Mapping genotypes to chromatin accessibility profiles in single cells.

In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1-3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT-ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from patients with myeloproliferative neoplasms with JAK2V617F-mutated haematopoiesis. Differential accessibility analysis between wild-type and JAK2V617F-mutant progenitors revealed both cell-intrinsic and cell-state-specific shifts within mutant haematopoietic precursors, including cell-intrinsic pro-inflammatory signatures in haematopoietic stem cells, and a distinct profibrotic inflammatory chromatin landscape in megakaryocytic progenitors. Integration of mitochondrial genome profiling and cell-surface protein expression measurement allowed expansion of genotyping onto DOGMA-seq through imputation, enabling single-cell capture of genotypes, chromatin accessibility, RNA expression and cell-surface protein expression. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner, influencing inflammation states and differentiation trajectories. We envision that GoT-ChA will empower broad future investigations of the critical link between somatic mutations and epigenetic alterations across clonal populations in malignant and non-malignant contexts.

CXCL8/CXCR2 signaling mediates bone marrow fibrosis and is a therapeutic target in myelofibrosis.

Proinflammatory signaling is a hallmark feature of human cancer, including in myeloproliferative neoplasms (MPNs), most notably myelofibrosis (MF). Dysregulated inflammatory signaling contributes to fibrotic progression in MF; however, the individual cytokine mediators elicited by malignant MPN cells to promote collagen-producing fibrosis and disease evolution are yet to be fully elucidated. Previously, we identified a critical role for combined constitutive JAK/STAT and aberrant NF-κB proinflammatory signaling in MF development. Using single-cell transcriptional and cytokine-secretion studies of primary cells from patients with MF and the human MPLW515L (hMPLW515L) murine model of MF, we extend our previous work and delineate the role of CXCL8/CXCR2 signaling in MF pathogenesis and bone marrow fibrosis progression. Hematopoietic stem/progenitor cells from patients with MF are enriched for a CXCL8/CXCR2 gene signature and display enhanced proliferation and fitness in response to an exogenous CXCL8 ligand in vitro. Genetic deletion of Cxcr2 in the hMPLW515L-adoptive transfer model abrogates fibrosis and extends overall survival, and pharmacologic inhibition of the CXCR1/2 pathway improves hematologic parameters, attenuates bone marrow fibrosis, and synergizes with JAK inhibitor therapy. Our mechanistic insights provide a rationale for therapeutic targeting of the CXCL8/CXCR2 pathway among patients with MF.

NCCN Guidelines® Insights: Systemic Mastocytosis, Version 3.2024.

Mastocytosis is a heterogeneous group of disorders comprising cutaneous mastocytosis, systemic mastocytosis, and mast cell sarcoma. It is associated with a variety of symptoms related to the release of mast cell mediators and mast cell tissue infiltration. Referral to specialized centers with expertise in the management of mastocytosis and multidisciplinary collaboration with subspecialists (eg, allergists for the management of anaphylaxis and drug hypersensitivities, anesthesiologists for invasive procedures or surgery, high-risk obstetrician for pregnancy) is recommended. The NCCN Guidelines for Systemic Mastocytosis provide evidence- and consensus-based recommendations for the diagnosis and comprehensive care of patients with systemic mastocytosis. The multidisciplinary panel of experts convenes at least once a year to review requested changes to the guidelines from both internal and external entities as well as to discuss data on existing and new therapies. These NCCN Guidelines Insights focus on some of the recent updates to the guidelines.

Genomic profiling identifies somatic mutations predicting thromboembolic risk in patients with solid tumors.

Venous thromboembolism (VTE) associated with cancer (CAT) is a well-described complication of cancer and a leading cause of death in patients with cancer. The purpose of this study was to assess potential associations of molecular signatures with CAT, including tumor-specific mutations and the presence of clonal hematopoiesis. We analyzed deep-coverage targeted DNA-sequencing data of >14 000 solid tumor samples using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets platform to identify somatic alterations associated with VTE. End point was defined as the first instance of cancer-associated pulmonary embolism and/or proximal/distal lower extremity deep vein thrombosis. Cause-specific Cox proportional hazards regression was used, adjusting for pertinent clinical covariates. Of 11 695 evaluable individuals, 72% had metastatic disease at time of analysis. Tumor-specific mutations in KRAS (hazard ratio [HR], 1.34; 95% confidence interval (CI), 1.09-1.64; adjusted P = .08), STK11 (HR, 2.12; 95% CI, 1.55-2.89; adjusted P < .001), KEAP1 (HR, 1.84; 95% CI, 1.21-2.79; adjusted P = .07), CTNNB1 (HR, 1.73; 95% CI, 1.15-2.60; adjusted P = .09), CDKN2B (HR, 1.45; 95% CI, 1.13-1.85; adjusted P = .07), and MET (HR, 1.83; 95% CI, 1.15-2.92; adjusted P = .09) were associated with a significantly increased risk of CAT independent of tumor type. Mutations in SETD2 were associated with a decreased risk of CAT (HR, 0.35; 95% CI, 0.16-0.79; adjusted P = .09). The presence of clonal hematopoiesis was not associated with an increased VTE rate. This is the first large-scale analysis to elucidate tumor-specific genomic events associated with CAT. Somatic tumor mutations of STK11, KRAS, CTNNB1, KEAP1, CDKN2B, and MET were associated with an increased risk of VTE in patients with solid tumors. Further analysis is needed to validate these findings and identify additional molecular signatures unique to individual tumor types.

Molecular predictors of immunophenotypic measurable residual disease clearance in acute myeloid leukemia.

Measurable residual disease (MRD) is a powerful prognostic factor in acute myeloid leukemia (AML). However, pre-treatment molecular predictors of immunophenotypic MRD clearance remain unclear. We analyzed a dataset of 211 patients with pre-treatment next-generation sequencing who received induction chemotherapy and had MRD assessed by serial immunophenotypic monitoring after induction, subsequent therapy, and allogeneic stem cell transplant (allo-SCT). Induction chemotherapy led to MRD- remission, MRD+ remission, and persistent disease in 35%, 27%, and 38% of patients, respectively. With subsequent therapy, 34% of patients with MRD+ and 26% of patients with persistent disease converted to MRD-. Mutations in CEBPA, NRAS, KRAS, and NPM1 predicted high rates of MRD- remission, while mutations in TP53, SF3B1, ASXL1, and RUNX1 and karyotypic abnormalities including inv (3), monosomy 5 or 7 predicted low rates of MRD- remission. Patients with fewer individual clones were more likely to achieve MRD- remission. Among 132 patients who underwent allo-SCT, outcomes were favorable whether patients achieved early MRD- after induction or later MRD- after subsequent therapy prior to allo-SCT. As MRD conversion with chemotherapy prior to allo-SCT is rarely achieved in patients with specific baseline mutational patterns and high clone numbers, upfront inclusion of these patients into clinical trials should be considered.

Synthesis and Characterization of Ether Adducts of Thorium Tetrahydroborate Th(BH4)4 and Chemical Vapor Deposition of Thorium Boride Thin Films.

Treating ThCl4 with LiBH4 in various ethereal solvents affords the adducts Th(BH4)4(Et2O)2, Th(BH4)4(thf)2, and Th(BH4)4(dme) (thf = tetrahydrofuran and dme = 1,2-dimethoxyethane). The structures of these three compounds have been established by single-crystal X-ray diffraction: if the tetrahydroborate groups are considered as occupying one coordination site, the Et2O and thf complexes adopt trans-octahedral coordination geometries, whereas the dme complex exhibits a cis-octahedral structure. All four BH4- ligands in each compound are tridentate, rendering each thorium center 14-coordinate. The Th···B distances range from 2.64 to 2.67 Å, and the Th-O bond lengths are 2.47-2.52 Å. We propose that crystals of Th(BH4)4(thf)2 are isomorphous with those of U(BH4)4(thf)2, but owing to pseudosymmetry the latter was reported in a unit cell that was too small by a factor of 2. IR spectra and 1H and 11B NMR data are reported as well. All three adducts are volatile, subliming readily at 60 °C and 10-4 Torr, making them potentially useful as precursors for the chemical vapor deposition (CVD) of thin films of thorium boride. Passage of Th(BH4)4(Et2O)2 over glass, Si(100), and aluminum substrates heated to 350 °C yields amorphous films of approximate stoichiometry ThB2; films deposited from Th(BH4)4(thf)2 have stoichiometries closer to ThB2.5 and contain some oxygen. Auger, XPS, XRD, and SEM studies of these films are reported.

Leukemia secondary to myeloproliferative neoplasms.

Secondary acute myeloid leukemias (AMLs) evolving from an antecedent myeloproliferative neoplasm (MPN) are characterized by a unique set of cytogenetic and molecular features distinct from de novo AML. Given the high frequency of poor-risk cytogenetic and molecular features, malignant clones are frequently insensitive to traditional AML chemotherapeutic agents. Allogeneic stem cell transplant, the only treatment modality shown to have any beneficial long-term outcome, is often not possible given the advanced age of patients at time of diagnosis and frequent presence of competing comorbidities. Even in this setting, relapse rates remain high. As a result, outcomes are generally poor and there remains a significant unmet need for novel therapeutic strategies. Although advances in cancer genomics have dramatically enhanced our understanding of the molecular events governing clonal evolution in MPNs, the cell-intrinsic and -extrinsic mechanisms driving leukemic transformation at this level remain poorly understood. Here, we review known risk factors for the development of leukemic transformation in MPNs, recent progress made in our understanding of the molecular features associated with leukemic transformation, current treatment strategies, and emerging therapeutic options for this high-risk myeloid malignancy.

Myeloproliferative Neoplasms, Version 3.2022, NCCN Clinical Practice Guidelines in Oncology.

The classic Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) consist of myelofibrosis, polycythemia vera, and essential thrombocythemia and are a heterogeneous group of clonal blood disorders characterized by an overproduction of blood cells. The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for MPN were developed as a result of meetings convened by a multidisciplinary panel with expertise in MPN, with the goal of providing recommendations for the management of MPN in adults. The Guidelines include recommendations for the diagnostic workup, risk stratification, treatment, and supportive care strategies for the management of myelofibrosis, polycythemia vera, and essential thrombocythemia. Assessment of symptoms at baseline and monitoring of symptom status during the course of treatment is recommended for all patients. This article focuses on the recommendations as outlined in the NCCN Guidelines for the diagnosis of MPN and the risk stratification, management, and supportive care relevant to MF.

Sodium Aminodiboranates Na(H3BNR2BH3): Structural and Spectroscopic Studies of Steric and Electronic Substituent Effects.

We describe the syntheses of a series of sodium aminodiboranate salts, Na(H3B-NR2-BH3), with different substituents on nitrogen, including sodium salts of the unsubstituted aminodiboranate, H3B-NH2-BH3-, and of the N-substituted anions H3B-NRR'-BH3-, where NRR' = NHMe, NHEt, NH(SiMe3), NEt2, N(i-Pr)2, N(SiMe3)2, NMe(i-Pr), NMe(t-Bu), NMe(SiMe3), and the pyrrolidide and piperidide derivatives NC4H8, NC5H10, and NC5H8-cis-2,6-Me2. The compounds have been characterized by 1H and 11B NMR spectroscopy and IR spectroscopy; crystallographic studies have been carried out for the unsolvated N,N-dimethylaminodiboranate salt Na(H3B-NMe2-BH3) and several sodium aminodiboranate salts in which the sodium ions are solvated with ethers (dioxane, diglyme, tetrahydrofuran, and 12-crown-4) or amines (N,N,N',N'-tetramethylethylenediamine). One of the structures contains a rare example of an ether ligand in which one oxygen atom bridges between two metal ions. General structural and spectroscopic trends as a function of the substituents on nitrogen are discussed.

X-ray Crystal Structure of Thorium Tetrahydroborate, Th(BH4)4, and Computational Studies of An(BH4)4 (An = Th, U).

The crystal structure of Th(BH4)4 is described. Two of the four BH4- ions are terminal and tridentate (κ3), whereas the other two bridge between neighboring ThIV centers in a κ2,κ2 (i.e., bis-bidentate) fashion. Thus, each thorium center is bound to six BH4- groups by 14 Th-H bonds. The six boron atoms describe a distorted octahedron in which the κ3-BH4- ions are mutually cis; the 14 ligating hydrogen atoms define a highly distorted bicapped hexagonal antiprism. The thorium centers are linked into a polymer consisting of interconnected helical chains wound about 4-fold screw axes. The structures of An(BH4)4 (An = Th, U) were also investigated by DFT. The geometries of [An(BH4)6]2-, [An3(BH4)16]4-, and [An5(BH4)26]6- fragments of the polymeric structures were optimized at the B3LYP and/or PBE levels. Most calculated geometries are 14-coordinate and agree with the experimental structures, but isolated [Th(BH4)6]2- units are predicted to feature 16-coordinate ThIV centers.

Myeloid/Lymphoid Neoplasms with Eosinophilia and TK Fusion Genes, Version 3.2021, NCCN Clinical Practice Guidelines in Oncology.

Eosinophilic disorders and related syndromes represent a heterogeneous group of neoplastic and nonneoplastic conditions, characterized by more eosinophils in the peripheral blood, and may involve eosinophil-induced organ damage. In the WHO classification of myeloid and lymphoid neoplasms, eosinophilic disorders characterized by dysregulated tyrosine kinase (TK) fusion genes are recognized as a new category termed, myeloid/lymphoid neoplasms with eosinophilia and rearrangement of PDGFRA, PDGFRB or FGFR1 or with PCM1-JAK2. In addition to these aforementioned TK fusion genes, rearrangements involving FLT3 and ABL1 genes have also been described. These new NCCN Guidelines include recommendations for the diagnosis, staging, and treatment of any one of the myeloid/lymphoid neoplasms with eosinophilia (MLN-Eo) and a TK fusion gene included in the 2017 WHO Classification, as well as MLN-Eo and a FLT3 or ABL1 rearrangement.

Synthesis and Characterization of Strontium N,N-Dimethylaminodiboranates as Possible Chemical Vapor Deposition Precursors.

The reaction of SrBr2 with 2 equiv of sodium N,N-dimethylaminodiboranate (DMADB; Na(H3BNMe2BH3)) in Et2O at 0 °C followed by crystallization and drying under vacuum gives the unsolvated strontium compound Sr(H3BNMe2BH3)2 (1). Before the vacuum-drying step, the colorless crystals obtained by crystallization consist of the diethyl ether adduct Sr(H3BNMe2BH3)2(Et2O)2 (2). If the reaction of SrBr2 with 2 equiv of Na(H3BNMe2BH3) is carried out in the more strongly coordinating solvent thf, the solvate Sr(H3BNMe2BH3)2(thf)3 (3) is obtained. Treating the thf adduct 3 with 1,2-dimethoxyethane (dme), bis(2-methoxyethyl) ether (diglyme), or N,N,N',N'-tetramethylethylenediamine (tmeda) in thf affords the new compounds Sr(H3BNMe2BH3)2(dme)2 (4), Sr(H3BNMe2BH3)2(diglyme) (5), and Sr(H3BNMe2BH3)2(tmeda) (6), respectively, in greater than 60% yields. Treatment of 3 with 2 equiv of the crown ether 12-crown-4 affords the charge-separated salt [Sr(H3BNMe2BH3)(12-crown-4)2][H3BNMe2BH3] (7). Crystal structures of all the Lewis base adducts are described. Compounds 2-6 all possess chelating κ2-BH3NMe2BH3-κ2 groups, in which two hydrogen atoms on each boron center are bound to strontium. Compound 6 is dinuclear because each metal atom is also coordinated to one hydrogen atom on a BH3NMe2BH3- ligand that chelates to the neighboring metal center. Compound 7 possesses an unusual κ1-BH3NMe2BH3- group owing to the near-complete encapsulation of the Sr atom by two 12-crown-4 molecules; the other BH3NMe2BH3- anion is a charge-separated counterion. When they are heated, the diglyme and tmeda compounds 5 and 6 melt without decomposition and can be sublimed readily under reduced pressure (1 Torr) at 120 °C. The diglyme and tmeda adducts are some of the most volatile strontium compounds known and are promising candidates as CVD precursors for the growth of strontium-containing thin films.

Loss of plasmacytoid dendritic cell differentiation is highly predictive for post-induction measurable residual disease and inferior outcomes in acute myeloid leukemia.

Measurable residual disease is associated with inferior outcomes in patients with acute myeloid leukemia (AML). Measurable residual disease monitoring enhances risk stratification and may guide therapeutic intervention. The European LeukemiaNet working party recently came to a consensus recommendation incorporating leukemia associated immunophenotype-based different from normal approach by multi-color flow cytometry for measurable residual disease evaluation. However, the analytical approach is highly expertise-dependent and difficult to standardize. Here we demonstrate that loss of plasmacytoid dendritic cell differentiation after 7+3 induction in AML is highly specific for measurable residual disease positivity (specificity 97.4%) in a uniformly treated patient cohort. Moreover, loss of plasmacytoid dendritic cell differentiation as determined by a blast-to-plasmacytoid dendritic cell ratio >10 was strongly associated with inferior overall and relapse-free survival (RFS) [Hazard ratio 2.79, 95% confidence interval (95%CI): 0.98-7.97; P=0.077) and 3.83 (95%CI: 1.51-9.74; P=0.007), respectively), which is similar in magnitude to measurable residual disease positivity. Importantly, measurable residual disease positive patients who reconstituted plasmacytoid dendritic cell differentiation (blast/ plasmacytoid dendritic cell ratio <10) showed a higher rate of measurable residual disease clearance at later pre-transplant time points compared to patients with loss of plasmacytoid dendritic cell differentiation (blast/ plasmacytoid dendritic cell ratio <10) (6 of 12, 50% vs 2 of 18, 11%; P=0.03). Furthermore pre-transplant plasmacytoid dendritic cell recovery was associated with superior outcome in measurable residual disease positive patients. Our study provides a novel, simple, broadly applicable, and quantitative multi-color flow cytometry approach to risk stratification in AML.

Hyaluronidase modulates bleomycin-induced lung injury detected noninvasively in small rodents by radial proton MRI.

PURPOSE: To assess whether hyaluronic acid, a building block of proteoglycans and extracellular matrix with hydrophilic characteristics, might contribute to magnetic resonance imaging (MRI)-detected proton signals elicited by bleomycin in the lung. To this end, hyaluronidase, which degrades hyaluronic acid, was administered to bleomycin-challenged animals. MATERIALS AND METHODS: Fibrosis was induced by oropharyngeal aspiration (OA) of bleomycin. Mice received bleomycin once daily (0.1 mg/kg) on 6 consecutive days, while rats were given a single dose (2 or 4 mg/kg). Hyaluronidase, budesonide, and the respective vehicles were also administered via OA. Animals were examined using a radial ultrashort echo time sequence. Histology of picrosirius reflecting collagen and tissue gene analysis were performed postmortem. RESULTS: In mice, hyaluronidase induced an increase of high intensity signals by 34 ± 12 µL (means ± SD, P = 0.007), consistent with the ability of the degradation products of hyaluronic acid to provoke acute inflammation. Budesonide was able to resolve hyaluronidase-induced signals or to prevent their formation. Combined administration of budesonide and hyaluronidase to bleomycin-treated rats resulted in an overall decrease (-17.1 ± 7%, P = 0.02) of the MRI-detected bleomycin-induced signals. Moreover, the relative gene expression of hyaluronidase was reduced (-61.8 ± 10.2%, P < 0.001) in fibrotic lungs. CONCLUSION: The present data indicate that hyaluronic acid contributes to the bleomycin-induced responses detected by MRI in the lung.

Adriamycin-induced nephropathy in rats: functional and cellular effects characterized by MRI.

PURPOSE: To assess with magnetic resonance imaging (MRI) adriamycin-induced nephropathy in living rats, an established model for proteinuric renal disease was used. MATERIALS AND METHODS: Functional information of contrast agent clearance was obtained with dynamic contrast-enhanced (DCE) imaging following intravenous Gd-DOTA administration. Perfusion data were obtained with a bolus tracking technique comprising intravenous injection of superparamagnetic iron oxide (SPIO) nanoparticles. Cellular information was derived from anatomical images acquired 24 hours after SPIO. Treatment with the transforming growth factor-ß123 (TGF-ß1,2,3 ) antibody, 1D11, started 1 week after adriamycin. Histology was performed at week 6 post-adriamycin. RESULTS: Tracer washout rates derived by DCE-MRI decreased by 65.5% with respect to baseline at week 6 post-adriamycin. The impaired kidney function agreed with glomerulopathy, nephropathy and fibrosis revealed histologically (picrosirius collagen staining in adriamycin-treated rats increased by 125.8% [P = 0.005] with respect to controls). Perfusion was reduced by 16.1%. Images acquired 24 hours after SPIO presented contrast changes that correlated inversely with the histologically determined iron content (R = -0.74, P = 2.6 × 10(-4) ). In adriamycin-challenged animals, iron was found in macrophages and in sclerotic tubuli, only in areas where macrophages were present. Treatment with 1D11 did not improve the adriamycin-induced renal injury. CONCLUSION: MRI provides longitudinal functional and cellular (macrophage infiltration) information that correlates with nephropathy development in adriamycin-challenged rats.

Anagostic interactions under pressure: attractive or repulsive?

Square-planar d(8)-ML4 complexes might display subtle but noticeable local Lewis acidic sites in axial direction in the valence shell of the metal atom. These sites of local charge depletion provide the electronic prerequisites to establish weakly attractive 3c-2e M⋅⋅⋅H-C agostic interactions, in contrast to earlier assumptions. Furthermore, we show that the use of the sign of the (1)H NMR shifts as major criterion to classify M⋅⋅⋅H-C interactions as attractive (agostic) or repulsive (anagostic) can be dubious. We therefore suggest a new characterization method to probe the response of these M⋅⋅⋅H-C interactions under pressure by combined high pressure IR and diffraction studies.

Lung volume quantified by MRI reflects extracellular-matrix deposition and altered pulmonary function in bleomycin models of fibrosis: effects of SOM230.

Idiopathic pulmonary fibrosis is a progressive and lethal disease, characterized by loss of lung elasticity and alveolar surface area, secondary to alveolar epithelial cell injury, reactive inflammation, proliferation of fibroblasts, and deposition of extracellular matrix. The effects of oropharyngeal aspiration of bleomycin in Sprague-Dawley rats and C57BL/6 mice, as well as of intratracheal administration of ovalbumin to actively sensitized Brown Norway rats on total lung volume as assessed noninvasively by magnetic resonance imaging (MRI) were investigated here. Lung injury and volume were quantified by using nongated or respiratory-gated MRI acquisitions [ultrashort echo time (UTE) or gradient-echo techniques]. Lung function of bleomycin-challenged rats was examined additionally using a flexiVent system. Postmortem analyses included histology of collagen and hydroxyproline assays. Bleomycin induced an increase of MRI-assessed total lung volume, lung dry and wet weights, and hydroxyproline content as well as collagen amount. In bleomycin-treated rats, gated MRI showed an increased volume of the lung in the inspiratory and expiratory phases of the respiratory cycle and a temporary decrease of tidal volume. Decreased dynamic lung compliance was found in bleomycin-challenged rats. Bleomycin-induced increase of MRI-detected lung volume was consistent with tissue deposition during fibrotic processes resulting in decreased lung elasticity, whereas influences by edema or emphysema could be excluded. In ovalbumin-challenged rats, total lung volume quantified by MRI remained unchanged. The somatostatin analog, SOM230, was shown to have therapeutic effects on established bleomycin-induced fibrosis in rats. This work suggests MRI-detected total lung volume as readout for tissue-deposition in small rodent bleomycin models of pulmonary fibrosis.