Blood Advances

Cyclin-dependent kinase 9 (CDK9) drives transcriptional elongation and supports the expression of short-lived oncogenic and anti-apoptotic proteins such as MYC and MCL1. PRT2527 is a potent, selective CDK9 inhibitor currently in early clinical development. We evaluated its preclinical activity in marginal zone lymphoma (MZL) models, including cell lines with acquired resistance to BTK, PI3K, and BCL2 inhibitors. Short exposure (4 hours) to PRT2527 produced nanomolar cytotoxicity across all tested MZL cell lines, with efficacy maintained in resistant derivatives. Transcriptomic profiling of VL51 cells showed broad gene repression, including MYC, IRF4, NF-{kappa}B-related genes, and MCL1, alongside increased expression of HLA class II genes. Moreover, comparison with additional CDK inhibitors revealed a similar transcriptional repression signature, underscoring a conserved CDK-dependent regulatory network. Protein analyses confirmed rapid depletion of MCL1, MYC, RNA polymerase II, and IRF4. Flow cytometry validated increased HLA class II and decreased HLA class I surface expression. Combination studies demonstrated additive to synergistic effects with BTK inhibition (ibrutinib) or dual PI3K/BCL2 inhibition (copanlisib plus venetoclax), independent of baseline drug sensitivity. Mechanistically, these combinations may enhance apoptosis by concurrently suppressing survival signaling and transcriptional addiction. Analysis of patient samples revealed high CDK9 expression, further supporting the biological relevance and therapeutic rationale for targeting CDK9 in this disease. Our findings support the development of CDK9-based combination strategies for relapsed/refractory MZL and other B-cell malignancies, with an additional potential for integration with immunotherapies. Key PointsO_LICDK9 inhibitor PRT2527 kills marginal zone lymphoma cells, regardless of whether they are resistant to other targeted drugs. C_LIO_LIPRT2527 boosts the effects of BTK, PI3K, and BCL2 inhibitors and alters immune-related gene expression. C_LI Draft of graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/705084v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@37b9e6org.highwire.dtl.DTLVardef@8de6a5org.highwire.dtl.DTLVardef@219771org.highwire.dtl.DTLVardef@15dabfe_HPS_FORMAT_FIGEXP M_FIG C_FIG

The distinct features of neonatal megakaryocytes, high proliferation and inefficient platelet production, have clinical repercussions. A diminished capacity for stress thrombopoiesis, the response to acute drops in platelet counts, contributes to the high prevalence of thrombocytopenia in premature infants and to impaired platelet recovery after umbilical cord blood stem cell transplantation. High proliferation also promotes leukemogenesis in babies with Down Syndrome (DS). The transcriptional coactivator Mkl1/MrtfA participates in programming the ontogenic shift from fetal/neonatal to adult-type megakaryopoiesis; in this activity it is opposed by the DS-associated kinase Dyrk1a. In a screen for downstream ontogenic effectors in human progenitors, we identified the kinesin Kifc3 as a factor selectively decreased in adult megakaryocytes and whose knockdown in neonatal megakaryocytes induced adult-type morphogenesis with augmented platelet release. Kifc3 acts as a minus-end directed motor for centrosomal delivery of various cargos. Centrosomal release of Cep192 has recently been found induce cellular process extensions through actin remodeling, reminiscent of megakaryocyte platelet release. In our studies, Cep192 showed striking upregulation and dispersion in adult vs neonatal megakaryocytes, and Kifc3 knockdown recapitulated this effect in neonatal megakaryocytes. A role for Cep192 in promoting megakaryocyte morphogenesis, distinct from its role in centrosome biogenesis, was demonstrated in vitro and in vivo. In silico screening for Kifc3 inhibitors identified a small molecule that affected neonatal megakaryocytes similarly to Kifc3 knockdown, indicating feasibility for therapeutic argeting of the Kifc3-Cep192 pathway in clinical conditions associated with fetal-type megakaryopoiesis. Key PointsO_LIThe motor protein Kifc3 dictates megakaryocyte ontogeny in association with its control of the centrosomal actin-remodeling factor Cep192. C_LIO_LIKnockdown or small molecule targeting of Kifc3 enhances neonatal megakaryocyte morphogenesis and thrombopoiesis. C_LI

Leptin Receptor-expressing (LepR+) stromal cells in the bone marrow are a critical source of growth factors for the maintenance of hematopoietic stem cells (HSCs) and most restricted hematopoietic progenitors. An important unresolved question is whether they also regulate terminal differentiation in some hematopoietic cells. We found that LepR+ cells promote thrombopoiesis by synthesizing the chemokine CXCL14, which is expressed in the bone marrow by a subset of LepR+ cells. Cxcl14-expressing LepR+ cells extend fine processes that wrap around perisinusoidal megakaryocytes. Deletion of Cxcl14 from LepR+ cells did not significantly alter HSC function or most aspects of bone marrow hematopoiesis, including megakaryocyte generation; however, it significantly reduced the numbers of proplatelet-forming megakaryocytes in the bone marrow and platelets in the blood. CXCL14 promoted platelet formation by remodeling lipid metabolism in megakaryocytes, increasing fatty acid transporter expression and enabling megakaryocytes to use more polyunsaturated fatty acids from the circulation. A high fat diet rescued the formation of proplatelet-forming megakaryocyte and platelets in Lepr-cre; Cxcl14 fl/fl mice. CXCL14 protein was sufficient to promote platelet formation by megakaryocytes in vitro and in vivo. LepR+ cells thus create a perisinusoidal niche for thrombopoiesis by producing CXCL14, which regulates lipid metabolism and terminal differentiation in megakaryocytes. Key pointsO_LILeptin Receptor+ stromal cells regulate terminal differentiation in megakaryocytes in addition to maintaining stem and progenitor cells C_LIO_LICXCL14 from Leptin Receptor+ cells promotes the formation of platelets by remodeling lipid metabolism in megakaryocytes in the bone marrow C_LI

Targeted immunotherapies have revolutionized outcomes for lymphoid malignancies, but success in myeloid neoplasms is limited by the lack of amenable targets and immunologically hostile tumor microenvironment (TME). Myeloproliferative neoplasms are chronic myeloid blood cancers, a third of which are driven by mutations in calreticulin (mutCALR). This yields a common neoepitope that binds to, and activates, the thrombopoietin receptor and results in display of the oncoprotein on the extracellular membrane of disease-driving cells, exposing a therapeutic vulnerability. Here, we present a first-in-class chimeric antigen receptor (CAR) T-cell therapy that specifically targets mutCALR+ cells, both in vitro and in vivo. The CAR T-cell therapy selectively depleted mutCALR+ stem cells from patients with myelofibrosis while sparing healthy stem cells, and improved survival in mutCALR leukemia xenografts. To mimic myelofibrotic marrow, we developed a bespoke human chimeroid model and showed no decrease in the potency of CAR T cell-mediated target cell killing even in a fibrotic tumor microenvironment. We also devised a method to boost cell surface expression of mutCALR in CD34+ cells isolated from patients with accelerated/blast phase MPN (defined as >10 % blasts in peripheral blood or bone marrow), enhancing CAR T targeting. This study presents a therapeutic with potential to eradicate mutCALR-driven malignancies and highlights an innovative strategy to evaluate blood cancer-targeting immunotherapies in a relevant TME. One Sentence SummaryA first-in-class CAR T-cell therapy targeting mutant calreticulin selectively depletes malignant stem cells in vivo and in fibrotic human organoids.

TP53 mutations represent one of the strongest adverse prognostic factors in myelodysplastic neoplasms (MDS). While multi-hit TP53 (TP53multiHit) alterations uniformly lead to very poor outcomes, the prognostic relevance of monoallelic TP53 (TP53mono) mutations remains controversial. TP53 variants can cause loss-of-function, dominant-negative, or gain-of-function effects. We hypothesized that functional heterogeneity among TP53 variants contributes to the variable clinical behavior observed in monoallelic TP53-mutated MDS. Therefore, we analyzed pretreatment samples from 4,505 patients with MDS from two independent cohorts (IWG, n=3,173; J-MDS, n=1,332), including 271 patients with TP53mono and 499 with TP53multiHit. Functional annotation of TP53 variants was performed using a previously published phenotype score (PS) derived from saturation mutagenesis screens, capturing dominant-negative and loss-of-function effects. Median overall survival (OS) differed significantly by TP53 allelic state (TP53 wild-type (TP53wt) 42.4 months; TP53mono 22.9 months; TP53multiHit 9.2 months; p < 0.001). Within the TP53mono subgroup, functional annotation identified marked heterogeneity. Patients with high PS ([&ge;]7) showed significantly inferior OS compared with those with low PS (median OS: 13.8 vs. 39.2 months; HR 1.68, 95% CI 1.16-2.42; p = 0.006), particularly for IPSS-R and IPSS-M low-risk cases. Combining PS and variant allele frequency (VAF) further improved risk stratification. TP53mono patients with PS [&ge;]7 and VAF [&ge;]22% had outcomes comparable to TP53multiHit (median OS: 8.8, p = 0.2), whereas those with PS <7 and VAF <22% exhibited survival similar to TP53wt (median OS: 49.7, p = 0.9). Overall, functional annotation of TP53 variants refines prognostication in TP53mono-mutated MDS and may enhance individualized risk assessment.

BackgroundChimeric antigen receptor (CAR) T cell therapy has transformed the treatment of B cell malignancies, but translation to acute myeloid leukemia (AML) has been hindered by on-target, off-tumor (OTOT) toxicity. In particular, endothelial cell (EC)-specific toxicity has limited clinical translation of promising leukemia stem cell-enriched targets such as CD93. Innovative strategies to mitigate EC damage while preserving antileukemic efficacy are needed. MethodsWe hypothesized that a NOT-gated CAR T cell strategy could circumvent EC toxicity associated with CD93 targeting. Considering CAR target antigen density and the pro-inflammatory microenvironment of CAR T cells, we identified VE-cadherin (VC), a highly specific EC marker, as an optimal inhibitory CAR target. We engineered a novel VC-specific single chain variable fragment (scFv), confirmed EC specificity in the context of a VC-specific second-generation activating CAR, then evaluated VC/CD93 NOT-gated CAR T cells for EC protection and antileukemic activity in in vitro cytotoxicity assays and in a three-dimensional vascularized microphysiological system. ResultsVC/CD93 NOT-gated CAR T cells maintain potent cytotoxicity against AML across multiple effector-to-target ratios, but preserve EC integrity, including in a three-dimensional vascular model system. Importantly, prior AML exposure did not impair the EC-protective function of the VC-specific iCAR, indicating durable NOT-gate activity under inflammatory conditions. Conversely, EC-induced iCAR inhibitory functions did not limit downstream antileukemic cytotoxicity, confirming a reversibility of both activation and inhibitory signals. Conclusions: These findings establish NOT-gated CAR T cells as an effective strategy to overcome EC-specific OTOT toxicity. Our results underscore the importance of CAR target discovery and validation across a spectrum of inflammatory states that can influence antigen expression and available therapeutic windows. This approach expands the potential CAR target landscape for AML and may be more broadly applicable to other malignancies where OTOT toxicity limits clinical translation.

Terminal erythroid differentiation involves dramatic cellular remodeling that culminates in the expulsion of the nucleus, a process known as enucleation. While enucleation is conserved across mammals and is crucial for the generation of fully functional erythrocytes, the mechanisms governing this process have remained largely unknown, in part because the absence of genetic material in mature, enucleated red blood cells hinders genetic experimentation. Here, we performed a pooled, forward-genetic CRISPR-Cas9 screen in enucleated red blood cells derived from primary human hematopoietic stem cells to identify genes required for enucleation. We found that Chloride Intracellular Channel 3 (CLIC3) and Vesicle-associated membrane protein 8 (VAMP8) are both necessary for terminal erythroid differentiation, yet likely act through different mechanisms. Knockdown of CLIC3 led to a delay in erythroblast differentiation, culminating in impaired enucleation. We found that the knockdown cells had increased p53 and p21 and exhibited cell cycle alterations, suggesting CLIC3 plays a crucial role in coordinating cell cycle progression during erythropoiesis. In comparison, VAMP8-depleted cells initially appear to undergo accelerated differentiation but then display a specific defect in enucleation. Transcriptional analysis of the VAMP8-knockdown cells suggested dysregulation of pathways for vesicle trafficking and actin binding, and imaging of late-stage erythroblasts revealed impaired nuclear polarization and disorganized actin. This work provides a new approach for functional genomics in enucleated cells and reveals novel factors important for terminal erythroid differentiation and enucleation. Key pointsO_LIA CROPseq-based CRISPR-Cas9 screen enables functional genomics in enucleated primary human red blood cells. C_LIO_LIChloride Intracellular Channel 3 (CLIC3) and Vesicle Associated Membrane Protein 8 (VAMP8) were identified as critical for terminal erythroid differentiation and enucleation, likely acting through two distinct mechanisms. C_LI

Abstract / SummarySurvival outcomes for pediatric Burkitt lymphoma (BL) substantially vary depending on geography (50-90%), which also serves as a proxy for the prevalence of Epstein-Barr virus (EBV) within the tumors. Although BL is considered an immunologically "cold" tumor with few tumor-infiltrating lymphocytes (TILs), their functional status has not been fully evaluated, especially for EBV-positive disease. Here, we characterize the exhaustion and activation profiles of T cells in the tumor microenvironment (TME) of EBV-positive BL using orthogonal methods, single-cell gene expression analysis, spectral flow cytometry, and immuno-histochemistry staining (IHC). We found that CD8+ TILs displayed a mosaic of immune inhibitory gene expression encoding, PD1, TIGIT, LAG3 and HAVCR2/TIM3. IHC validated the expression of PD1 and TIGIT on CD8+ TILs, as well as their respective ligands, PDL-1, PVR, and Nectin-2 on malignant B cells. Despite exhaustion-associated signatures, CD8+ TILs retain cytotoxic potential, expressing granules (i.e. Granzyme A, Perforin) and cytokines (i.e. IFN{gamma}) and demonstrate an increased uptake of metabolites such as glucose, arginine, and methionine. In peripheral blood, pediatric BL patients exhibited a significantly higher abundance of PD1+TIGIT+ CD8+ T cells compared to healthy children. Notably, these circulating T cells from BL patients express significantly lower levels of TOX, suggesting they are not irreversibly dysfunctional. Together, our results indicate that CD8+ T cells both in the TME and in circulation of children with BL are not terminally exhausted but remain poised for functional re-invigoration. These findings support the potential integration of immune checkpoint inhibitors into combination chemotherapeutic regimens to improve outcomes for these children. SignificanceEBV-positive BL tumors contain functional, metabolically active CD8+ T cells. Circulating PD1+TIGIT+CD8+ T cells found in BL patients blood are a biomarker for those in the tumor microenvironment.

Background/ObjectivesIdentification of prognostic biomarkers that capture biologically aggressive disease remains a major need in chronic lymphocytic leukemia (CLL). Aberrant calcium signaling contributes to leukemic survival; however, the clinical relevance of Ca{superscript 2}/calmodulin-dependent protein kinase kinase 2 (CaMKK2), a calcium-responsive kinase, has not been defined. This study evaluated CaMKK2 as a candidate prognostic biomarker and functional regulator in CLL. MethodsCaMKK2 expression was quantified in purified CD19 CLL cells from a clinically annotated cohort balanced by immunoglobulin heavy chain variable region (IGHV) mutation status. Associations with time-to-treatment and overall survival were analyzed. Functional relevance was assessed by pharmacologic inhibition of CaMKK2 in primary CLL cells using metabolic (MTS) and apoptosis (Annexin V/PI) assays. Correlations between CaMKK2 expression and inhibitor sensitivity were determined. The impact of CaMKK2 inhibition on nurse-like cell (NLC) differentiation and macrophage-mediated leukemic support was evaluated in ex vivo culture systems. ResultsElevated CaMKK2 expression was enriched in IGHV-unmutated CLL and associated with shorter time-to-treatment and inferior overall survival. CaMKK2 inhibition reduced primary CLL viability in a dose-dependent manner and induced apoptosis, with sensitivity correlating with CaMKK2 expression levels. Inhibition also attenuated CD163 macrophage polarization and impaired NLC-mediated support of leukemic cells. ConclusionsCaMKK2 expression identifies biologically aggressive CLL and functionally contributes to leukemic persistence. These findings position CaMKK2 as a prognostically relevant biomarker with therapeutic implications, supporting further evaluation of CaMKK2-targeted strategies in high-risk CLL. Sample SummaryChronic lymphocytic leukemia (CLL) shows marked variability in clinical outcome, highlighting the need for biomarkers that identify patients at higher risk of progression and guide therapeutic strategies. Calcium signaling supports leukemia cell survival, yet the clinical relevance of the calcium-responsive enzyme CaMKK2 has not been established. In this study, we demonstrate that elevated CaMKK2 expression in patient-derived leukemia cells is associated with more aggressive disease and earlier need for treatment. Laboratory experiments further show that inhibiting CaMKK2 reduces leukemia cell survival and disrupts supportive macrophage-like cells within the tumor microenvironment. These results position CaMKK2 as a candidate prognostic biomarker that reflects biologically high-risk disease and may inform therapeutic development. Future studies are warranted to determine whether CaMKK2-based risk stratification or targeted inhibition could improve management of patients with CLL.

BackgroundClassical myeloproliferative neoplasms (MPN)--essential thrombocythemia, polycythemia vera, and primary myelofibrosis--are characterized by clonal hematopoiesis, overproduction of mature blood cells, and a high burden of thromboembolic events. Although thrombosis is the leading cause of morbidity and mortality in MPN, the contribution of the vascular endothelium remains incompletely defined. We investigated patient-derived endothelial colony-forming cells (ECFCs) as a surrogate for vascular endothelium in individuals with JAK2 V617F-mutated MPN. MethodsECFCs were cultured from peripheral blood of patients with MPN and healthy controls, phenotyped for thrombo-inflammatory and adhesive markers, tested for JAK2 V617F, and profiled by bulk RNA sequencing. Functional assays assessed endothelial-dependent factor Xa generation. Transcriptomes were benchmarked against public HUVEC reference datasets processed through an identical quantification pipeline. ResultsECFCs were obtained more frequently and in greater numbers from patients with MPN than from controls, indicating enhanced endothelial regenerative or activation potential. MPN ECFCs exhibited increased von Willebrand factor and P-selectin expression and release, along with elevated endothelial cell-dependent factor Xa generation, consistent with a thrombo-inflammatory, procoagulant phenotype. JAK2 V617F was not detected in any ECFC colonies, supporting a non-clonal origin of these endothelial abnormalities. Transcriptomic analysis identified 289 differentially expressed genes in MPN versus control ECFCs, with pathway enrichment revealing coordinated dysregulation of blood coagulation, platelet activation, plasminogen regulation, vascular permeability, extracellular matrix organization, and angiogenesis. Benchmarking against HUVEC datasets confirmed strong endothelial identity of ECFC-derived cells, with MPN-associated changes reflecting endothelial activation rather than loss of endothelialness. ConclusionsECFCs from patients with JAK2-mutated MPN display functional and transcriptomic signatures of endothelial dysfunction in the absence of detectable driver mutations. These findings support a model in which a primed, thrombo-inflammatory endothelium cooperates with clonal hematopoiesis to promote the heightened thrombotic risk characteristic of MPN.

ObjectivesThe therapeutic efficacy of rituximab has reduced the discriminatory power of the International Prognostic Index (IPI) in diffuse large B-cell lymphoma (DLBCL), particularly within intermediate-risk categories. To address this "risk dilution," we aimed to develop and internally validate the AB-IPI (Albumin-BCL2 Refined Prognostic Index) using a hypothesis-driven approach that integrates tumor burden, host fitness, and tumor biology. MethodsThis multi-center retrospective study analyzed 289 patients with de novo DLBCL treated uniformly with R-CHOP immunochemotherapy. We combined the standard IPI with serum albumin < 3.6 g/dL (representing host fitness/rituximab pharmacokinetics) and BCL2 protein expression > 50% (representing tumor biology). The model was validated internally using bootstrapping with 1,000 resamples in accordance with TRIPOD Type 1b guidelines. This study adhered to the TRIPOD (Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis) statement for model development and internal validation (Type 1b). ResultsDuring the observation period, 115 death events were recorded. Multivariate Cox regression identified albumin < 3.6 g/dL (Hazard Ratio 2.62), IPI score > 2 (HR 2.13), and BCL2 > 50% (HR 1.72) as independent prognostic factors. The model maintained a robust Events Per Variable (EPV) ratio of 38.3. The AB-IPI stratified patients into four distinct risk groups with 5-year overall survival rates of 88.0% (Low), 76.1% (Intermediate-1), 45.0% (Intermediate-2), and 29.0% (High). The calibration plot demonstrated excellent agreement between predicted and observed probabilities, with a calibration slope of 0.98, indicating minimal optimism and robust risk estimation. Decision Curve Analysis (DCA) demonstrated that the AB-IPI provided a superior Net Benefit across a wide range of clinically relevant threshold probabilities. ConclusionsThe AB-IPI demonstrates superior clinical utility and calibration compared to the standard IPI. By identifying patients with compounded biological risks who are unlikely to be cured by R-CHOP alone, this score offers a practical framework for optimizing therapeutic strategies, such as the allocation of polatuzumab vedotin.

BackgroundSickle Cell Anaemia (SCA), a genetic blood disorder caused by a single mutation in the beta globin gene, displays a highly variable clinical course. Hydroxyurea (HU), an effective treatment, has an unclear mechanism of action. Plasma proteins can act as biomarkers for understanding disease states and response to HU treatment in SCA patients. MethodsPlasma proteome profiling of 31 healthy individuals and 76 SCA patients, including those with and without HU treatment, was performed using a high-performance liquid chromatography system and Orbitrap mass spectrometer. Statistical analysis was performed to identify differentially abundant proteins (DAPs) between SCA patients and healthy controls. Subgroup analyses were performed to look at the impact of HU treatment on plasma proteome. ResultsOur analysis yielded 43 DAPs in the plasma of SCA patients. Global correlation and protein-protein network analysis revealed that these proteins are part of a robust interaction network. Proteins showing higher abundance (LBP, ORM1 and TFRC) were primarily associated with immune response whereas those with reduced abundance (FBLN1 and F13B) were linked to blood coagulation and proteolysis. Differential abundance of several proteins such as CD14, FCN3, LFALS3BP, LAP and TGFBI was observed in either male or female patients indicating influence of gender. Importantly, HU treatment was associated with elevated levels of haptoglobin (HP) and hemopexin (HPX), key proteins involved in free hemoglobin scavenging. Notably, DAPs such as F10, LPA, and FCN3 overlapped with proteins previously reported to be differentially abundant in beta-thalassemia patients. Moreover, multiple proteins, including APOL1, AZGP1, FBLN1, GPLD1, HPX, LGALS3BP, and TFRC correlated with clinical parameters, such as blood transfusion frequency and, vaso-occlusive crisis, and WBC and platelet counts. ConclusionsThis study identifies novel differentially abundant plasma proteins in SCA, expanding the current repertoire of disease-associated biomarkers and proteins modulated by hydroxyurea therapy. The observed overlap with beta-thalassemia associated signatures reinforces shared pathophysiological mechanisms between these hemoglobinopathies. Several of these proteins show significant correlations with key clinical parameters and disease complications, offering insights into disease mechanisms and potential utility in disease management. Collectively, these findings provide a strong foundation for translational validation in larger, independent cohorts.

Acute myeloid leukemia (AML) is a heterogeneous malignancy whose characterization relies on immunophenotyping and molecular profiling. While hemolysis is recommended for leukocyte isolation in clinical diagnostics, Ficoll-based density gradient centrifugation is widely used in research and biobanking. Here, we evaluated the impact of Ficoll isolation on commonly performed analyses of AML samples. Ficoll altered flow cytometry-based characterization by systematically enriching lymphocytes and AML blasts while depleting granulocytes. The increased T-cell content impaired AML engraftment in NSG mice, as T cells mediated terminal graft-versus-host disease. Although Ficoll had minimal impact on ex vivo AML blast expansion or chemotherapy response, RNA sequencing identified 1,136 differentially expressed genes compared with hemolysis, with Ficoll-processed samples notably leading to an overestimation of leukemic stem cell gene set expression. Immunogenomic deconvolution highlighted that Ficoll leads to an overestimation of CD8+ T-cell and monocyte abundances in sequenced samples. Mutation calling from RNA-seq data revealed substantial discrepancies between methods, including failure to detect a clinically relevant DNMT3A R882 mutation in a Ficoll-processed sample. Together, these findings support the systematic use of hemolysis to preserve cellular diversity and avoid unpredictable biases introduced by Ficoll-based isolation.

Mantle cell lymphoma (MCL) is one of the deadliest forms of Non-Hodgkins B-cell lymphoma. Typically, patients present with both overexpression of CyclinD1 and secondary mutations identified by genomic sequencing. Although MCL patients may initially respond to treatment, they eventually relapse and succumb to disease, highlighting the essential need to identify new targets for treatment. Here we performed proteomic profiling of healthy B cells and three different forms of B-cell malignancies, including MCL, to define the proteomic signature of MCL. We compared the proteome of each to MCL and identified 10 proteins that are specifically upregulated in MCL. Of these 10 proteins, seven of them show no transcriptional changes and have been overlooked by conventional RNA expression analysis. Further analysis of the proteomic signature reveals potential avenues for dual targeting in CAR T-cell therapy and provides guidance for personalized therapeutics based on protein expression. STATEMENT OF SIGNIFICANCEWe present a resource defining the protein landscape of MCL, CLL, and FL as compared to healthy b cells identified utilizing quantitative proteomics from primary patient samples. Applied to MCL, our results identify 10 proteins specifically upregulated in MCL that may prove to be therapeutic targets to treat the disease.

Hematopoietic progenitors downstream of hematopoietic stem cells (HSC) are now recognized as the main drivers of day-to-day hematopoiesis. While embryonic and adult HSC fates have been studied in detail, less information exists on stages downstream from HSC, notably in the multipotent progenitor compartment. The early postnatal period represents an important growth phase of the animal and its immune system. Developing immune lineages must be generated in large numbers rapidly, and populate expanding organ niches. To shed light on this critical period, we focused our experiments on early postnatal Flt3+ hematopoietic progenitors, and combined genetic single progenitor barcoding using Polylox with Flt3-driven, inducible fate mapping. Key immune cell types, including T and B lymphocytes (lymphocytes), innate lymphocytes (ILC) 1-3, NK cells, and granulocytes and monocytes (myeloid) emerged from Flt3+ hematopoietic progenitors. Barcode analysis revealed that about 75% of Flt3+ hematopoietic progenitors had unipotent fates for lymphocytes, or ILC or myeloid cells, while the remaining fraction showed unprecedented fate combinations for these lineages. Focusing on ILC only, we uncovered clonal fate restriction towards ILC1, or ILC2, or ILC3 in tissues. These data indicate early tissue seeding by progenitors, and further differentiation towards discrete subsets in situ. In addition to these fate analyses, induction of fluorescent marker at this intermediate stage of hematopoiesis showed that Flt3+ progenitors generated a wave of progeny lasting for over one year. The washout of these cells over time provided kinetic data of cell turnover in major immune cell compartments (in the circulation and in tissues) in vivo. In conclusion, we tracked the fate of large numbers (in the order of hundreds) of Flt3+ progenitor clones in situ. These intermediate progenitors downstream of HSC displayed mostly lineage-restricted fates as well as strong fate complexity, thus serving as a source for early tissue seeding and durable immune lineage.

BackgroundDistinguishing benign proliferative nodules (PNs) from melanoma arising within congenital melanocytic nevi remains a major diagnostic challenge. Copy number alteration (CNA) analysis is widely used to support classification, but current criteria were developed using array comparative genomic hybridization (aCGH). The performance of alternative platforms such as shallow whole-genome sequencing (sWGS) and methylation arrays in this setting is poorly defined. ObjectivesThe objective of this study is to compare CNA profiles obtained from aCGH, sWGS, and methylation arrays in atypical nodules arising within congenital nevi, and to correlate these molecular findings with clinical outcomes. MethodsSixteen samples from fourteen patients were retrospectively analyzed using all three platforms. CNAs were cataloged, concordance across methods was quantified using the Jaccard index, and molecular classifications were compared. Clinical follow-up was reviewed to provide clinical context. ResultsaCGH detected 39 CNAs, sWGS 60, and methylation profiling 66. Concordance was highest between sWGS and methylation (mean Jaccard 0.67), followed by aCGH versus sWGS (0.64) and aCGH versus methylation (0.49). Cases with high aneuploidy demonstrated strong cross-platform agreement, whereas low-burden lesions exhibited greater variability between methods. Divergent molecular classifications were observed in six cases. ConclusionsWhile all methods reliably detect broad chromosomal changes, sWGS and methylation arrays identify many additional focal CNAs that may not align with CGH-based diagnostic criteria. Until platform-specific thresholds are established, aCGH remains the most conservative and clinically validated approach for evaluating proliferative nodules in congenital nevi. SIGNIFICANCEAccurate molecular classification of melanocytic proliferations in congenital nevi is essential but challenging, particularly in patients with multiple proliferative nodules. This study provides the first systematic comparison of aCGH, sWGS, and methylation-based CNA profiling in this setting. We show that higher-resolution platforms detect substantially more focal aberrations, which can lead to discordant and potentially overcalled malignancy assessments when applying CGH-derived criteria. Our findings highlight the need for platform-adapted diagnostic frameworks and support continued use of CGH as the most conservative and clinically validated method for risk stratification. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=118 HEIGHT=200 SRC="FIGDIR/small/26347388v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1d7b155org.highwire.dtl.DTLVardef@1bb7081org.highwire.dtl.DTLVardef@d72e3forg.highwire.dtl.DTLVardef@11d3f0b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Allogeneic hematopoietic cell transplantation (allo-HCT) hinges on a delicate trade-off between graft-versus-tumor control and graft-versus-host disease (GvHD), mediated by donor T-cell recognition of antigens presented by recipient human leukocyte antigen (HLA) molecules. We hypothesized that, beyond allele-level matching, sequence divergence at peptide-binding grooves across donor and recipient HLA loci shapes these responses. To this end, we evaluated the effect of HLA evolutionary divergence (HED), a metric quantifying amino acid variability at HLA peptide-binding sites, on selected hematological malignancies in 4,695 patients undergoing allo-HCT from a 9/10 mismatched unrelated donor (MMUD), reported to the EBMT database. We examined (i) locus-specific recipient HED (HED-R) and (ii) "HED-mismatch" (HED-MM), capturing immunopeptidome divergence at the mismatched locus. While dichotomous mismatch status explained differences in survival and acute GvHD risk (with overall greater detriment for class I loci), HED metrics uncovered substantial within-mismatch heterogeneity. In DRB1 mismatched subgroup, HED-MM at this locus, independently predicted inferior relapse-free survival (RFS) with an attenuating time-dependent association, further modulated by cross-locus HED-R. In this subgroup, higher HED-R at HLA-A and HLA-C associated with increased risks of acute GvHD and non-relapse mortality, respectively. Among HLA-B-mismatched pairs, higher DRB1 HED-R associated with worse overall survival (OS) and RFS and higher relapse risk. In the HLA-A-mismatched subgroup, higher HED-R at HLA-A increased chronic GvHD risk. Collectively, HED-derived metrics complement conventional mismatch classification by capturing qualitative differences in donor-recipient immunopeptidome interactions and reveal a complex, non-linear interplay among alleles across mismatch subgroups that modulates the clinical impact of mismatching. KeypointsO_LIIn mismatched unrelated HCT, baseline risk varies across mismatch constellations, with class I mismatches more detrimental than class II. C_LIO_LIHED complements conventional HLA mismatch classification by capturing qualitative donor-recipient immunopeptidome interactions. C_LI

Prolonged cytopenias are a frequent complication of chimeric antigen receptor (CAR) T-cell therapies and are associated with increased infection risk and non-relapse mortality. Although inflammatory cytokines released during CAR-T cell activation have been implicated in immune effector cell-associated hematotoxicity (ICAHT), their direct effects on human hematopoietic stem and progenitor cells' (HSPCs) function remains incompletely understood. Here, we established a reductionist model of CAR-T-associated hematotoxicity using conditioned media (CM) derived from activated CD19 CAR-T cells. Sustained exposure of human HSPCs to CAR-T-derived inflammatory secretome impaired HSPC expansion and reduced long-term repopulating capacity in xenotransplantation assays. In contrast, short-term exposure did not abrogate HSPC function, indicating that brief inflammatory signals can initiate durable reprogramming events, with functional consequences emerging during subsequent proliferative expansion. Mechanistically, CAR-T CM induced IFN gamma- (IFNg) and TNF alpha- (TNFa) responsive transcriptional programs in HSPCs and promoted inflammatory myeloid skewing without evidence of apoptosis-dependent stem cell loss. Combined inhibition of IFNg and TNFa restored HSPC expansion, normalized lineage output, reversed inflammatory transcriptional signatures, and rescued in vivo repopulating capacity without impairing CAR-T cytotoxic activity. These findings demonstrate that CAR-T-derived inflammatory signaling can directly impair human HSC function and identify dual IFNg/TNFa blockade as a potential strategy to mitigate CAR-T-associated hematotoxicity while preserving antitumor efficacy.

Diffuse large B-cell lymphoma (DLBCL), the most common aggressive lymphoma, encompasses histologically similar but genetically distinct cancers. Recent genetic studies have defined at least six molecular subtypes, yet none account for Epstein-Barr virus (EBV), despite 5-15% of DLBCLs being EBV-associated. By reanalyzing published whole-exome and RNA-sequencing data from 481 tumors, we identified 19 EBV-positive cases. These were significantly enriched in the BN2 subtype (6/19), while most (11/19) remained unclassified. In BN2 tumors, several subtype-defining mutations were reduced in frequency among EBV-positive cases, supporting the hypothesis that EBV oncogenes substitute for specific cellular alterations and may confound DLBCL classification algorithms. Extending our analysis to cell lines, we found that the widely used Val cell line harbors the B95-8 laboratory EBV strain; other EBV-positive lines appeared authentic but modeled only non-BN2 subtypes and expressed an atypical viral latency III program, whereas some DLBCL tumors expressed the atypical latency III program and others latency I or II. Together, these findings demonstrate that EBV-positive DLBCL, like DLBCL itself, is not a single disease, and that current in vitro models only partially capture its biological heterogeneity. Key pointsO_LIEBV-positive DLBCL is not a single disease and EBV status can impact genetic-based classifications. C_LIO_LICurrent EBV-positive DLBCL cell lines do not adequately capture tumor complexity; we determined that Val is a problematic cell line. C_LI

Fibrotic remodeling of the bone marrow (BM) niche is a characteristic feature of myelofibrosis (MF) that contributes to disease progression. In MF, mesenchymal stromal cells (MSCs) produce excessive amounts of inflammatory cytokines and extracellular matrix, leading to BM fibrosis, impaired blood production, extramedullary hematopoiesis, and progressive BM failure. While the genetic events that initiate MF in hematopoietic cells are well defined, our understanding of the mechanisms responsible for BM fibrosis remains incomplete. Here, we show that transcription factor EBF1 is a key regulator of the fibrotic gene program in mouse and human MSCs. EBF1 is upregulated in pre-fibrotic MSCs, while mice with MSC-specific deletion of Ebf1 exhibit reduced BM fibrosis, decreased expansion of myeloid cells and splenomegaly when transplanted with hematopoietic progenitors harboring the MF driver mutation MPLW515L. Moreover, we identify ITGB8 as an EBF1-regulated gene with therapeutic potential. MF mice treated with ITGB8-neutralizing antibodies or with MSC-specific Itgb8 deletion show reduced disease burden, as indicated by decreased marrow fibrosis, significantly reduced frequencies of MPL mutant cells, and reduced inflammation in the BM. Our data indicate that targeting the EBF1-ITGB8 axis in the MF MSCs may have therapeutic benefits.