cheminform 2018, PMID: 30109435). For each pocket, we used the structure-guided diffusion model DiffSBDD (Nat Comput Sci 2024, PMID: 39653846) to generate previously unseen chemical structures that differ substantially from existing drugs, thereby enabling the exploration of novel chemical space. The model was further fine-tuned using direct preference optimization (NeurIPS 2023) against a curated dataset of known inhibitors to enrich for favorable binding profiles (low binding free energy, ΔG) and calibrated against drug-likeness (QED), synthetic accessibility (SA), lipophilicity (logP), and Lipinski's rule compliance. Additionally, our pipeline integrates ligand–protein contact maps with CRISPR-hypersensitive positions to assess spatial interactions, prioritizing ligands that effectively mask biologically essential residues with high affinity. The utility of CRISPR-TICA.ai in AML drug discovery was evaluated- we selected the top 100 leukemia-essential genes from the DepMap database (https://depmap.org/portal/) and generated custom CRISPR libraries for high-resolution gene tiling screens. These libraries comprised 20,233 sgRNAs to tile-scan all 100 genes (47,901 amino acid residues) in Molm13 AML cells at an average resolution of 2.4 amino acids per sgRNA. This dataset provided in-depth structural and functional input for CRISPR-TICA.ai to examine AI-enabled ligand design for over 300 high-confidence druggable pockets in AML. We further developed a user-friendly, web-based 3D visualization platform that interactively maps functional CRISPR hotspots alongside predicted pockets and ligands to enhance accessibility and reproducibility. This tool allows visualization of CRISPR tiling scores, predicted binding pockets, and ligand prioritization, enabling interactive exploration and application. To annotate therapeutically relevant sites, we incorporated data from multiple genomic and proteomic resources, including AlphaFold protein models, Pfam domain annotations, post-translational modification (PTM) sites, and COSMIC leukemia mutational data. Exportable files and GitHub integration are also provided for advanced users to deploy CRISPR-TICA.ai within their facilities.In summary, our study introduces a scalable, leukemia-focused framework for de novo therapeutic discovery. By integrating high-density CRISPR mutagenesis with diffusion-based GenAI modeling, CRISPR-TICA.ai provides a rational roadmap for compound design targeting residues essential for leukemia maintenance. Importantly, the CRISPR-TICA.ai pipeline is adaptable to CRISPR tiling datasets from solid tumors (e.g., the Novartis dataset), highlighting its versatility across diverse cancer types. This approach is especially promising for addressing historically undruggable and resistance-prone targets in AML and beyond.

Abstract Introduction AL amyloidosis is a rare disorder caused by amyloid fibrils produced by clonal plasma cells, leading to serious organ dysfunction. Cardiac involvement is a major risk factor for poor survival. CD38-binding Daratumumab (D) targets plasma cells and, with bortezomib, cyclophosphamide and dexamethasone (VCd) is the only approved regimen for newly diagnosed AL amyloidosis. The ANDROMEDA phase 3 study showed significant improvements in hematologic responses, major organ deterioration progression free survival and overall survival, compared with VCd alone. The AQUARIUS study (NCT05250973) evaluated cardiac safety of different D-VCd schedules and potential cardiac toxicity mitigation strategies. Methods This multicenter, open-label, phase 2 study enrolled 151 newly diagnosed AL amyloidosis patients at 37 sites in 10 countries. Patients enrolled in either Cohort 1 (n=120, cardiac involvement [Mayo 2004 stage II/IIIA], randomized 2:1 to receive D + immediate VCd or D + deferred VCd) or Cohort 2 (n=31, racial or ethnic minorities with ≥1 any organ involvement, treated with D + immediate VCd). Immediate VCd began on Cycle 1, deferred VCd on Cycle 4. The primary safety endpoint was the incidence of cardiac treatment emergent adverse events (TEAEs). Cardiac assessments included HS TroponinT, NT-proBNP, echocardiogram (ECHO), ECG, NYHA, and the 6-minute walk test (6MWT). Clinical cardiac signs and symptoms (S&S) were assessed at baseline and monthly. Selected, clinically relevant grade ≥3 and/or serious cardiac TEAEs were defined as Major Cardiac TEAE and were assessed by an independent adjudication committee for causality. Patients were followed for 12 treatment cycles or 12 months from first dose (if treatment discontinued prior to 12 cycles). Results 142 patients from both cohorts had cardiac involvement and received at least one dose of D + immediate VCd (n=103) or D + deferred VCd (n=39). Baseline characteristics were balanced between the two groups, including Mayo 2004 stage (IIIa: immediate VCd, 35.0%; deferred VCd, 35.9%; II: immediate VCd, 62.1%; deferred VCd, 53.8%). Treatment duration (median: 10.4 months) and proportion completing ≥10 cycles (79% vs 85%) were similar. Serious cardiac TEAEs occurred at similar rates across groups (immediate VCd, 7.8%; deferred VCd, 7.7%). The most common serious cardiac TEAE (MedDRA term) was cardiac failure (immediate VCd, 5.8%; deferred VCd, 2.6%). Two deaths occurred within 60 days of first study treatment, both were in the immediate VCd group, cardiac-related and unrelated to treatment. The immediate VCd group had fewer cardiac TEAEs overall (48.5% vs 61.5%) but experienced them more frequently during Cycles 1-3 than deferred VCd (35.9% vs 28.2%). This trend reversed for Cycles 4-6 (immediate VCd, 17.7%; deferred VCd, 28.9%). Cardiac TEAEs were low for both groups for Cycles 7-9 (immediate VCd, 9.3%; deferred VCd, 12.1%) and Cycles 10-12 (immediate VCd, 7.4%; deferred VCd, 12.1%). Levels of NT-proBNP, HS troponin T, the 6MWT, and overall cardiac S&S improved similarly for both treatment groups. Rate of cardiac TEAEs of any grade was similar for Mayo stage III patients in the two groups (immediate VCd, 73.0%; deferred VCd, 68.8%) whereas for Mayo stage II patients the incidence was higher in the deferred group (35.9% vs 57.1%). Twenty patients (Immediate VCd, 13; deferred VCd, 7) experienced 30 Major Cardiac TEAEs (selected grade ≥3 and/or serious). Adjudicators attributed 28 events primarily to amyloid cardiomyopathy and 2 events primarily to treatment. These 20 patients had higher baseline Mayo stage (IIIa: 70% vs 29.5%) than the remaining patients (n=122), higher baseline median NT-proBNP (4862 ng/L vs 1723 ng/L) and overall S&S score (7.5 vs 4.0). Several ECHO measures were worse at baseline in these 20 patients (notably, median GLS: -8.8% vs -13.7% and E prime lateral: 4.4 cm/s vs 6.1 cm/s) as was 6MWT (median distance: 319 m vs 363 m). Complete Response (CR) rates were similar in both groups: immediate VCd, 62.1%; deferred VCd, 59.0%. Median time to CR was 64 days for the immediate VCd group and 113 days for the deferred VCd group. Conclusion The D-VCd regimen (immediate or deferred) had a manageable safety profile consistent with previous studies. Cardiac TEAEs were similar between regimens, and their emergence correlated with the start of VCd. Major cardiac events were associated with underlying disease and baseline risk factors that are quantifiable and monitorable.

Abstract Background: For patients with B-cell acute lymphoblastic leukemia (B-ALL), extramedullary relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) carries an extremely unfavorable prognosis. As a new immunotherapy, chimeric antigen receptor T (CAR-T) cell therapy has shown remarkable effects in refractory or relapsed B-ALL (r/r B-ALL). However, there is still a lack of evidence for its efficacy and safety in patients with extramedullary relapse after allo-HSCT. The aim of this study was to evaluate the safety and efficacy of allogeneic CAR-T in such high-risk populations. Method: We conducted a prospective clinical study, during which 7 patients with B-ALL who experienced extramedullary relapse after allo-HSCT were enrolled between October 2019 and January 2025. These patients all received allogeneic CD19 CAR-T cell therapy. We prospectively evaluated the safety, efficacy, and survival outcomes following CAR-T treatment. This study was registered at www.chictr.org.cn (No. ChiCTR2000036350). Results: This study included 7 patients with extramedullary relapse after allo-HSCT. Median age was 21 years (range: 15 - 46 years), and the median follow-up time was 415 days (range: 130 - 1320 days). The last follow-up was conducted until July 5, 2025. All the patients were classified as high-risk patients before transplantation. Four of them were Philadelphia chromosome/BCR-ABL positive (Ph+). The sites of extramedullary relapse included: 5 cases of central nervous system (among which 2 cases were accompanied by BCR-ABL molecular relapse in the bone marrow), 1 case of testicular relapse, and 1 case of extensive extramedullary relapse. The median interval from transplantation to extramedullary relapse was 628 days (44 - 1225 days). All patients received chemotherapy, radiotherapy or targeted therapy to reduce tumor burden before infusion. The infusion dose of CAR-T cells was 4 - 10 × 10⁶/kg. After infusion, one patient developed grade 3 cytokine release syndrome (CRS) and grade 4 immune effector cell-related neurotoxicity syndrome (ICANS), while the remaining patients did not experience grade 2 or higher CRS or ICANS. No patients developed graft-versus-host disease (GVHD), and all adverse events were resolved. In terms of therapeutic efficacy, one patient was considered unresponsive at the first assessment after infusion (54 days after infusion). The remaining 6 patients all achieved complete remission (CR) efficacy. The median duration of CR was 275 days (range: 120 - 1305 days). During the follow-up period, one patient suffered from central nervous system relapse again at 275 days post-infusion, while the other 5 maintained a continuous CR. The expansion of CAR-T cells in peripheral blood peaked between days 8 to 15 post-infusion, with a median peak of 1.90E+05 copies/μg DNA (range: 1.78E+04 – 3.18E+05 copies/μg DNA), and the longest duration of detectable expansion was 1320 days. Furthermore, CAR-T cells were detected in the cerebrospinal fluid of three patients, indicating their capability for targeted migration and central nervous system infiltration. Conclusion: Overall, allogeneic CAR-T therapy has demonstrated excellent safety and durable anti-leukemia effects in high-risk ALL patients with extramedullary relapse after transplantation.

Abstract Introduction: Multiple myeloma (MM) is an incurable plasma cell (PC) malignancy, in which nearly all patients are expected to relapse and undergo multiple lines of treatment over the course of their disease. By the time patients receive CAR-T cell therapy, they have typically been exposed to numerous prior therapies, including high-dose melphalan (HDM). Chemotherapeutic agents that cause genotoxic stress, such as HDM, can induce cellular senescence in normal cells. More recently, it has been demonstrated that tumor cells can also exhibit features of therapy-induced senescence (TIS). TIS in tumor cells is associated with distinct gene expression patterns that have been implicated in resistance to therapy and relapse. To investigate whether TIS is activated in MM cells following exposure to chemotherapies, particularly in the context of late-stage disease, we performed an integrated analysis of single-cell RNA sequencing (scRNA-seq) datasets. Methods: We integrated scRNA-seq data from bone marrow plasma cells and MM cells using the following three sources: 1) Boiarsky, et al. (GSE193531, dbGaP: phs001323.v3.p1), which includes healthy donors, MGUS, SMM, and newly diagnosed MM (NDMM) patients; 2) Dhodapkar, et al. (GSE210079), which includes late-stage MM patients pre- and post-CAR-T cell therapy; and 3) newly generated scRNA-seq data from healthy donor (N=3) and late-stage MM patients pre- (N=10) and post- (N=2) CAR-T cell therapy. Non-plasma cells were excluded based on canonical plasma cell markers. We used Seurat v4.3 for data integration, employing canonical correlation analysis (CCA) to define anchors using the FindIntegrationAnchors and IntegrateData functions. Integration quality across datasets was validated by the consistent clustering of healthy plasma cells and expected expression patterns of chromosomal translocation markers CCND1 in t(11;14) cases and FGFR3 in t(4;14) cases, as previously described (PMID: 36396631). To evaluate senescence, we applied single-cell gene set enrichment analysis (scGSEA) using previously published gene sets (PMID: 40164720): SenUp (Senescence Upregulated), SenGA (Senescence Growth Arrest), and SCAPs (Senescent Cell Anti-apoptosis Pathways). We also curated a Plasma Cell Senescence (PCSen) gene set, composed of senescence-related genes that were differentially upregulated in pre-malignant plasma cells across two independent datasets (GSE5900, GSE47552).A normal plasma cell gene set was also generated, comprising genes differentially expressed between healthy and abnormal plasma cells in GSE193531. Results:In the integrated dataset, scGSEA revealed significantly higher enrichment of PCSen, SenUp, SenGA, and SCAPs in late-stage MM cells (both pre- and post-CAR-T cell therapy) compared to NDMM and healthy donors (p<0.05, Kruskal-Wallis with Dunn's posttest). Conversely, the Normal gene set was significantly enriched in healthy plasma cells relative to MM (p<0.05). Expression of CDKN2A, which encodes the senescence marker p16, was also increased in late-stage MM relative to NDMM or healthy plasma cells. Notably, in our newly generated scRNA-seq samples collected within 6 months before CAR-T therapy, we observed a significant inverse correlation between senescence marker expression and progression free survival (PFS) post-CAR-T, suggesting that MM cells exhibiting TIS may be more resistant to T cell mediated cytotoxicity. Supporting this, preliminary in vitro experiments showed that MM cells treated with HDM displayed reduced sensitivity to T cell-mediated cytotoxicity, consistent with a senescence-associated resistant phenotype. Conclusion: Our findings demonstrate that late-stage MM cells exhibit transcriptional signatures consistent with therapy-induced senescence, potentially driven by prior exposure to chemotherapy. This senescent phenotype may contribute to resistance to immunotherapies, including CAR-T cells. These data highlight senescence as a mechanism of resistance and a potential biomarker for predicting CAR-T outcomes. Further studies are needed to explore senescence-targeted strategies to enhance immunotherapeutic efficacy in MM.

Abstract Introduction: cBTKi have made a substantial impact in pts w/ MCL, but pts who develop PD while on treatment w/ cBTKi have historically had poor responses to subsequent lines of therapy (LOT). Brexucel, lisocel, and the non-covalent BTKi pirto have been approved in this population. While two RW studies have substantiated the benefit of brexucel, similar data for pirto are lacking. Accordingly, we aimed to evaluate the outcomes of pts treated w/ pirto in the RW setting. Methods: We performed a multi-center retrospective cohort study of adult pts w/ a diagnosis of MCL who experienced PD after any approved cBTKi and subsequently received pirto. Pts who received pirto w/ bridging intent and those who switched to pirto due to intolerance of cBTKi were excluded. The 95% exact binomial confidence intervals (CI) were calculated for overall response rate (ORR) and complete response rate (CRR). Progression-free survival (PFS) and overall survival (OS) were defined as the time from pirto start to PD or death, whichever occurred first, and the time from pirto start to death, respectively, and calculated w/ the Kaplan-Meier method. The log-rank test was used to compare survival curves. A multivariate (MV) Cox proportional hazard model was built to calculate adjusted hazard ratio (aHR). Analyses were performed w/ SAS, version 9.4. Results: Data on 111 pts w/ MCL treated across 21 institutions were collected. Median (mdn) age was 72 (range 33 – 93) years. Twenty-seven pts (24%) were female, 3 (3%) were Asian, 5 (5%) Black, 9 (8%) Hispanic, 86 (77%) White. Among the 53 (48%) pts w/ available MIPI-c at diagnosis, 28 (53%) pts were high-risk. Ki67 at diagnosis was available in 84 (76%) pts: of those, 58 (69%) had a Ki67 ≥30%, and 41 (49%) ≥50%. TP53 mutational status was available in 70 (63%) pts: 33 (47%) had documented TP53 mutation and 10/52 (19%) pts had a disease w/ complex karyotype. Pts had a mdn of 3 (range 1 – 9) prior LOT (n=106). Ninety-one pts (86%) received chemo-immunotherapy (CIT), 16 (15%) autologous stem cell transplant, 19 (18%) venetoclax (ven), 29 (27%) chimeric antigen receptor T-cell, 4 (4%) allogeneic stem cell transplant. For cBTKi, 39 (35%) pts received ibrutinib, 56 (50%) pts acalabrutinib, 33 (30%) pts zanubrutinib, and 17 (15%) pts received more than one cBTKi. The mdn time from the last dose of cBTKi to pirto start was 55 (range 0 – 2587) days, w/ 51 (46%) pts who switched from a cBTKi directly to pirto. Thirty (27%) pts had no response (stable disease or PD as best response) to cBTKi, and 40 (36%) pts had no response to the last LOT. Two (2%) pts received pirto in combination w/ CIT, 8 (7%) w/ an anti-CD20 monoclonal antibody (mAb), 11 (10%) w/ ven ± a mAb, while 86 (77%) pts as single agent. In 104 (94%) pts, pirto was given at full dose, 10 (9%) pts had a subsequent dose reduction. A total of 35 serious (grade ≥3) adverse events (AE) were documented in 27 (24%) pts: 4 (4%) pts had a serious bleeding AE, 5 (5%) pts a serious cardiac AE, 10 (9%) a serious GI AE, and 16 (14%) a serious infectious AE. Ninety-eight (88%) pts were evaluable for response. The ORR was 40% (95% CI 30% – 50%) w/ a CRR of 29% (95% CI 20%– 39%). At the last follow-up, 29 (26%) pts remained on pirto w/ a mdn treatment duration of 15.1 months (range 0.4 – 26). Fifty-eight (52%) pts died, 35 (78%) because of PD. At a mdn follow-up of 15.8 (range 0.4 – 26) months among survivors, the mdn PFS was 4.7 months (95% CI 3.3 – 8.2) and the mdn OS was 13 months (95% CI 9.2 – not available). Using the log-rank test, age (quartile groups), number of LOT (1-2 vs. 3-4 vs. 5+), time from cBTKi to pirto (quartile groups), Ki67≥30%, and high MIPI-C did not result in a statistically significant difference in PFS (p>0.05). Presence of TP53 mutation was associated w/ a non-statistically significant adverse trend in PFS (p=0.0585). No response to cBTKi and Ki67≥50% were associated w/ a statistically significant inferior PFS in log-rank test (p=<0.05), which persisted in a MV Cox regression model (aHR 2.4, 95% CI 1.4-4.2, and aHR 2.6, 95% CI 1.6-4.4, respectively). Conclusions: This is the first RW report on pirto in MCL pts. In this high-risk population, ORR to pirto was comparable to the BRUIN trial, while PFS was significantly worse, especially in pts w/ no response to cBTKi and w/ a high Ki67. However, prolonged remissions were seen in a subset of pts, suggesting that a better characterization of this population w/ durable benefit from pirto is needed.