Epstein-Barr virus (EBV) infects >90% of humans and is associated with both hematological and epithelial malignancies. Here, we analyzed 990 EBV genomes (319 newly sequenced and 671 from public databases) from patients with various diseases to comprehensively characterize genomic variations, including single nucleotide variations (SNVs) and structural variations (SVs). Although most SNVs were a result of conservative evolution and reflected the geographical origins of the viral genomes, we identified several convergent SNV hot spots within the central homology domain of EBNA3B, the transactivation domain of EBNA2, and the second transmembrane domain of LMP1. These convergent SNVs seem to fine-tune viral protein functionality and immunogenicity. SVs, particularly large deletions, were frequently observed in chronic active EBV disease (28%), EBV-positive diffuse large B-cell lymphoma (48%), extranodal natural killer/T-cell lymphoma (41%), and Burkitt lymphoma (25%), but were less common in infectious mononucleosis (11%), posttransplant lymphoproliferative disorder (7%), and epithelial malignancies (5%). In hematological malignancies, deletions often targeted viral microRNA clusters, potentially promoting viral reactivation and lymphomagenesis. Nondeletion SVs, such as inversions, were also prevalent, with several inversions disrupting the C promoter to suppress latent gene expression, thereby maintaining viral dormancy. Furthermore, recurrent EBNA3B deletions suggested that this viral transcription factor functions as a tumor suppressor. EBNA3B knockout experiments in vitro revealed downregulation of human tumor suppressors, including PTEN and RB1, which could explain the enhanced lymphomagenesis observed in EBNA3B-deficient lymphoblastoid cell line xenografts. Our findings highlight both disease-specific and general contributions of EBV genomic alterations to human cancers, particularly in hematological malignancies.

Loss-of-function (LoF) mutations frequently found in human cancers are generally intractable by classical small molecule inhibitor approaches. Among them are mutations affecting Polycomb-group (PcG) epigenetic regulators, enhancer of zeste homolog 2 (EZH2) and Additional sex combs like 1 (ASXL1), frequently found in hematological malignancies of myeloid or lymphoid lineage, and their concurrent mutations associates with particularly poor prognosis. Although there is a clear need to develop novel and effective treatments for these patients, the lack of appropriate disease models and mechanistic insights have significantly hindered the progress. Here, we show that genetic inactivation of Asxl1 and Ezh2 in murine hematopoietic stem/progenitor cells results in highly penetrant hematological malignancies as observed in corresponding human diseases. These PcG proteins regulate both coding and noncoding genomes, leading to marked reactivation of transposable elements (TEs) and DNA damage responses in PcG LoF-mutated cells, which create a novel vulnerability for poly(ADP-ribose) polymerase (PARP) inhibitor (PARPi)-induced synthetic lethality. Using both mouse models and primary patient samples, we demonstrate that Asxl1/Ezh2-mutated cells are highly sensitive to PARPis that induce excessive DNA damage and significantly extend disease latency. Intriguingly, the observed PARPi sensitivity can be specifically overridden by reverse transcriptase inhibitors that interrupt target site-primed reverse transcription and life cycle of TEs. This mechanism is contrastingly different from the current concept of BRCAness associated PARPi-induced synthetic lethality, which largely rely on deficient homologous recombination, and is independent on reverse transcriptase inhibitors. Together, this study reveals a novel application and mechanism of PARPi-induced synthetic lethal targeting of blood cancers with reactivated TEs such as those carrying PcG epigenetic mutations.

Acquired somatic mutations are incorporated in the classification and prognosis of myelodysplastic syndromes/neoplasms (MDSs). However, the predictive role of molecular features in MDS needs to be elucidated, especially in the lower-risk subtypes (LR-MDS), where treatment has become heterogeneous and predictive biomarkers are lacking. In this study, we investigated genetic markers associated with erythropoiesis-stimulating agents (ESAs) response in LR-MDS. A European cohort of 535 patients with LR-MDS was analyzed using targeted next-generation sequencing (t-NGS) to calculate molecular prognostic scores (International Prognostic Scoring System, molecular [IPSS-M]). The integration of IPSS-M score among the 2 known variables, serum erythropoietin (sEPO) and transfusion dependence (TD), refined the capability to predict response (area under the curve [AUC], 0.71 vs 0.63, P = .0004). Based on these 3 variables, a molecular predictive score, which we named ESA-PSS-M (-0.05 × [sEPO U/L] -4.5 × [IPSS-M score] -5 × [TD (yes = 1; no = 0)]; specificity 76%; sensitivity 57%), was generated and validated in an external cohort (n = 223 patients with LR-MDS). Despite the impact of IPSS-M score, no single mutated gene was linked to ESA response; however, when we stratified cases by sex at birth, the X-linked STAG2 gene mutations were significantly associated with ESA resistance in males with LR-MDS (odds ratio, 0.13; P = .003). To our knowledge, this is the first study based on a large multicenter cohort of patients suggesting that the integration of IPSS-M score and sex-specific mutations can characterize ESA resistance and guide first-line (1L) therapeutic choices for anemic LR-MDS (ie, ESAs vs luspatercept).

Liver sinusoidal endothelial cells (LSECs) are essential for maintaining liver function by actively sensing nutrients and producing angiocrine factors. LSECs also regulate systemic iron metabolism by secreting bone morphogenetic proteins (BMPs), which are key modulators of systemic iron homeostasis. However, the mechanism by which LSECs sense iron to regulate iron metabolism remains unclear. Here, we identify that the endothelial transcriptional factor forkhead box protein O1 (Foxo1) and its upstream protein kinase, mechanistic target of rapamycin complex 2 (mTORC2), as critical iron sensors. In response to iron, Foxo1 undergoes acute and dynamic nuclear translocation to activate the transcription of Bmp2 and Bmp6, thereby stimulating the synthesis of iron-regulatory hormone hepcidin in adjacent hepatocytes. Foxo1 directly binds evolutionally conserved Foxo binding sites within the Bmp2 and Bmp6 promoters to mediate this response. Mechanistically, iron triggers the lysosomal degradation of the mTORC2-specific component rapamycin-insensitive companion of mTOR (Rictor), enhancing Foxo1 activation. Endothelial-specific Foxo1 deletion reduces the expressions of hepatic Bmp2/6 and hepcidin, leading to systemic iron overload, whereas endothelial Rictor deletion increases the expressions of hepatic Bmp2/6 and hepcidin, producing an iron-deficient phenotype. Moreover, endothelial-targeted lipid nanoparticles expressing endothelial-specific and constitutively active Foxo1 alleviate iron overload in a murine model of hereditary hemochromatosis. Collectively, our study establishes the endothelial mTORC2-Foxo1 axis as an iron-responsive regulator of Bmp2 and Bmp6 expression and identifies it as a promising target for iron-related disorders.

Cell-free RNA (cf-RNA) has emerged as a critical mediator of intercellular communication and a potential regulator of hemostasis. In this study, plasminogen (Plg), the zymogen precursor of plasmin, was demonstrated to function as a secreted ribonucleoprotein that carries regulatory, extracellular small noncoding RNAs (sRNAs). Purified human and bovine Plg, isolated via lysine-affinity chromatography, were found to transport 25- to 60-nucleotide-long sRNAs derived from both host and microbial sources. In vitro studies revealed that Plg accepted sRNA cargo from primary macrophages and bound candidate sRNAs with moderate (micromolar) affinity. Notably, Plg-sRNA complexes exhibited a distinct RNA profile compared to high-density lipoproteins, and their compositions were sensitive to hypercholesterolemic conditions. Functionally, removal of sRNA cargo from Plg via ribonuclease digestion significantly increased plasmin enzymatic activity and accelerated clot lysis, while also attenuating Plg-induced proinflammatory cytokine expression in both mouse and human macrophages. These findings reveal a dual regulatory role for sRNAs in modulating both the fibrinolytic and immunogenic properties of Plg, offering novel insights into the cross talk between cf-RNA biology and coagulation pathways. This work positions Plg-sRNA interactions as promising targets for therapeutic intervention in thrombotic and inflammatory diseases.

Neutrophils play a key role in innate immunity by killing microbes through phagocytosis and superoxide anion production by the phagocyte reduced NAD phosphate (NADPH) oxidase. The signaling pathways regulating NADPH oxidase activation in neutrophils have been extensively studied using soluble agonists, but are less understood during phagocytosis, a fundamental function of neutrophils. The aim of this study was to investigate the phosphorylation of the cytosolic NADPH oxidase protein p47phox in human neutrophils stimulated by serum-opsonized zymosan (OZ), which induces phagocytosis, using antibodies against phosphorylated sites. The results show that OZ induced rapid phosphorylation of p47phox on Ser304, Ser315, Ser320, and Ser328, followed by rapid dephosphorylation. Interestingly, despite the transient nature of p47phox phosphorylation, OZ-induced NADPH oxidase activity was sustained for a longer period in cells and in isolated membranes. OZ-induced p47phox phosphorylation was concentration dependent and preceded particle ingestion. Immunoglobulin G (IgG)- and complement protein fragment 3bi (C3bi)-opsonized zymosan similarly induced rapid phosphorylation and dephosphorylation of p47phox on Ser304 to Ser328, suggesting that IgG Fc-gamma receptors (FcγR) and complement receptor 3 (CR3) are involved in this process. Inhibitors of sarcome (Src) tyrosine kinase, spleen tyrosine kinase (Syk), phosphoinositide 3-kinase (PI3K), phospholipase C (PLC), phospholipase D (PLD), Ca2+, and protein kinase C beta 2 (PKCβ2) inhibited OZ-induced phosphorylation of p47phox. These results suggest that (1) OZ-induced p47phox phosphorylation on Ser304 to Ser328 is required for the initiation of NADPH oxidase activation but not for its maintenance during phagocytosis, (2 )the membrane receptors FcγR and CR3 mediate this phosphorylation, and (3) Src and Syk tyrosine kinases, PI3K, PLD, Ca2+, and PKCβ2 control the phosphorylation of p47phox during phagocytosis.

NPM1 is a multifunctional phosphoprotein with key roles in ribosome biogenesis among its many functions. NPM1 gene mutations drive 30% of acute myeloid leukemia (AML) cases. The mutations disrupt a nucleolar localization signal and create a novel nuclear export signal, leading to cytoplasmic displacement of the protein (NPM1c). NPM1c mutations prime hematopoietic progenitors to leukemic transformation, but their precise molecular consequences remain elusive. Here, we first evaluate the effects of isolated NPM1c mutations on the global proteome of preleukemic hematopoietic stem and progenitor cells (HSPCs) using conditional knockin Npm1cA/+ mice. We discover that many proteins involved in ribosome biogenesis are significantly depleted in these murine HSPCs, but also importantly in human NPM1-mutant AMLs. In line with this, we found that preleukemic Npm1cA/+ HSPCs display higher sensitivity to RNA polymerase I inhibitors, including actinomycin D (ActD), compared with Npm1+/+ cells. Combination treatment with ActD and venetoclax inhibited the growth and colony-forming ability of preleukemic and leukemic NPM1c+ cells, whereas low-dose ActD treatment was able to resensitize resistant NPM1c+ cells to venetoclax. Furthermore, using data from CRISPR dropout screens, we identified and validated TSR3, a 40S ribosomal maturation factor whose knockout preferentially inhibited the proliferation of NPM1c+ AML cells by activating a p53-dependent apoptotic response. Similarly, to low-dose ActD treatment, TSR3 depletion could partially restore sensitivity to venetoclax in therapy-resistant NPM1c+ AML models. Our findings propose that targeted disruption of ribosome biogenesis should be explored as a therapeutic strategy against NPM1-mutant AML.

Immunological memory in adaptive and innate immune cells is well characterized, enabling enhanced responses upon secondary challenges. However, it has only been recently appreciated that the nonimmune target cells of inflammation, particularly organ-specific stem cells (SCs), also exhibit memory of previous inflammatory exposures. Previous inflammation experience imprints on the SCs and influences their regenerative potential and responses to subsequent inflammatory insults. This phenomenon has been observed in hematopoietic, intestinal, and skin epithelial SCs, with profound implications for tissue homeostasis, disease progression, and therapeutic strategies. Herein, we expand and develop the notion of inflammatory memory of SCs and explore recent insights in the field. We discuss the emerging understanding of the molecular underpinnings and their potential clinical and biological implications. Inflammatory memory is driven by spatiotemporal changes in gene loci and transcription regulated by DNA and histones' epigenetic modifications, metabolic reprogramming, and chromatin accessibility changes. Understanding these mechanisms is critical for improving the outcomes of hematologic diseases, hematopoietic SC transplantation, and cellular immunotherapies.

Immunodeficiency in telomere biology disorders (TBDs) has been described in pediatric patients with severe phenotypes, but is less characterized within the broader TBD spectrum. We collected complete blood counts, lymphocyte subsets, and infection history from 88 consecutive patients with TBD with a median age of 38 years (range, 6-76). Most patients were >18 years old (80/88; 90%) and harbored either a TERT (45%) or TERC germ line mutation (32%). Thirty-two patients (36%) experienced significant infections (opportunistic, recurrent, and/or requiring hospitalization); 47% had lymphopenia, and 3% severe neutropenia. Absolute lymphocyte counts (ALCs) of <0.96 and <1.1 × 103/μL, but not severe neutropenia, were associated with increased infection risk and lower overall survival, respectively. Decreased CD3+ T cells, both CD4+ and CD8+, were associated with bone marrow failure, increased infection risk, and reduced survival. Low CD3+ and CD4+ T cells were associated with solid cancers. Telomere length was shortened across the cohort without correlation with ALC or lymphocyte subsets. In a predominantly adult cohort of TBDs, immunodeficiency was marked by T-cell lymphopenia, possibly a consequence of accelerated aging in the hematopoietic compartment. An ALC cutoff of <1.1 × 103/μL may be a useful biomarker to identify patients with an increased risk of infection, a major cause of death in patients with TBD.

Children with Down syndrome (DS) have a high risk of GATA1-associated myeloid leukemia (ML-DS) before age 4 years. Somatic N-terminal GATA1 mutations (GATA1s) are necessary, but not sufficient, for ML-DS, but their significance at birth for individual babies and whether mutations occur after birth is unclear. To address these questions, we performed a prospective study of newborns with DS using next-generation sequencing-based GATA1 mutation analysis, with hematologic and clinical evaluation and follow-up for the window of ML-DS risk. Of 450 neonates with DS, 113 (25%) had GATA1s mutations, among whom 20/113 (17.7%) had multiple mutations and 59 (52%) were clinically silent. Variant allele frequency (VAF) varied from 0.3% to 89%. VAF positively correlated (P < .0001) with the percent blasts, leukocytes, dyserythropoiesis and dysmegakaryopoiesis scores, and clinical disease severity, and negatively with hemoglobin, although only 4/113 were anemic. GATA1s mutations were detected from 28 weeks gestation; the highest frequency (45%) was at 34 to 35 weeks, whereas mutation frequency in early fetal samples (<20 weeks) was <4% (2/57). GATA1s clones (VAF, percent blasts) fell rapidly postnatally, becoming undetectable by 6 months, except in neonates who developed ML-DS. Of 110 surviving neonates, 7 (6.4%) developed ML-DS at a median age of 17.5 months. GATA1s clone size at birth was the only predictor of ML-DS. No neonates lacking GATA1s mutations acquired mutations after birth or developed ML-DS. Taken together, the fetal environment is essential for GATA1s mutation selection and expansion of GATA1s clones. Rates of leukemic transformation of GATA1s clones detected at birth are low, but clones that persist >6 months transformed.

Mutations in TP53 are mutually exclusive with other known drivers of myeloid transformation and define a distinct molecular subtype within de novo acute myeloid leukemia (AML) that is associated with a complex karyotype, resistance to chemotherapy, and poor prognosis. Although TP53 defects are rare in de novo AML, biallelic mutations are a defining molecular feature of erythroleukemia. The genetic alterations that cooperate with defective TP53 to transform erythroid progenitors remain unknown. We found that loss of BAP1 (BRCA1-associated protein 1) co-occurs in one-third of patients with TP53-mutated AML, is associated with an erythroid-primed gene expression signature, and confers an additional adverse effect on overall survival. BAP1 is a tumor suppressor involved in the DNA damage response as well as epigenetic regulation through histone H2AK119 deubiquitination. Although Bap1KO mice develop myelodysplasia with prominent dyserythropoiesis, combined deletion of Bap1 and Trp53 caused transplantable erythroleukemia, and occasionally mixed AML, mirroring the heterogeneity of human disease. Bulk and single-cell RNA sequencing coupled to chromatin immunoprecipitation sequencing in hematopoietic progenitors revealed that Bap1 loss triggers a proinflammatory response and cooperates with Trp53 deficiency to transform erythroid-primed multipotent progenitors. Mechanistically, genomic instability led to the development of erythroleukemia, whereas epigenetic deregulation caused myelomonocytic skewing suggesting a dichotomous and context dependent role for BAP1. We also demonstrate that BAP1-deficient erythroleukemia is dependent on BCL2L1 expression and is sensitive to B-cell lymphoma-extra large inhibitors in vivo.

In inflammation, circulating neutrophils indirectly damage the skeleton by inducing formation of bone-resorbing osteoclasts. However, neutrophil progenitors in marrow have no known physiological function. A bone-protective role for the neutrophil lineage was recently suggested when a profound defect in bone structure was observed in mice with neutropenia due to granulocyte colony-stimulating factor deletion coupled with STAT3 hyperactivation in bone cells. Here, we tested the existence of this protective effect by manipulating neutrophil progenitors in bone marrow using anti-Ly6G (αLy6G) treatment. Two protocols revealed an inverse relationship between marrow neutrophil progenitors and osteoclasts. Two weeks of αLy6G treatment increased marrow immature neutrophils by 25%, and halved osteoclast markers in cortical bone. In contrast, 6 weeks of αLy6G, combined with anti-rat immunoglobulin G2a to maintain antigenicity, reduced marrow preneutrophils by 50%. This latter treatment doubled trabecular osteoclast surface, halved trabecular bone mass, and significantly reduced high-density bone mass, both in control mice and in mice with bone-specific STAT3 hyperactivation. In culture, isolated preneutrophils dose-dependently inhibited osteoclastogenesis, independent of direct contact. We conclude that neutrophil progenitors directly inhibit osteoclast formation by releasing soluble factors. This identifies a novel action of hematopoietic cells in marrow to protect bone structure.

Platelet shape and volume changes are early mechanical events contributing to platelet activation and thrombosis. Here, we identify single-nucleotide polymorphisms in leucine-rich repeat-containing 8 (LRRC8) protein subunits that form the volume-regulated anion channel (VRAC), which are independently associated with altered mean platelet volume. LRRC8A is required for functional VRAC in megakaryocytes (MKs) and regulates platelet volume; adhesion; and agonist-stimulated activation, aggregation, adenosine triphosphate (ATP) secretion, and calcium mobilization. MK-specific LRRC8A conditional knockout mice have reduced laser injury-induced cremaster arteriolar thrombus formation and prolonged FeCl3 induced carotid arterial thrombosis without prolonged bleeding times. Mechanistically, platelet LRRC8A mediates swell-induced cytosolic ATP release to amplify agonist-stimulated calcium-phosphoinositide 3-kinase-protein kinase B signaling. Small-molecule LRRC8 channel inhibitors recapitulate defects observed in LRRC8A-null platelets in vitro and in vivo. These studies identify the mechanoresponsive LRRC8 channel complex as an ATP release channel in platelets, which positively regulates platelet function and thrombosis, providing a proof of concept for a novel antithrombotic drug target.

Disease-defining signatures in lymphomas, driven by intricate molecular mechanisms, have advanced molecular taxonomies, refined classification, and may guide clinical management; however, the role of these signatures in driving disease hallmarks, including subtype-specific organotropism, remains largely unexplored. Primary mediastinal large B-cell lymphoma (PMBCL) is an exemplary lymphoma characterized by disease manifestations in the thymic niche, unique genetic alterations, and immune escape. Here, we identified interferon regulatory factor 4 (IRF4)-C99R mutations uniquely occurring in PMBCL through mutational meta-analysis of large-scale data sets. By integrating multiomics approaches with genome editing in PMBCL cells, we revealed that IRF4-C99R contributes to a differentiation block phenotype. Specifically, we showed that IRF4-C99R reduces its binding to the interferon-stimulated response element (ISRE) motif within PRDM1, encoding a key transcriptional regulator of B-cell differentiation, resulting in decreased PRDM1 expression. Additionally, IRF4-C99R suppresses Traf2 and Nck-interacting kinase, a key interferon gamma (IFN-γ) pathway regulator, by impairing ISRE motif binding, thereby reducing IFN-γ signaling and increasing thymus and activation-regulated chemokine (TARC) expression, which drives TARC-mediated chemotaxis of T regulatory cells. We also revealed that IRF4-C99R upregulates ephrin type-B receptor 1 (EPHB1) through noncanonical activating protein 1-IRF composite motif binding and showed that overexpression of EPHB1 in an immunocompetent syngeneic lymphoma model influenced organotropism to favor thymic localization, without affecting overall tumor burden. IRF4-C99R mutation-induced phenotypes were validated in primary PMBCL tissues using single-nuclei RNA sequencing, confirming that the molecular mechanisms observed in vitro align with the pathophysiology of PMBCL in patients. Together, these findings demonstrate how a single genetic mutation orchestrates the coordinated regulation of hallmark traits including thymus-specific tropism in PMBCL.