Journal of Hematology & Oncology

Children with acute lymphoblastic leukemia (ALL) are treated with multiagent chemotherapy that causes profound changes to the immune system. There are limited data on how disease and therapy impact antigen-specific immune memory, leading to inconsistent guidelines on best practices for revaccination of this population. Here, to inform vaccine guidance, we investigated whether immunity derived from routine childhood measles and varicella zoster virus (VZV) vaccines is maintained during and after therapy for childhood ALL. We report that antibodies against measles and VZV were significantly reduced in children with ALL (n=45) compared to healthy controls (n=13), particularly in older children in whom a longer time had passed since their most recent vaccine dose. However, the avidity of the measles and VZV-specific antibodies was indistinguishable between groups. Despite changes to the composition of the T cell compartment, both overall and antigen-specific T cell function were preserved in children with ALL. These data provide compelling evidence for revaccination of children following ALL treatment. Intact T cell responses suggest that post-treatment revaccination would be effective.

Despite considerable advances, the emergence of treatment resistance to tyrosine kinase inhibitors (TKIs) therapy remains a significant challenge in chronic myeloid leukemia (CML). Here, we report the first clinical case of resistance to combined ponatinib and asciminib therapy in a CML patient who relapsed with B lymphoblastic blast crisis. While at presentation the patient harbored the canonical e13a2 BCR::ABL1 fusion, at relapse his disease harbored the T315I mutation together with a novel e6a3 BCR::ABL1 fusion, arisen by internal deletion in the original translocated allele. Structural modeling and biochemical analyses demonstrated that deletion of exon 2-encoded residues of ABL1 destabilizes the autoinhibited conformation, resulting in a hyperactive kinase with increased propensity for B-cell differentiation. Functional studies revealed that both BCR::ABL1e6a3 and BCR::ABL1e6a3/T315I conferred resistance to ponatinib and asciminib, alone or in combination. BCR::ABL1e6a3 demonstrated enhanced sensitivity to active-state selective inhibitors dasatinib and bosutinib, whereas BCR::ABL1e6a3/T315I remained resistant. Combined drug sensitivity assays showed that axitinib restored inhibitory activity when combined with ponatinib or asciminib. Strikingly, a combination of axitinib and asciminib with low dose ponatinib fully suppressed enzymatic activity of BCR::ABL1e6a3/T315I and cellular proliferation. These data show that treatment with asciminib and ponatinib can select for mutations with notably elevated enzymatic activity, effectively targeted by an axitinib-based triple combination. These data highlight the remarkable mutability of the BCR::ABL1 kinase, including through novel isoforms and provides a strong rationale for the clinical assessment of a triple inhibitor combination as a strategy to overcome resistance to dual ponatinib and asciminib therapy.

CAR-T immunotherapy has achieved remarkable efficacy in hematologic malignancies. However, the widespread clinical adoption of autologous CAR-T products remains constrained by high costs, lengthy manufacturing process, and limited accessibility. Universal or off the shelf CAR-T (UCAR-T) cells derived from healthy donors offer a promising alternative, enabling immediate treatment at a lower cost. However, the allogeneic nature of UCAR-T cells triggers immune rejection by the host immune system after infusion, thereby compromising their persistence and therapeutic efficacy. Current strategies to circumvent this rejection focus on disrupting HLA class I expression. Although this modification allows UCAR-T cells to successfully evade T cell mediated elimination, the loss of HLA class I molecules renders them vulnerable to attack by host natural killer (NK) cells. In contrast to previous approaches that attempt to retain certain non-classical HLA molecules (such as HLA-E or HLA-G) to inhibit NK cells, we directly focused on editing the ligands that mediate NK cell rejection. Through transcriptomic and in vitro validation analyses, we found that UL16 binding proteins (ULBP) 2/5/6 were substantially upregulated in UCAR-T cells compared with nontransduced donor T cells. Elevated ULBP expression effectively activates the NKG2D receptor on allogeneic NK cells and leads to killing of UCAR-T cells, thereby impairing UCAR-T function. To test whether abrogating this NK activating signal could improve UCAR-T persistence and antitumor efficacy, we generated ULBP knockout UCAR-T cells using CRISPR-Cas9 editing. Deletion of ULBP2/5/6 significantly reduced NK cell mediated killing in vitro without affecting CAR expression or T cell effector function. Compared with wild type UCAR-T cells, ULBP deficient UCAR-T cells exhibited enhanced tumor killing efficacy in the presence of NK cells. Collectively, our findings identify ULBP upregulation as one of the mechanisms underlying NK cell mediated rejection of HLA deficient UCAR-T cells. Targeted ablation of ULBP molecules provides a novel strategy to confer resistance to host NK cells, thereby improving the therapeutic potential of universal CAR T products.

Chimeric antigen receptor T-cell (CAR-T) therapy targeting CD19 has transformed outcomes for children with relapsed or refractory (R/R) B-cell acute lymphoblastic leukemia (B-ALL), yet the influence of molecular subtype on outcomes remains unclear. We evaluated the impact of cytogenetic and molecular signatures on complete response (CR), overall survival (OS), and leukemia-free survival (LFS) after CD19 CAR-T therapy in eighty-six pediatric patients with R/R B-ALL treated with tisagenlecleucel. CR was assessed 30 days after infusion. Cytogenetic data were available for 84 patients and molecular profiling for 62. Survival analyses included 72 patients who received CD19 CAR-T as the sole cellular therapy. Seventy-seven patients achieved CR (89.5%). Pre-infusion bone marrow blasts of [&ge;]20% were associated with lower CR rates (53.8% vs 95.9%, p<0.0001) and significantly reduced OS and LFS (both p<0.0001). Among molecular markers, RAS mutations correlated with inferior OS (p=0.0222) and LFS (0.0402). In multivariate analysis, bone marrow blasts >20% and RAS mutations independently predicted inferior OS. Post CAR-T, CD19 negative relapses showed almost twice higher prevalence of RAS mutations (66% vs 37.5%). These findings highlight RAS mutations as a key molecular predictor of outcome after CD19 CAR-T therapy and suggest emergence of unique risk stratification for patients receiving CD19-targeting therapy. Key PointsO_LIRAS mutations independently predict unfavorable survival after CAR-T CD19 in pediatric B-ALL. C_LIO_LIRAS mutations increase risk of CD19 negative relapse after CAR-T CD19 therapy in pediatric B-ALL. C_LI

Chimeric antigen receptor (CAR) T-cell therapy has transformed treatment for relapsed /refractory(r/r) lymphoid malignancies. Yet, these cellular immunotherapies are often associated with immune-related adverse events (irAEs), namely cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS), that pose significant risks to patient safety and limit broader clinical implementation of CAR T-cell therapies. In the current study, we used proteomics technology to establish circulating protein signatures that would predict severe CRS and ICANS in r/r lymphoma patients that subsequently received CAR T-cell therapy. Initial discovery was performed using plasma samples collected preceding CAR T-cell infusion from 39 r/r lymphoma patients at MD Anderson Cancer Center. A 5-marker and 8-marker protein panel was developed for predicting Grade [&ge;] 2 CRS and ICANS respectively, yielding respective AUCs of 0.85 [95% CI: 0.72-0.98] and 0.91 [95% CI: 0.81-1.00]. Independent testing of the CRS and ICANS panel was performed in a cohort of 59 r/r lymphoma patients from the Moffitt Cancer Center, with resultant AUCs of 0.76 [95% CI: 0.63-0.89] and 0.67 [95% CI: 0.51-0.84] for the CRS and ICANS panel, respectively. Patients were further classified into low-, intermediate-, and high-risk groups based on panel score tertiles. In the combined dataset (MDACC + Moffitt), compared to patients in the low-risk group (reference), patients in the intermediate- and high-risk groups were 3.15 [95% CI: 0.92-12.71] and 13.84 [95% CI: 4.21-56.26] more likely to have Grade [&ge;] 2 CRS, and 1.21 [95% CI: 0.36-4.23] and 8.59 [95% CI: 2.87-29.09] more likely to have Grade [&ge;]2 ICANS. The protein biomarker panels provide a means to risk stratify patients who are at high risk for developing severe CRS and ICANS, to inform on the need for prophylactic interventions and improve patient outcomes.

PURPOSEBispecific antibodies (BsAbs) represent a major advancement in the management of relapsed/refractory multiple myeloma (RRMM), offering high response rates even in heavily pretreated patients. However, their use presents operational, safety, and supportive care complexities that require coordinated care teams, and evolving infrastructure. This manuscript summarizes best practice recommendations for adverse event (AE) management, outpatient operational models, referral pathways, and emerging strategies to optimize long-term tolerability. METHODSMedlive--A PlatformQ Health Brand conducted qualitative interviews of academic and community-based clinicians. Discussions focused on BsAb implementation, patient selection and counseling, and AE management. Experts provided recommendations on team-based protocols, transitions of care, and inpatient versus outpatient considerations. RESULTSTen hematologists/oncologists (academic n=4; community n=6) described practice patterns, barriers, and perspectives on BsAb use. BsAbs were consistently regarded as highly effective across multiple lines of therapy, particularly for patients without alternatives. Cytokine release syndrome (CRS) was the most common acute toxicity, generally low grade and managed effectively with early tocilizumab, including prophylactic use in outpatient settings. Immune effector cell-associated neurotoxicity syndrome (ICANS) was rare, mild, and best mitigated through early recognition and caregiver support. Infections, largely from BCMA-associated hypogammaglobulinemia, frequently interrupted therapy, necessitating antiviral prophylaxis, pneumocystis jirovecii pneumonia (PJP) prophylaxis, and intravenous immunoglobulin (IVIG). Outpatient step-up dosing is expanding, supported by prophylactic strategies and academic-community collaboration. Timely referral was emphasized to preserving eligibility. Major outpatient challenges included sequencing, infrastructure readiness, and standardized caregiver and staff education. CONCLUSIONEffective community implementation of BsAbs requires multidisciplinary coordination, standardized AE protocols, infection prevention, and infrastructure to support monitoring, referrals, and equitable access. These measures are critical to ensure safe, sustainable integration of bispecific therapies and to optimize patient outcomes.

Abstract/SummaryImmune checkpoint blockade can produce long-lasting responses in patients with metastatic melanoma; notably, combined CTLA-4/PD-1 blockade has been associated with approximately 52% melanoma specific 10-year survival (1). Yet, nearly half of patients experience minimal clinical benefit, and intensified regimens come with substantial risk of severe immune-related toxicity. The precise determinants of immunotherapy response are incompletely defined, reflecting a complex interplay between tumor biology and host immunity. This is especially consequential for patients whose disease progresses on checkpoint blockade, for whom effective salvage options are limited. In a series of patients with NRAS-mutated melanoma refractory to checkpoint inhibitors, we found that intratumoral administration of talimogene laherparepvec (T-VEC) combined with MEK inhibitor binimetinib induced exceptional clinical responses by amplification of pre-existing T cell responses and induction of de novo tumor-reactive immunity.

Curative-intent immunochemotherapy fails in ~30% of patients with large B-cell lymphoma (LBCL), yet no validated molecular tool enables early identification of high-risk individuals to guide treatment intensification. Using shallow whole genome sequencing (sWGS) of plasma cell-free DNA from 190 LBCL patients, we developed and validated the ACT score (Aberrations, fragment Composition, Terminal motifs), a composite classifier integrating genomic and fragmentomic features from a single post-cycle-1 sample. ACT-positive patients had worse 2-year outcomes versus ACT-negative patients: time-to-progression 29% vs. 83% (HR 4.4, 95% CI 1.9 - 10.0; P = 1.5 x 10 - 4) and overall survival 47% vs. 93% (HR 8.7, 95% CI 3.0 - 25.4; P = 1.8 x 10-6). ACT score was independently prognostic of the International Prognostic Index, and their combination identified the highest-risk patients. Unlike mutation-based approaches, this assay requires neither tumor tissue, germline control nor a baseline plasma sample. Built on open-source tools and sWGS, the ACT score offers a feasible scalable strategy for early risk stratification in aggressive LBCL.

Casein Kinase 2 (CK2) is a constitutively active kinase regulating proliferation and immune signaling and is frequently dysregulated in cancer, including acute myeloid leukemia (AML), making it a therapeutic target. CK2 comprises two catalytic subunits, CK2 or CK2, with two regulatory {beta} subunits. The role of CK2, the predominant catalytic subunit and principal mediator of CK2 kinase activity in hematopoietic cells, in steady-state hematopoiesis remains undefined. To define how CK2 shapes hematopoietic cells, we used bone marrow and spleen tissue samples of wild type control and conditional knock out (KO) of CK2 (Csnk2a1) in the hematopoietic compartment of transgenic mice. Using single-cell RNA sequencing, we profiled the transcriptomic changes associated with CK2 loss. Although HSC abundance was comparable between the control and CK2-deficient samples, HSCs experienced the largest transcriptional response to CK2 loss among all cell types. CK2-deficient HSCs displayed transcriptional remodeling for inflammatory and immune-associated programs, interferon signaling, and antigen presentation. Expression of inflammatory genes such as S100a8 and S100a9, changed in opposite directions in bone marrow and spleen HSCs, demonstrating the transcriptional consequences of CK2 loss shaped by tissue context. Using a network-based approach, we identified immune-associated transcription factors Nfkb1, Rfx5, Hes1, and AP-1 family members as regulatory hubs driving these inflammatory transcriptional states in CK2-deficient HSCs. Cell-cell communication profiling revealed multiple gains and losses in ligand-receptor communication between the HSCs and their immune microenvironment in KO. Our findings identify CK2 as a regulator of immune transcriptional programs in HSCs and suggest that disruption of CK2 signaling influences stem cell behavior and immune activation in contexts relevant to hematologic malignancies and CK2-targeted cancer therapies. Statement of significanceThis study reveals that inhibiting the protein CK2 forces blood stem cells into a stressed, immune-primed state. These tissue-specific findings highlight potential side effects for cancer therapies targeting this essential regulatory kinase.

Children with relapsed or refractory acute lymphoblastic leukemia (ALL) require more effective and less toxic therapies. We established a prospective, multicenter Drug Response Profiling (DRP) registry (NCT06550102) integrating functional testing into precision-guided treatment. DRP was performed for 340 patients from 17 European countries with a turn-around time of two-weeks. Image-based drug screening with over 135000 unique perturbations revealed a heterogeneous landscape of ex vivo responses to 88 drugs on average. Ranking drug responses across the patient cohort defined individual drug fingerprints, identifying "DRP twins" by similarity in sensitivity and resistance independent of genetic ALL subtypes. Of 239 high-risk patients with follow-up, DRP-informed interventions were reported for 63 patients (26%). Patients received combination therapies based on venetoclax, tyrosine kinase inhibitors, trametinib, bortezomib or selinexor, resulting in objective clinical responses in 43 cases (68%). Precision-guided treatments allowed bridging to cellular therapies in 42 patients among whom 28 (67%) were still alive with a median follow-up of 21 months after DRP (IQR: 14.7-26.6 months). Top responders to venetoclax, ranked within the first tertile of the cohort, had superior 1-year event-survival compared to venetoclax non-responders (0.57 [95% CI, 0.39-0.85] vs. 0.25 [95% CI, 0.11-0.58]). Collectively, these findings demonstrate the feasibility and clinical relevance of functional profiling within an international network. This scalable framework enables individualized therapy selection for enrolment in adaptive precision trials for high-risk pediatric ALL.

Long-term follow-up of the CASSIOPEIA trial (NCT02541383) demonstrated superior progression-free survival (PFS) with daratumumab, both in combination with bortezomib, thalidomide, and dexamethasone during induction and consolidation, and during maintenance therapy, in transplant- eligible patients newly diagnosed with multiple myeloma (MM). However, outcomes among CASSIOPEIA patients remain heterogeneous across treatment groups. Measurable residual disease (MRD) is a strong indicator of the depth and duration of therapeutic response and is independently associated with both PFS and overall survival (OS), but it does not fully capture the biological diversity of MM. We performed a risk prediction analysis based on transcriptomic subgroups in CASSIOPEIA patients. A subset of 628 patients was characterized using RNA sequencing and consensus clustering identified five transcriptomic subtypes of MM. Long-term follow-up allowed the definition of three transcriptomic risk categories, with estimated 72-month PFS rates of 70%, 51%, and 27% for low, intermediate, and high-risk groups, respectively, among patients who received daratumumab in at least one treatment phase. In these patients, MRD negativity rates after consolidation and six months later were significantly higher in the low and high-risk groups compared with the intermediate-risk group. In the high-risk group, MRD status was not associated with PFS or OS. This suggests that, although daratumumab administered during both the induction/consolidation and maintenance phases improves the clinical outcomes of patients with activation of NSD2 or overexpressing members of the MAF family, highly aggressive minor clones may rapidly expand. These findings emphasize the need for novel therapeutic strategies in this high-risk population.

Multiple myeloma (MM) is a clonal plasma cell malignancy characterized by bone marrow infiltration, monoclonal immunoglobulin production, and microenvironmental dysregulation that leads to systemic organ damage. The advent of B-cell maturation antigen (BCMA)-directed chimeric antigen receptor (CAR) T-cell therapy has induced unprecedented responses and durability for patients with relapsed/refractory MM. These outcomes are rarely observed with prior salvage strategies, although relapse remains the predominant long-term challenge for most patients. The two currently approved BCMA CAR-T cell products use viral vectors to semi-randomly insert the CAR gene, which results in heterogeneous genomic composition and variability in efficacy, safety, and product consistency. To address these challenges, we integrated targeted CRISPR genome engineering with precise CAR transgene insertion at the T-cell receptor alpha constant (TRAC) locus, 1XX CAR signaling architecture to enhance potency and durability, and non-viral manufacturing with a single-stranded DNA repair template to improve efficiency and yield. This approach confers physiological CAR expression, reduces insertional mutagenesis, and improves persistence by mitigating tonic signaling and exhaustion. Our GMP manufacturing process consistently achieved high CAR integration (37.7-72.7%) and yields across all full-scale runs and met predefined release criteria for identity, purity, safety, and quality. In NSG mouse models of MM, the UCCT-BCMA-1 product exhibited exceptionally potent tumor control, CAR-T cell expansion 100-1000-fold greater than that of lentiviral constructs, and durable clearance of myeloma cells after multiple rechallenges. These findings establish a CRISPR-edited, fully non-viral manufacturing platform for next-generation 1XX-BCMA CAR-T therapies with enhanced persistence, safety, and efficacy. One Sentence SummaryCRISPR-engineered, TRAC-targeted 1XX-BCMA CAR-T therapy with improved safety, potency, and persistence in relapsed and refractory multiple myeloma.

Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy can induce durable remissions in patients with large B-cell lymphoma (LBCL), yet outcomes remain variable. Reliable pre-treatment predictors of durable response remain limited, leaving a critical gap in patient management. To address this, we profiled pre-treatment plasma cell-free RNA (cfRNA) from 91 LBCL patients treated with axicabtagene ciloleucel (axi-cel, Yescarta) across three independent cohorts. We first demonstrated that signatures of "lymph node-like" tumor microenvironments (TMEs), previously identified in tumor biopsies and shown to correlate with favorable outcomes, are specifically elevated in the pre-treatment plasma cfRNA of responders, but not in matched peripheral blood mononuclear cells (PBMCs). These observations indicate that cfRNA captures TME tissue-derived signals not reflected in circulating immune cells. Next, using unbiased approaches, we identified additional cfRNA signatures associated with one-year clinical outcomes that capture the underlying biological landscape of treatment response. Collectively, these findings support pre-treatment plasma cfRNA as a minimally invasive surrogate of TME state to prospectively inform durable CAR T-cell therapy outcomes and guide risk stratification and TME-modulating adjunct therapies.

Allogeneic hematopoietic stem cell transplantation (HSCT) is a life-saving treatment for hematologic malignancies, but long-term survivors present with lower muscle mass and functional capacity. In adult HSCT survivors 10-20 years after treatment, single nucleus RNA sequencing uncovered elevated XRRA1 expression levels in all muscle nuclei populations, which was retained in primary muscle stem cell cultures. HSCT survivors were characterized in vivo by impaired neuromuscular innervation that associated with muscle weakness, and lower muscle stem cell neurotrophic action. Despite these impairments, the molecular and physiological responses to heavy resistance training (HReT) were preserved in HSCT survivors, as demonstrated in a pre-registered clinical trial (ClinicalTrials.gov: NCT04922970). After 12 weeks of HReT, gains in muscle mass and strength were similar in HSCT survivors and healthy controls. In addition, we observed that [~]9% of muscle-resident immune cells persist into adulthood and that bone marrow derived cells do not adopt alternative cell fates in muscle tissue, resolving long-standing questions in human muscle biology. Together, these findings uncover molecular mechanisms of HSCT sequelae in muscle nuclei and muscle stem cells, which, importantly, can at least partly be overcome by mechanical loading. Given the growing population of HSCT survivors and the multitude of benefits of HReT for all organ systems, our findings support the importance of HReT in this population to promote healthspan. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/26351644v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@14322d1org.highwire.dtl.DTLVardef@a30589org.highwire.dtl.DTLVardef@c07930org.highwire.dtl.DTLVardef@544b02_HPS_FORMAT_FIGEXP M_FIG C_FIG

Chimeric antigen receptor (CAR) T cell therapy utilizes genetically engineered patient-derived T cells to target cancer cells. Despite its clinical successes in multiple cancer types, the underlying molecular mechanisms by which molecules on CAR-T cells and surrounding cells interact with other proteins and collectively determine treatment efficacy remain elusive. Most previous studies have relied on transcriptome profiling, which does not fully reflect protein-level organization and interactions. In this study, we developed an antibody-oligonucleotide conjugate targeting the FMC63 region of CAR and integrated it into molecular pixelation (MPX). This approach enabled profiling of the dynamics of CAR molecules on cell surfaces as well as their colocalization with other proteins at the single-cell level. By applying MPX to longitudinal samples from three patients undergoing CAR-T cell therapy, we characterized the dynamic changes in CAR-associated protein organization in both pre-infusion CAR products and post-infusion peripheral blood. While CAR protein abundance and polarization showed limited variation across clinical courses, remodeling of a CAR-centered co-localization network was observed over time, including different retentions of specific molecular associations between patients with different clinical outcomes. Although derived from a limited cohort, our study identifies insights from this methodological framework beyond those gained by conventional omics analyses and offers results of a systematic investigation to predict and enhance CAR therapeutic outcomes. Key pointsO_LIMolecular pixelation was applied for chimeric antigen receptor (CAR) profiling at single-molecule and single-cell resolutions. C_LIO_LIProtein and transcriptome analyses of the CAR molecule showed dynamic remodeling during CAR-T therapy in patients with non-Hodgkin lymphoma. C_LI

The ABACUS study was a single arm, phase II trial evaluating neoadjuvant atezolizumab in operable urothelial carcinoma. Initial bulk transcriptomic and immunohistochemistry analyses suggested links between immune activation, tissue remodeling, and resistance pathways such as transforming growth factor {beta} that were associated with clinical outcome. To further characterize spatial and phenotypic changes at high resolution, artificial intelligence-assisted digital image analysis of hematoxylin and eosin sections and spatial transcriptomics were performed on paired tissue samples. In baseline samples, cells residing in lymphoid aggregates and tertiary lymphoid structures were more abundant in stable disease than in relapse and exhibited gene expression programs associated with improved survival in urothelial carcinoma. Most spatial features reflected shared pharmacodynamic changes between stable disease and relapse; however, carcinoma-endothelial adjacency was reduced significantly following treatment and differed between groups, accompanied by distinct transcriptional programs. Together, these findings indicate that atezolizumab induces localized immune and stromal remodeling within the tumor microenvironment, while non-response despite immune expansion is associated with persistent spatial immune exclusion and carcinoma-endothelial adjacency. Spatial and phenotypic biomarkers identified here may inform rational combination strategies for immune checkpoint inhibitor-refractory urothelial carcinoma.

Myelodysplastic neoplasms (MDS) and related myeloid neoplasms such as chronic myelomonocytic leukaemia (CMML) are clonal haematopoietic stem cell disorders characterised by ineffective and dysplastic haematopoiesis. They are associated with peripheral cytopaenias, variable increases in immature blasts, and a risk of progression to acute myeloid leukaemia. Hypomethylating agents (HMA) can improve blood counts and reduce blasts, but responses are usually limited. Epigenetic rewiring of haematopoietic stem and progenitor cells (HSPC) by HMA enhances hematopoietic output but is influenced by clonal mosaicism, which requires tracking of response at the single cell level to achieve full understanding. We developed SCIMETAR-seq for single-cell interrogation of DNA methylation, target amplicons, and mRNA in FACS-indexed HSPC, then deployed SCIMETAR-seq on CD34+ HSPC from longitudinal HMA-treated patient BM in vitro and in vivo. HMA-induced LINE-1 (L1) demethylation was positively correlated with cell cycling; being lowest in quiescent HSC and highest in erythrocyte progenitors. Erythrocyte progenitor frequencies were particularly increased by HMA exposure. SRSF2 p.P95 genotype did not influence HMA-induced L1 demethylation but was enriched into cells with a CMP immunophenotype, which were transcriptionally biased away from MEP towards granulocytic progenitors. Despite a lack of L1 demethylation in quiescent HSC/MPP after 7 days of HMA treatment in vivo, their transcriptomes were enriched for TNF-, TGF{beta}- and WNT-signaling, suggesting that extrinsic factors secreted by other BM cells in response to HMA mediates reprogramming of quiescent HSC during HMA therapy in vivo.

Somatic mutations in the RAS pathway are highly prevalent in B-Cell Acute Lymphoblastic Leukemia (B-ALL), yet their impact on the bone marrow immune microenvironment and response to immunotherapy remains poorly defined. In this study, we integrated bulk RNA-sequencing, single-cell RNA-sequencing (scRNA-seq), and spectral flow cytometry to characterize the immune landscape of RAS-mutant B-ALL. We identified pathogenic mutations in KRAS, NRAS, PTPN11, or BRAF in 42% of the cohort, predominantly as clonal events. Despite similar T-cell frequencies by flow cytometry, bulk transcriptomes from RAS-mutant samples showed suppression of immune-response and T-cell-activation pathways, and T cells from RAS-mutant patients exhibited impaired proliferation ex vivo. Single-cell analysis revealed higher CD8 dysfunction scores and enrichment of regulatory T cells (Tregs) in RAS-mutant bone marrow. These findings were validated by spectral flow cytometry and by CIBERSORTx deconvolution of bulk data. Trajectory analysis supported a higher CD4 to Treg differentiation in the RAS-mutant niche, and CellChat mapping identified contact-dependent and checkpoint interactions (including TIGIT-NECTIN2 and CTLA-4-CD86/ICOSL) enriched in RAS-mutant samples. Functionally, blinatumomab produced limited leukemic-cell killing ex vivo overall, but addition of CTLA-4 blockade (ipilimumab) selectively restored blinatumomab efficacy in RAS-mutant samples. Together, these results indicate that RAS-pathway activation associates with a Treg-enriched, immunosuppressive bone-marrow microenvironment and point to CTLA-4-targeted strategies to enhance T-cell-engager efficacy in this subgroup.

BackgroundChimeric antigen receptor (CAR)-T cell therapies efficacy in solid tumors remains limited, largely due to the profoundly immunosuppressive tumor microenvironment (TME) which drives CAR-T cells to dysfunction and poor persistence. A comprehensive understanding of the dynamic interplay between CAR-T cells and the TME is therefore critical for the rational design of more effective CAR-T strategies for solid cancers. MethodsHere, we performed single-cell RNA sequencing of tumor samples from immunocompetent mice treated with stroma-targeting EDA-CAR-T cells, profiling CAR-T cell states and TME programs at the peak of antitumor response and during subsequent tumor progression. ResultsOur analysis revealed a marked temporal remodeling of EDA-CAR-T cells within the TME, where early antitumor efficacy is associated with concurrent expansion of cytotoxic effector CD8 CAR-T cells and activation of memory CD4 CAR-T subsets. Moreover, EDA-CAR-T cells effectively engaged the myeloid compartment, resulting in strengthened communication networks involving T cell activation. However, by tumor progression, EDA-CAR-T cells suffered a widespread transcriptional reprogramming towards dysfunction, characterized by loss of effector programs alongside induction of exhaustion and immunoregulatory pathways within the TME, including PD-L1/PD-L2 and TGF{beta} signaling, which impairs sustained immune responses. Notably, early CAR-T cell activation led to increased susceptibility to TME-mediated immunosuppression, revealing EDA-CAR-T-specific soluble galectin-mediated cell-to-cell interaction networks. ConclusionsTogether, this works offers a high-resolution view of CAR-T cell dynamics within the solid TME, uncovering cellular and molecular mechanisms of rapid functional decline and identifying regulatory pathways within the TME that can be exploited to improve CAR-T cell therapy efficacy in solid tumors. KEY MESSAGES OF THE ARTICLEO_ST_ABSWhat is already known on this topicC_ST_ABSThe determinants of CAR-T cell therapeutic efficacy in solid tumors remain poorly defined, largely due to the complexity of the immunosuppressive tumor microenvironment. In this effort, it is necessary to perform comprehensive and detailed mechanistic studies that capture CAR-T cell dynamics within the solid tumor microenvironment to understand treatment failure. What this study addsWe performed single-cell profiling of stroma-targeting EDA-CAR-T cells, revealing their dynamic reprogramming toward dysfunction within the solid tumor microenvironment. We dissected CAR-T cell states and their cell-to-cell interactions with the tumor microenvironment across response and tumor progression and identified mechanisms linking CAR-T cell functionality and therapeutic failure. How this study might affect research, practice or policyThis study provides comprehensive mechanistic insights from an immunocompetent model that can be leveraged to identify shared determinants of CAR-T cell functionality in solid tumors and potentially guide the rational development of improved CAR-T cell therapies.

Carbohydrates are classically catabolized by fermentation or oxidation, a choice that impacts many cellular functions including proliferation. Proliferating cells including somatic stem and progenitor cells are thought to favor fermentation over oxidation, and most proliferating cells in vitro depend on lactate production. However, it has not been tested if fermentation and oxidation are the universal obligatory terminal fates for carbohydrates in vivo because the key enzymes, lactate dehydrogenase (LDH) and pyruvate dehydrogenase (PDH), have not been simultaneously deleted in any cell type. Here we show that both fermentation and oxidation are dispensable for the survival and function of hematopoietic stem cells (HSC). Combined LDHA and LDHB deletion to ablate LDH did not impair HSC function, suggesting that HSCs and rapidly proliferating hematopoietic progenitors surprisingly do not require fermentation. Combined LDHA, LDHB, and PDH deletion abolished both glucose oxidation and fermentation, but did not impair HSC function. Glycolysis was preserved, suggesting the operation of an alternative endpoint. LDH/PDH-deficient HSCs terminated glycolysis through pyruvate export. Pyruvate export by HSCs and progenitors was a physiological response to changing nutrient levels. Quadruple deletion of LDHA/B, PDH, and the pyruvate transporter MCT1 impaired HSC function. This suggested that an essential role of glycolysis termination is not to produce acetyl-CoA or lactate but to remove pyruvate. Therefore, in contrast to classical theories and to in vitro metabolism, carbohydrate metabolism in vivo does not require oxidation or fermentation but can terminate directly in pyruvate export, and this alternative pathway is sufficient to support stem cell function.