Novel cell adhesion/migration pathways are predictive markers of HDAC inhibitor resistance in cutaneous T cell lymphoma

BACKGROUND: Treatment for Cutaneous T Cell Lymphoma (CTCL) is generally not curative. Therefore, selecting therapy that is effective and tolerable is critical to clinical decision-making. Histone deacetylase inhibitors (HDACi), epigenetic modifier drugs, are commonly used but effective in only ~30% of patients. There are no predictive markers of HDACi response and the CTCL histone acetylation landscape remains unmapped. We sought to identify pre-treatment molecular markers of resistance in CTCL that progressed on HDACi therapy. METHODS: Purified T cells from 39 pre/post-treatment peripheral blood samples and skin biopsies from 20 patients were subjected to RNA-seq and ChIP-seq for histone acetylation marks (H3K14/9 ac, H3K27ac). We correlated significant differences in histone acetylation with gene expression in HDACi-resistant/sensitive CTCL. We extended these findings in additional CTCL patient cohorts (RNA-seq, microarray) and using ELISA in matched CTCL patient plasma. FINDINGS: Resistant CTCL exhibited high levels of histone acetylation, which correlated with increased expression of 338 genes (FDR \u3c 0·05), including some novel to CTCL: BIRC5 (anti-apoptotic); RRM2 (cell cycle); TXNDC5, GSTM1 (redox); and CXCR4, LAIR2 (cell adhesion/migration). Several of these, including LAIR2, were elevated pre-treatment in HDACi-resistant CTCL. In CTCL patient plasma (n = 6), LAIR2 protein was also elevated (p \u3c 0·01) compared to controls. INTERPRETATION: This study is the first to connect genome-wide differences in chromatin acetylation and gene expression to HDACi-resistance in primary CTCL. Our results identify novel markers with high pre-treatment expression, such as LAIR2, as potential prognostic and/or predictors of HDACi-resistance in CTCL. FUNDING: NIH:CA156690, CA188286; NCATS: WU-ICTS UL1 TR000448; Siteman Cancer Center: CA091842

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM

Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample. DXM does not require prior knowledge of the number of subpopulations or types of cells to expect. We benchmark DXM\u27s performance and demonstrate improvement over existing methods. We further experimentally validate DXM predicted allelic subpopulation-methylation profiles in four Diffuse Large B-Cell Lymphomas (DLBCLs). Lastly, as proof-of-concept, we apply DXM to a cohort of 31 DLBCLs and relate allelic subpopulation methylation profiles to relapse. We thus demonstrate that DXM can robustly find allelic subpopulation methylation profiles that may contribute to disease progression using bisulfite sequencing data of any heterogeneous sample

Nuclear-localized human respiratory syncytial virus NS1 protein modulates host gene transcription

Human respiratory syncytial virus (RSV) is a common cause of lower respiratory tract infections in the pediatric, elderly, and immunocompromised individuals. RSV non-structural protein NS1 is a known cytosolic immune antagonist, but how NS1 modulates host responses remains poorly defined. Here, we observe NS1 partitioning into the nucleus of RSV-infected cells, including the human airway epithelium. Nuclear NS1 coimmunoprecipitates with Mediator complex and is chromatin associated. Chromatin-immunoprecipitation demonstrates enrichment of NS1 that overlaps Mediator and transcription factor binding within the promoters and enhancers of differentially expressed genes during RSV infection. Mutation of the NS1 C-terminal helix reduces NS1 impact on host gene expression. These data suggest that nuclear NS1 alters host responses to RSV infection by binding at regulatory elements of immune response genes and modulating host gene transcription. Our study identifies another layer of regulation by virally encoded proteins that shapes host response and impacts immunity to RSV

Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers

BACKGROUND: The most common B-cell cancers, chronic lymphocytic leukemia/lymphoma (CLL), follicular and diffuse large B-cell (FL, DLBCL) lymphomas, have distinct clinical courses, yet overlapping cell-of-origin . Dynamic changes to the epigenome are essential regulators of B-cell differentiation. Therefore, we reasoned that these distinct cancers may be driven by shared mechanisms of disruption in transcriptional circuitry. METHODS: We compared purified malignant B-cells from 52 patients with normal B-cell subsets (germinal center centrocytes and centroblasts, naïve and memory B-cells) from 36 donor tonsils using \u3e325 high-resolution molecular profiling assays for histone modifications, open chromatin (ChIP-, FAIRE-seq), transcriptome (RNA-seq), transcription factor (TF) binding, and genome copy number (microarrays). FINDINGS: From the resulting data, we identified gains in active chromatin in enhancers/super-enhancers that likely promote unchecked B-cell receptor signaling, including one we validated near the immunoglobulin superfamily receptors FCMR and PIGR. More striking and pervasive was the profound loss of key B-cell identity TFs, tumor suppressors and their super-enhancers, including EBF1, OCT2(POU2F2), and RUNX3. Using a novel approach to identify transcriptional feedback, we showed that these core transcriptional circuitries are self-regulating. Their selective gain and loss form a complex, iterative, and interactive process that likely curbs B-cell maturation and spurs proliferation. INTERPRETATION: Our study is the first to map the transcriptional circuitry of the most common blood cancers. We demonstrate that a critical subset of B-cell TFs and their cognate enhancers form self-regulatory transcriptional feedback loops whose disruption is a shared mechanism underlying these diverse subtypes of B-cell lymphoma. FUNDING: National Institute of Health, Siteman Cancer Center, Barnes-Jewish Hospital Foundation, Doris Duke Foundation

Investigating the Lower Mass Gap with Low Mass X-ray Binary Population Synthesis

Mass measurements from low-mass black hole X-ray binaries (LMXBs) and radio pulsars have been used to identify a gap between the most massive neutron stars (NSs) and the least massive black holes (BHs). BH mass measurements in LMXBs are typically only possible for transient systems: outburst periods enable detection via all-sky X-ray monitors, while quiescent periods enable radial-velocity measurements of the low-mass donor. We quantitatively study selection biases due to the requirement of transient behavior for BH mass measurements. Using rapid population synthesis simulations (COSMIC), detailed binary stellar-evolution models (MESA), and the disk instability model of transient behavior, we demonstrate that transient-LMXB selection effects introduce observational biases, and can suppress mass-gap BHs in the observed sample. However, we find a population of transient LMXBs with mass-gap BHs form through accretion-induced collapse of a NS during the LMXB phase, which is inconsistent with observations. These results are robust against variations of binary evolution prescriptions. The significance of this accretion-induced collapse population depends upon the maximum NS birth mass $M_\mathrm{ NS, birth-max}$. To reflect the observed dearth of low-mass BHs, COSMIC and MESA models favor $M_\mathrm{ NS, birth-max} \lesssim2M_{\odot}$. In the absence of further observational biases against LMXBs with mass-gap BHs, our results indicate the need for additional physics connected to the modeling of LMXB formation and evolution.Comment: 21 pages, accepted to Ap

Data needs and challenges for quantum dot devices automation

Gate-defined quantum dots are a promising candidate system for realizing scalable, coupled qubit systems and serving as a fundamental building block for quantum computers. However, present-day quantum dot devices suffer from imperfections that must be accounted for, which hinders the characterization, tuning, and operation process. Moreover, with an increasing number of quantum dot qubits, the relevant parameter space grows sufficiently to make heuristic control infeasible. Thus, it is imperative that reliable and scalable autonomous tuning approaches are developed. This meeting report outlines current challenges in automating quantum dot device tuning and operation with a particular focus on datasets, benchmarking, and standardization. We also present insights and ideas put forward by the quantum dot community on how to overcome them. We aim to provide guidance and inspiration to researchers invested in automation efforts

MagAO Imaging of Long-period Objects (MILO). II. A Puzzling White Dwarf around the Sun-like Star HD 11112

The version of record, Rodigas, T. J. et al, 'MagAO Imaging of long-period objects (MILO). II. A puzzling white dwarf around the sun-like star HD 11112', The Astrophysical Journal, 831:177, November 2016, is available online via doi: 10.3847/0004-637X/831/2/177 © 2016. The American Astronomical Society. All rights reserved.HD 11112 is an old, Sun-like star that has a long-term radial velocity (RV) trend indicative of a massive companion on a wide orbit. Here we present direct images of the source responsible for the trend using the Magellan Adaptive Optics system. We detect the object (HD 11112B) at a separation of 2\fasec 2 (100 AU) at multiple wavelengths spanning 0.6-4 \microns ~and show that it is most likely a gravitationally-bound cool white dwarf. Modeling its spectral energy distribution (SED) suggests that its mass is 0.9-1.1 \msun, which corresponds to very high-eccentricity, near edge-on orbits from Markov chain Monte Carlo analysis of the RV and imaging data together. The total age of the white dwarf is $>2\sigma$ discrepant with that of the primary star under most assumptions. The problem can be resolved if the white dwarf progenitor was initially a double white dwarf binary that then merged into the observed high-mass white dwarf. HD 11112B is a unique and intriguing benchmark object that can be used to calibrate atmospheric and evolutionary models of cool white dwarfs and should thus continue to be monitored by RV and direct imaging over the coming years.Peer reviewedFinal Published versio

Mosaic: A Satellite Constellation to Enable Groundbreaking Mars Climate System Science and Prepare for Human Exploration

The Martian climate system has been revealed to rival the complexity of Earth\u27s. Over the last 20 yr, a fragmented and incomplete picture has emerged of its structure and variability; we remain largely ignorant of many of the physical processes driving matter and energy flow between and within Mars\u27 diverse climate domains. Mars Orbiters for Surface, Atmosphere, and Ionosphere Connections (MOSAIC) is a constellation of ten platforms focused on understanding these climate connections, with orbits and instruments tailored to observe the Martian climate system from three complementary perspectives. First, low-circular near-polar Sun-synchronous orbits (a large mothership and three smallsats spaced in local time) enable vertical profiling of wind, aerosols, water, and temperature, as well as mapping of surface and subsurface ice. Second, elliptical orbits sampling all of Mars\u27 plasma regions enable multipoint measurements necessary to understand mass/energy transport and ion-driven escape, also enabling, with the polar orbiters, dense radio occultation coverage. Last, longitudinally spaced areostationary orbits enable synoptic views of the lower atmosphere necessary to understand global and mesoscale dynamics, global views of the hydrogen and oxygen exospheres, and upstream measurements of space weather conditions. MOSAIC will characterize climate system variability diurnally and seasonally, on meso-, regional, and global scales, targeting the shallow subsurface all the way out to the solar wind, making many first-of-their-kind measurements. Importantly, these measurements will also prepare for human exploration and habitation of Mars by providing water resource prospecting, operational forecasting of dust and radiation hazards, and ionospheric communication/positioning disruptions