483 research outputs found

    T-BET and EOMES sustain mature human NK cell identity and antitumor function

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    Since the T-box transcription factors (TFs) T-BET and EOMES are necessary for initiation of NK cell development, their ongoing requirement for mature NK cell homeostasis, function, and molecular programming remains unclear. To address this, T-BET and EOMES were deleted in unexpanded primary human NK cells using CRISPR/Cas9. Deleting these TFs compromised in vivo antitumor response of human NK cells. Mechanistically, T-BET and EOMES were required for normal NK cell proliferation and persistence in vivo. NK cells lacking T-BET and EOMES also exhibited defective responses to cytokine stimulation. Single-cell RNA-Seq revealed a specific T-box transcriptional program in human NK cells, which was rapidly lost following T-BET and EOMES deletion. Further, T-BET- and EOMES-deleted CD56bright NK cells acquired an innate lymphoid cell precursor-like (ILCP-like) profile with increased expression of the ILC-3-associated TFs RORC and AHR, revealing a role for T-box TFs in maintaining mature NK cell phenotypes and an unexpected role of suppressing alternative ILC lineages. Our study reveals the critical importance of sustained EOMES and T-BET expression to orchestrate mature NK cell function and identity

    Ultra-deep sequencing reveals the mutational landscape of classical Hodgkin lymphoma

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    UNLABELLED: The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified \u3e95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE: Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient

    Catalog of Radio Galaxies with z>0.3. I:Construction of the Sample

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    The procedure of the construction of a sample of distant (z>0.3z>0.3) radio galaxies using NED, SDSS, and CATS databases for further application in statistical tests is described. The sample is assumed to be cleaned from objects with quasar properties. Primary statistical analysis of the list is performed and the regression dependence of the spectral index on redshift is found.Comment: 9 pages, 6 figures, 2 table

    The SEC\u27s Misguided Climate Disclosure Rule Proposal

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    The following article adapts and consolidates two comment letters submitted last spring by a group of twenty-two professors of finance and law on the SEC’s proposed climate change disclosure rules. The professors reiterate their recommendation that the SEC withdraw its proposal as legally misguided, while outlining some of the issues that the proposal will face when challenged in court

    Observation of two new Ξb\Xi_b^- baryon resonances

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    Two structures are observed close to the kinematic threshold in the Ξb0π\Xi_b^0 \pi^- mass spectrum in a sample of proton-proton collision data, corresponding to an integrated luminosity of 3.0 fb1^{-1} recorded by the LHCb experiment. In the quark model, two baryonic resonances with quark content bdsbds are expected in this mass region: the spin-parity JP=12+J^P = \frac{1}{2}^+ and JP=32+J^P=\frac{3}{2}^+ states, denoted Ξb\Xi_b^{\prime -} and Ξb\Xi_b^{*-}. Interpreting the structures as these resonances, we measure the mass differences and the width of the heavier state to be m(Ξb)m(Ξb0)m(π)=3.653±0.018±0.006m(\Xi_b^{\prime -}) - m(\Xi_b^0) - m(\pi^{-}) = 3.653 \pm 0.018 \pm 0.006 MeV/c2/c^2, m(Ξb)m(Ξb0)m(π)=23.96±0.12±0.06m(\Xi_b^{*-}) - m(\Xi_b^0) - m(\pi^{-}) = 23.96 \pm 0.12 \pm 0.06 MeV/c2/c^2, Γ(Ξb)=1.65±0.31±0.10\Gamma(\Xi_b^{*-}) = 1.65 \pm 0.31 \pm 0.10 MeV, where the first and second uncertainties are statistical and systematic, respectively. The width of the lighter state is consistent with zero, and we place an upper limit of Γ(Ξb)<0.08\Gamma(\Xi_b^{\prime -}) < 0.08 MeV at 95% confidence level. Relative production rates of these states are also reported.Comment: 17 pages, 2 figure

    Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns

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    The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical X-ray diffraction patterns of DNA contain information about the flexibility, interactions and sequence-related variations encoded within the helical structure. To extract this information, we have developed a new diffraction theory that accounts for these effects. We show how double helix non-ideality and fluctuations broaden the diffraction peaks. Meridional intensity profiles of the peaks at the first three helical layer lines reveal information about structural adaptation and intermolecular interactions. The meridional width of the fifth layer line peaks is inversely proportional to the helical coherence length that characterizes sequence-related and thermal variations in the double helix structure. Analysis of measured fiber diffraction patterns based on this theory yields important parameters that control DNA structure, packing and function
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