Coronavirus disease 2019: a clinical review

In December 2019, an outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in Wuhan, China, and it subsequently spread in many countries around the world. Many efforts have been applied to control and prevent the spread of COVID-19, and many scientific studies have been conducted in a short period of time. Here we present an overview of the viral structure, pathogenesis, diagnosis, and clinical features of COVID-19 based on the current state of knowledge, and we compare its clinical characteristics with SARS and Middle East Respiratory Syndrome (MERS). Current researches on potentially effective treatment alternatives are discussed. We hope this review can help medical workers and researchers around the world contain the current COVID-19 pandemic.

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of information transferred from a potential regulator to its downstream target. We apply Scribe and other leading approaches for causal network reconstruction to several types of single-cell measurements and show that there is a dramatic drop in performance for "pseudotime"-ordered single-cell data compared with true time-series data. We demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods such as "RNA velocity" restore some degree of coupling through an analysis of chromaffin cell fate commitment. These analyses highlight a shortcoming in experimental and computational methods for analyzing gene regulation at single-cell resolution and suggest ways of overcoming it.

Current updates on the role of reactive oxygen species in bladder cancer pathogenesis and therapeutics

Bladder cancer (BCa) is the fourth most common urological malignancy in the world, it has become the costliest cancer to manage due to its high rate of recurrence and lack of effective treatment modalities. As a natural byproduct of cellular metabolism, reactive oxygen species (ROS) have an important role in cell signaling and homeostasis. Although up-regulation of ROS is known to induce tumorigenesis, growing evidence suggests a number of agents that can selectively kill cancer cells through ROS induction. In particular, accumulation of ROS results in oxidative stress-induced apoptosis in cancer cells. So, ROS is a double-edged sword. A modest level of ROS is required for cancer cells to survive, whereas excessive levels kill them. This review summarizes the up-to-date findings of oxidative stress-regulated signaling pathways and transcription factors involved in the etiology and progression of BCa and explores the possible therapeutic implications of ROS regulators as therapeutic agents for BCa.

Feasibility of three-dimensional constructive interference in steady state sequences for evaluating the anterolateral ligament

AIM

The purpose of the study was to determine the feasibility of three-dimensional (3D) constructive interference in steady state (CISS) sequences for evaluating the anterolateral ligament (ALL).

MATERIALS AND METHODS

Magnetic resonance imaging (MRI) of the right knee joint in 30 healthy volunteers was performed using a 3 T MRI machine. Axial T2-weighted imaging with fat saturation (T2WI-FS), coronal proton-density-weighted imaging with fat saturation (PDWI-FS), and 3D-CISS were included in the protocol. Multiplanar reconstruction (MPR) and rotating stretched curved planar reconstructions (CPRs) of the ALL at 30°, 60°, 90°, 120°, and 150° were generated from the 3D-CISS images. The visibility of the femoral part, meniscal part, tibial part, meniscal insertion, femoral footprint, and tibial footprint of the ALL on the imaging of all sequences was recorded.

RESULTS

Based on the CPR of 3D-CISS MRI, the presence of tibial and femoral footprints of the ALL was rated superior to MPR and PDWI-FS (96.67% and 96.67%, respectively; p<0.017). Rotating CPR of 3D-CISS MRI imaging was rated superior to PDWI-FS with respect to the tibial part, meniscal part, and meniscal insertion of the ALL (96.67%, 83.33%, and 83.33%, respectively; p<0.05). Rotating CPR of 3D-CISS MRI was rated superior to PDWI-FS with respect to the femoral part of the ALL, but the difference was not statistically significant (p=0.095). The angle between the ALL and lateral collateral ligament (LCL) on the oblique sagittal image was 18.34±1.88°.

CONCLUSIONS

The MRI 3D-CISS sequences significantly enhanced the ability to identify the ALL compared to the 2D MRI sequences.

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

Integrating single-cell trajectory analysis with pooled genetic screening could reveal the genetic architecture that guides cellular decisions in development and disease. We applied this paradigm to probe the genetic circuitry that controls epithelial-to-mesenchymal transition (EMT). We used single-cell RNA sequencing to profile epithelial cells undergoing a spontaneous spatially determined EMT in the presence or absence of transforming growth factor-β. Pseudospatial trajectory analysis identified continuous waves of gene regulation as opposed to discrete 'partial' stages of EMT. KRAS was connected to the exit from the epithelial state and the acquisition of a fully mesenchymal phenotype. A pooled single-cell CRISPR-Cas9 screen identified EMT-associated receptors and transcription factors, including regulators of KRAS, whose loss impeded progress along the EMT. Inhibiting the KRAS effector MEK and its upstream activators EGFR and MET demonstrates that interruption of key signaling events reveals regulatory 'checkpoints' in the EMT continuum that mimic discrete stages, and reconciles opposing views of the program that controls EMT.

Wavelength detection of model-sharing fiber Bragg grating sensor networks using long short-term memory neural network

In this paper, an effective wavelength detection approach based on long short-term memory (LSTM) network is proposed for fiber Bragg grating (FBG) sensor networks. The FBG sensor network utilizes a model-sharing mechanism, where the whole spectral wavelength is divided into several shareable regions and spectral overlap is allowed in each region. LSTM, a representative recurrent neural network in deep learning, is applied to learn the features directly from the spectra of FBGs and build the wavelength detection model. By feeding the spectra sequentially into the well-trained model, the Bragg wavelengths of FBGs can be quickly determined under overlap. The obtained LSTM model can be repeatedly used without re-training to improve the multiplexing capability. The results demonstrate that the LSTM-based method can realize high-accuracy and high-speed wavelength detection in the spectral overlapping situations. The proposed approach offers a flexible tool to enhance the sensing capacity of FBG sensor networks.

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest derived pigment cells of the adult stripe pattern, limiting melanophore population expansion, yet increasing yellow/orange xanthophore numbers. To learn how TH elicits seemingly opposite responses in cells having a common embryological origin, we analyzed individual transcriptomes from thousands of neural crest-derived cells, reconstructed developmental trajectories, identified pigment cell-lineage specific responses to TH, and assessed roles for TH receptors. We show that TH promotes maturation of both cell types but in distinct ways. In melanophores, TH drives terminal differentiation, limiting final cell numbers. In xanthophores, TH promotes accumulation of orange carotenoids, making the cells visible. TH receptors act primarily to repress these programs when TH is limiting. Our findings show how a single endocrine factor integrates very different cellular activities during the generation of adult form.

Search for Sterile Neutrinos in MINOS and MINOS+ Using a Two-Detector Fit

A search for mixing between active neutrinos and light sterile neutrinos has been performed by looking for muon neutrino disappearance in two detectors at baselines of 1.04 and 735 km, using a combined MINOS and MINOS+ exposure of 16.36×10^{20} protons on target. A simultaneous fit to the charged-current muon neutrino and neutral-current neutrino energy spectra in the two detectors yields no evidence for sterile neutrino mixing using a 3+1 model. The most stringent limit to date is set on the mixing parameter sin^{2}θ_{24} for most values of the sterile neutrino mass splitting Δm_{41}^{2}>10^{-4}  eV^{2}.

The single-cell transcriptional landscape of mammalian organogenesis

Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting 'mouse organogenesis cell atlas' (MOCA) provides a global view of developmental processes during this critical window. We use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes. We explore the dynamics of gene expression within cell types and trajectories over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle.

Revealing Color Forces with Transverse Polarized Electron Scattering

The Spin Asymmetries of the Nucleon Experiment measured two double spin asymmetries using a polarized proton target and polarized electron beam at two beam energies, 4.7 and 5.9 GeV. A large-acceptance open-configuration detector package identified scattered electrons at 40° and covered a wide range in Bjorken x (0.3<x<0.8). Proportional to an average color Lorentz force, the twist-3 matrix element, d[over ˜]_{2}^{p}, was extracted from the measured asymmetries at Q^{2} values ranging from 2.0 to 6.0  GeV^{2}. The data display the opposite sign compared to most quark models, including the lattice QCD result, and an unexpected scale dependence. Furthermore, when combined with the neutron data in the same Q^{2} range the results suggest a flavor independent average color Lorentz force.

Skeletal muscle mitoflashes, pH, and the role of uncoupling protein-3

Mitochondrial reactive oxygen species (ROS) are important cellular signaling molecules, but can cause oxidative damage if not kept within tolerable limits. An important proximal form of ROS in mitochondria is superoxide. Its production is thought to occur in regulated stochastic bursts, but current methods using mitochondrial targeted cpYFP to assess superoxide flashes are confounded by changes in pH. Accordingly, these flashes are generally referred to as 'mitoflashes'. Here we provide regulatory insights into mitoflashes and pH fluctuations in skeletal muscle, and the role of uncoupling protein-3 (UCP3). Using quantitative confocal microscopy of mitoflashes in intact muscle fibers, we show that the mitoflash magnitude significantly correlates with the degree of mitochondrial inner membrane depolarization and ablation of UCP3 did not affect this correlation. We assessed the effects of the absence of UCP3 on mitoflash activity in intact skeletal muscle fibers, and found no effects on mitoflash frequency, amplitude or duration, with a slight reduction in the average size of mitoflashes. We further investigated the regulation of pH flashes (pHlashes, presumably a component of mitoflash) by UCP3 using mitochondrial targeted SypHer (mt-SypHer) in skeletal muscle fibers. The frequency of pHlashes was significantly reduced in the absence of UCP3, without changes in other flash properties. ROS scavenger, tiron, did not alter pHlash frequency in either WT or UCP3KO mice. High resolution respirometry revealed that in the absence of UCP3 there is impaired proton leak and Complex I-driven respiration and maximal coupled respiration. Total cellular production of hydrogen peroxide (H₂O₂) as detected by Amplex-UltraRed was unaffected. Altogether, we demonstrate a correlation between mitochondrial membrane potential and mitoflash magnitude in skeletal muscle fibers that is independent of UCP3, and a role for UCP3 in the control of pHlash frequency and of proton leak- and Complex I coupled-respiration in skeletal muscle fibers. The differential regulation of mitoflashes and pHlashes by UCP3 and tiron also indicate that the two events, though may be related, are not identical events.

Accuracy of interferon-γ-induced protein 10 for diagnosing latent tuberculosis infection: a systematic review and meta-analysis

BACKGROUND

Effective diagnostic methods for detecting latent tuberculosis infection (LTBI) are important for its eradication. A number of studies have evaluated the use of interferon-γ-induced protein 10 (IP-10), which is elevated after tuberculosis infection, as a biomarker for LTBI, but conclusive results regarding its effectiveness have not been reported.

OBJECTIVES

Our objective was to assess the diagnostic value of IP-10 for LTBI.

DATA SOURCES

We searched the PubMed, Embase, the Cochrane Library and Web of Science databases to find eligible studies.

STUDY ELIGIBILITY CRITERIA

We included cohort, case-control and cross-sectional studies that evaluated IP-10 in LTBI participants in comparison with tuberculin skin tests (TST) and interferon-γ release assays (IGRA).

PARTICIPANTS

Individuals with LTBI and uninfected participants.

INTERVENTIONS

IP-10 (index test) compared with TST and IGRA (reference standard) for diagnosing LTBI.

METHODS

PubMed, Embase, the Cochrane Library, and Web of Science databases were searched up to June 2018. A hierarchical summary receiver operating characteristic (HSROC) model was used to evaluate the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and HSROC curve for the diagnostic efficiency of IP-10.

RESULTS

Twelve studies including 1023 participants and 1122 samples were included. The overall pooled sensitivity was 0.85 (95% CI 0.80-0.88), specificity was 0.89 (95% CI 0.84-0.92), PLR was 7.55 (95% CI 5.20-10.97), NLR was 0.17 (95% CI 0.13-0.22) and DOR was 44.23 (95% CI 28.86-67.79), indicating a high accuracy for diagnosing LTBI. Based on a meta-regression analysis, high-burden countries, study design, IP-10 method, reference standard and the IP-10 cut-off could not explain the heterogeneity (p >0.05).

CONCLUSIONS

Our results suggested that IP-10 is a promising biomarker for the diagnosis of LTBI.

[Safety and efficacy of percutaneous intervention for children with combined congenital heart abnormality solely guided by transthoracic echocardiography]

Objective: To investigate the safety and efficacy of percutaneous intervention of children with combined congenital heart abnormality solely guided by transthoracic echocardiography (TTE) . Methods: From September 2015 to June 2017, 21 children with combined congenital heart abnormality undergoing percutaneous interventional guided by TTE in Fuwai hospital were enrolled in our study, and the clinical data were retrospective analyzed. The atrial septal defect(ASD) closure, ventricular septal defect(VSD) closure, patent ductus arteriosus(PDA) closure or balloon pulmonary valvuloplasty were performed under the guidance of TTE. The procedural effect was evaluated by TTE after operation. The patients were followed up after discharged from the hospital. Results: The age was (37.3±11.6) months, and there were 9 male and 12 female patients. There were 4 cases with ASD and VSD, 6 cases with VSD and PDA, 6 cases with ASD and PDA, 2 cases with VSD and pulmonary stenosis, 3 cases with ASD and pulmonary stenosis. The operations were successfully performed in all patients. No one required extra X ray guidance or open heart surgery. The operation time was (44.6±7.5)min. All patients did not require blood transfusion, inotropic support, and analgesia. There were no complications such as peripheral vascular injury and pericardialeffusion after the operation. The length of hospital stay time was (3.5±0.6) days. All patients were recovered well. The follow-up was (17.6±5.2) months, and post-procedural conduction disturbances, residual shunts, occlude fall off, thrombosis, and new onset of valvular regurgitation were not observed in these patients. Conclusion: Percutaneous interventional of children with combined congenital heart abnormality solely guided by TTE is safe and effective, and the procedure can avoid the potential injuries of X ray and contrast agent.

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of "chromatin hubs"-they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression. Pseudotemporal analysis revealed that most DNA elements remain in chromatin hubs throughout differentiation. A subset of elements bound by MYOD1 in myoblasts exhibit early opening in a PBX1- and MEIS1-dependent manner. Our strategy can be applied to dissect the architecture, sequence determinants, and mechanisms of cis-regulation on a genome-wide scale.

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome

Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy and for revealing principles of gene regulation. However, most reprogramming systems are inefficient, converting only a fraction of cells to the desired state. Here, we analyze MYOD-mediated reprogramming of human fibroblasts to myotubes, a well-characterized model system for direct conversion by defined factors, at pseudotemporal resolution using single-cell RNA-seq. To expose barriers to efficient conversion, we introduce a novel analytic technique, trajectory alignment, which enables quantitative comparison of gene expression kinetics across two biological processes. Reprogrammed cells navigate a trajectory with branch points that correspond to two alternative decision points, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Analysis of these branch points revealed insulin and BMP signaling as crucial molecular determinants of reprogramming. Single-cell trajectory alignment enables rigorous quantitative comparisons between biological trajectories found in diverse processes in development, reprogramming, and other contexts.

Gestational dyslipidaemia and adverse birthweight outcomes: a systematic review and meta-analysis

BACKGROUND

Low and high birthweight is known to increase the risk of acute and longer-term adverse outcomes, such as stillbirth, infant mortality, obesity, type 2 diabetes and cardiovascular diseases. Gestational dyslipidaemia is associated with a numbers of adverse birth outcomes, but evidence regarding birthweight is still inconsistent to reliably inform clinical practice and treatment recommendations.

OBJECTIVE

The aim of this study was to explore the relationship between maternal gestational dyslipidaemia and neonatal health outcomes, namely, birthweight, metabolic factors and inflammatory parameters.

METHODS

We searched systematically Embase, MEDLINE, PubMed, CINAHL Plus and Cochrane Library up to 1 August 2016 (with an updated search in MEDLINE at the end of July 2017) for longitudinal studies that assessed the association of maternal lipid levels during pregnancy with neonatal birthweight, or metabolic and inflammatory parameters up to 3 years old.

RESULTS

Data from 46 publications including 31,402 pregnancies suggest that maternal high triglycerides and low high-density-lipoprotein cholesterol levels throughout pregnancy are associated with increased birthweight, higher risk of large for gestational age and macrosomia and lower risk of small-for-gestational age. The findings were consistent across the studied populations, but stronger associations were observed in women who were overweight or obese prior to pregnancy.

CONCLUSIONS

This meta-analysis suggested that the potential under-recognized adverse effects of intrauterine exposure to maternal dyslipidaemia may warrant further investigation into the relationship between maternal dyslipidaemia and birthweight in large prospective cohorts or in randomized trials.

PIG3 suppresses gastric cancer proliferation by regulating p53- mediated apoptosis

Gastric cancer (GC), the third leading cause of cancer mortality and the fifth most common cancer in the world, still is an important health problem worldwide. P53-inducible gene 3 (PIG3) was initially isolated in an investigation to identify the genes that were induced by p53 in human colorectal cancer cells. PIG3 can also regulate the stability of p53 through suppressing the process of the MDM2-mediated ubiquitination of p53. The aim of this study is to explore the expression level of PIG3 in human GC and further investigate the function and mechanism of PIG3 in human GC. Five cell lines and 30 matched GC tissue samples and adjacent tissue samples were used for this study, and MTT assay, colony formation assay, flow cytometry analysis and Western blot were carried out. Expression of PIG3 was found to be frequently reduced in GC. Restoration of the expression of PIG3 inhibited cell proliferation, induced cell apoptosis and further activated P53 signaling in BGC823 cells. In conclusion, we demonstrated that expression of PIG3 is frequently reduced in GC tissue, and PIG3 suppressed human GC growth through p53- mediated apoptosis. PIG3 may act as a potential diagnostic marker and a potential therapeutic target of GC.

[Safety and efficacy of omalizumab for the treatment of allergic rhinitis:Meta-analysis of randomized clinical trials]

Objective:To assess the efficacy and safety of omalizumab in patients with allergic rhinitis(AR) in a meta-analysis of clinical trial results, and provide evidence for the clinical treatment of AR.Method:Pubmed, Medline, Cochrane and Embase were searched through August 2014 using the terms 'allergic rhinitis, omalizumab, efficacy, safety, and randomized controlled trial(RCT)'without language restriction. Relevant reviews, publications, and abstracts of meetings were also retrieved. RevMan5.3 software was used for meta-analysis after data extraction. Result: Nine RCTs were included(n =1764).Of the 1764 participants,859 patients were treated by omalizumab and the other 905 received a placebo.The meta-analysis revealed that patients treated with omalizumab had significantly reduced total and individual symptoms scorescompared with the placebo group(P <0.05). And there was no significantly differences in adverse events between placebo and omalizumab(P <0.05).The WMD rate and 95%CI were as follows：total nasal symptom scores(0.04, - 0.10 to 0.19), rhinorrhea(-0.32, -0.44 to -0.21), nasal stuffiness(-0.33,-0.38 to -0.27), nasal itching (-0.08,-0.25 to 0.09), and sneezing(-0.24, -0.27 to -0.21), and non-nasal symptoms scores(0.30,0.04 to 0.55).Conclusion:Compared to the placebo,omalizumab can effectively and safely reduce symptoms scores of patients with AR.

[Prevention for glucocorticoid-induced osteonecrosis of femoral head: a long-term clinical follow-up trail]

Objective: To evaluated the outcome of prevention and treatment for glucocorticoid-induced osteonecrosis of femoral head with anticoagulant and vasodilator drugs. Methods: A prospective, randomized, double-blind study was performed. From August 2003 to August 2006, 58 patients with large amounts of hormone therapy in the Zhongshan Hospital Affiliated Dalian University were enrolled and randomly assigned to the control group (placebo) or preventive group (anticoagulant and vasodilator drugs). And we prospectively analyzed the clinical outcomes of 24 patients with glucocorticoid-induced osteonecrosis of femoral head early stage (treatment group)treated by anticoagulant and vasodilator drugsat the same time. Disease incidence rate and progression were evaluated by radiography and magnetic resonance imaging (MRI), Follow-up of patients with femoral head survival curve was drawn. The Harris Hip Score and the Short Form 36 health survey were used to rate hip function and quality of life, respectively. Results: Thus, a total of 80 patients were assessed in this study, 24 cases in control group[follow up from 7.5 to 13.0(10.7±1.6)years], 22 cases in preventive group and 24 cases in treatment group. There was significant difference in theincidence rate of Osteonecrosis of femoral head, survive rate of femoral head and HHS score between the control groupand preventive group(41.7% vs 13.6%, 66.7% vs 70.8% , P<0.01). Conclusion: Anticoagulant and vasodilator drugs could effect on preventing theglucocorticoid-induced osteonecrosis of femoral head, reducing disease progression, or improving life quality.

Proteotoxic Stress Desensitizes TGF-beta Signaling Through Receptor Downregulation in Retinal Pigment Epithelial Cells

Background:

Proteotoxic stress and transforming growth factor (TGFβ)-induced epithelial-mesenchymal transition (EMT) are two main contributors of intraocular fibrotic disorders, including proliferative vitreoretinopathy (PVR) and proliferative diabetic retinopathy (PDR). However, how these two factors communicate with each other is not well-characterized.

Objective:

The aim was to investigate the regulatory role of proteotoxic stress on TGFβ signaling in retinal pigment epithelium.

Methods:

ARPE-19 cells and primary human retinal pigment epithelial (RPE) cells were treated with proteasome inhibitor MG132 and TGFβ. Cell proliferation was analyzed by CCK-8 assay. The levels of mesenchymal markers α-SMA, fibronectin, and vimentin were analyzed by real-time polymerase chain reaction (PCR), western blot, and immunofluorescence. Cell migration was analyzed by scratch wound assay. The levels of p-Smad2, total Smad2, p-extracellular signal-regulated kinase 1/2 (ERK1/2), total ERK1/2, p-focal adhesion kinase (FAK), and total FAK were analyzed by western blot. The mRNA and protein levels of TGFβ receptor-II (TGFβR-II) were measured by real-time PCR and western blot, respectively.

Results:

MG132-induced proteotoxic stress resulted in reduced cell proliferation. MG132 significantly suppressed TGFβ-induced upregulation of α-SMA, fibronectin, and vimentin, as well as TGFβ-induced cell migration. The phosphorylation levels of Smad2, ERK1/2, and FAK were also suppressed by MG132. Additionally, the mRNA level and protein level of TGFβR-II decreased upon MG132 treatment.

Conclusion:

Proteotoxic stress suppressed TGFβ-induced EMT through downregulation of TGFβR-II and subsequent blockade of Smad2, ERK1/2, and FAK activation.

The cis-regulatory dynamics of embryonic development at single-cell resolution

Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring single cell gene expression are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain elusive. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single cell resolution. Using single cell combinatorial indexing assay for transposase accessible chromatin (sci-ATAC-seq)1, we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila embryos spanning three landmark embryonic stages: 2-4 hours (hrs) after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises ~6,000 multipotent cells; 6-8hrs (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12hrs (predominantly stage 13), when each of the embryo’s >20,000 cells are undergoing terminal differentiation. Our results reveal spatial heterogeneity in the usage of the regulatory genome prior to gastrulation, a feature that aligns with future cell fate, and nuclei can be temporally ordered along developmental trajectories. During mid-embryogenesis, tissue granularity emerges such that individual cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. The data reveal overlapping usage of regulatory elements between cells of the endoderm and non-myogenic mesoderm, suggesting a common developmental program reminiscent of the mesendoderm lineage in other species2–4. Altogether, we identify over 30,000 distal regulatory elements exhibiting tissue-specific accessibility. We validated the germ layer specificity of a subset of these predicted enhancers in transgenic embryos, achieving 90% accuracy. Overall, our results demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in the chromatin landscape during development, and to uncover the cis-regulatory programs of metazoan germ layers and cell types.

Prokaryotic functional expression and activity comparison of three CYP9A genes from the polyphagous pest Helicoverpa armigera

Cytochrome P450s (CYPs or P450s) have been long recognized as very important enzymes in the metabolism of xenobiotic and endogenous compounds, but only a few CYPs have been functionally characterized in insects. The effort in functional characterization of insect P450s is heavily hindered by technical difficulties in preparing active, individual P450 enzymes directly from the target insect. In this paper, we describe the functional expression of two additional pyrethroid resistance-associated CYP9A genes (CYP9A12 and CYP9A17) from the polyphagous pest Helicoverpa armigera in the facile Escherichia coli. The functionality of E. coli produced CYP9A12, CYP9A14, and CYP9A17 was investigated and activities of these CYP9As were compared against three probe substrates after reconstitution with NADPH-dependent cytochrome P450 reductase. The results showed that active forms of CYP9A12 and CYP9A17 were expressed in E. coli with a content of about 1.0-1.5 nmol mg-1 protein in membrane preparations. In vitro assays showed that CYP9A14 was capable of catalyzing O-dealkylation of methoxyresorufin (MROD), ethoxyresorufin (EROD), and benzyloxyresorufin (BROD), while CYP9A12 and CYP9A17 exhibited only MROD and EROD activities. Kinetic studies demonstrated that CYP9A14 had the greatest k cat/K m value for MROD, and CYP9A17 for EROD, while the lowest k cat/K m values for both MROD and EROD were observed for CYP9A12. The distinct biochemical traits suggest that the three paralogous CYP9As may play different roles in xenobiotic metabolism in this important pest.

Double trouble: Co-occurrence of testosterone deficiency and body fatness associated with all-cause mortality in US men

BACKGROUND

Testosterone deficiency (TD, total testosterone ≤350 ng/dL [12.15 nmol L^-1 ]) and obesity epidemic are growing in parallel in the United States. Yet, the sequelae of TD and obesity on the risk of mortality remain unclear.

OBJECTIVE

To investigate whether the co-occurrence of TD and overall obesity (body mass index ≥30 kg/m² ), and abdominal obesity (waist circumference ≥102 cm), is associated with a risk of all-cause mortality in American men.

DESIGN

The data were obtained from the NHANES 1999-2004 and the Linked Mortality File (December 31, 2011). A total of 948 participants aged ≥20 years old with endogenous sex hormones and adiposity measurements data were included in this study.

RESULTS

Over a median of 9.5 years of follow-up, 142 men died of any cause in this cohort. Multivariable analysis showed a 2.60 fold increased risk of death among men with TD compared with men without TD (Hazard Ratio [HR] = 2.60; 95% confidence interval [CI] = 1.20-5.80). No evidence for interaction between TD and overall or abdominal obesity with risk of death (P_interaction ≥ .80). However, only after comparing men with TD and abdominal obesity with men without TD and no abdominal obesity, we found a 3.30 fold increased risk of death (HR = 3.30, 95% CI = 1.21-8.71).

CONCLUSION

Men with co-occurrence of TD and abdominal obesity have a higher risk of mortality. The effect of co-occurrence of TD and abdominal obesity should be further explored with a larger and longer follow-up time study.

Comprehensive single-cell transcriptional profiling of a multicellular organism

To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 larval stage, which provided >50-fold "shotgun" cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. We integrated these profiles with whole-animal chromatin immunoprecipitation sequencing data to deconvolve the cell type-specific effects of transcription factors. The data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.

Identification of translationally controlled tumor protein in promotion of DNA homologous recombination repair in cancer cells by affinity proteomics

Translationally controlled tumor protein(TCTP) has been implicated in the regulation of apoptosis, DNA repair and drug resistance. However, the underlying molecular mechanisms are poorly defined. To better understand the molecular mechanisms underlying TCTP involved in cellular processes, we performed an affinity purification-based proteomic profiling to identify proteins interacting with TCTP in human cervical cancer HeLa cells. We found that a group of proteins involved in DNA repair are enriched in the potential TCTP interactome. Silencing TCTP by short hairpin RNA in breast carcinoma MCF-7 cells leads to the declined repair efficiency for DNA double-strand breaks on the GFP-Pem1 reporter gene by homologous recombination, the persistent activation and the prolonged retention of γH2AX and Rad51 foci following ionizing radiation. Reciprocal immunoprecipitations indicated that TCTP forms complexes with Rad51 in vivo, and the stability maintenance of Rad51 requires TCTP in MCF-7 cells under normal cell culture conditions. Moreover, inactivation of TCTP by sertraline treatment enhances UVC irradiation-induced apoptosis in MCF-7 cells, and causes sensitization to DNA-damaging drug etoposide and DNA repair inhibitor olaparib. Thus, we have identified an important role of TCTP in promoting DNA double-stand break repair via facilitating DNA homologous recombination processes and highlighted the great potential of TCTP as a drug target to enhance conventional chemotherapy for cancer patients with high levels of TCTP expression.

Reversed graph embedding resolves complex single-cell trajectories

Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with two or more branches remains a challenging computational problem. We present Monocle 2, which uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. Applied to two studies of blood development, Monocle 2 revealed that mutations in key lineage transcription factors diverts cells to alternative fates.

[Feasibility of device closure for multiple atrial septal defects using 3D printing and ultrasound-guided intervention technique]

Objective: To investigate the feasibility of trans-catheter closure of multiple atrial septal defects (ASD) monitored by trans-thoracic echocardiography (TTE) under the guidance of 3D printing heart model. Methods: Between April and August 2016, a total of 21 patients (8 male and 13 female) with multiple ASD in Fuwai Hospital of Chinese Academy of Medical Sciences underwent CT scan and 3-dimensional echocardiography for heart disease model produced by 3D printing technique. The best occlusion program was determined through the simulation test on the model. Percutaneous device closure of multiple ASD was performed follow the predetermined program guided by TTE. Clinical follow-up including electrocardiogram and TTE was arranged at 1 month after the procedure. Results: The trans-catheter procedure was successful in all 21 patients using a single atrial septal occluder. Mild residual shunt was found in 5 patient in the immediate postoperative period, 3 of them were disappeared during postoperative follow-up. There was no death, vascular damage, arrhythmia, device migration, thromboembolism, valvular dysfunction during the follow-up period. Conclusion: The use of 3D printing heart model provides a useful reference for transcatheter device closure of multiple ASD achieving through ultrasound-guided intervention technique, which appears to be safe and feasible with good outcomes of short-term follow-up.

Abstract B29: Innate immune modulation: The novel immunotherapeutic Imprime PGG triggers the anti-cancer immunity cycle in concert with tumor-targeting, anti-angiogenic and checkpoint inhibitor antibodies

Cancer immunotherapeutics largely focus on awakening T cell mediated recognition and eradication of tumor cells. Indeed, checkpoint inhibitor antibodies (e.g. pembrolizumab) unleash T cells already involved in anti-cancer responses and have shown remarkable clinical activity, though only in ~20-30% of solid tumor patients. Numerous approaches are being explored to enhance the percent of patients who benefit from checkpoint inhibitor therapies. Chief amongst these are the innate immune modulating therapies collectively designated as PAMPs- pathogen- associated molecular patterns. PAMPs operate as the critical non-self signals that, in response to pathogen infection, ignite the function of the innate immune system to trigger the immunity cycle. TLR and STING agonists acts as PAMPs and reflect bacterial and viral danger signals that can drive dendritic cell maturation, enhancing T cell function. These agents are in development in combination with other immunotherapies, including checkpoint inhibitors, but inspire intolerable cytokine storms and are thereby limited to direct intra-tumoral delivery approaches. We therefore sought to discover and develop a novel, systemically administered PAMP- Imprime PGG (Imprime). Ex vivo studies with whole blood from healthy human donors show that Imprime consistently elicits the activation of innate immune cells. M2 state macrophages repolarize, showing increased expression of M1 markers (CD86, PD-L1) with coincident reduction in M2 markers (CD163, CD206). Dendritic cells (DCs) mature, showing enhanced surface expression of CD80, CD86 and MHC class II. Functionally, the antigen presentation capability of these re-polarized macrophages and activated DCs is substantially enhanced and drives the robust expansion of co-cultured CD8 T cells as well as the marked upregulation of the potent anti-tumor cytokine interferon gamma. In preclinical tumor studies, Imprime is administered IV and profoundly enhances the efficacy of numerous antibody therapies. Using the B16 experimental metastasis model, we show that Imprime (administered IV) synergizes with the anti-TRP1 tumor-targeting antibody TA-99, nearly eradicating B16 metastases as measured by visual counts, TRP-1 RT-PCR and in situ immunofluorescence for TRP1. In the H441 and H1299 non-small cell lung cancer xenografts, Imprime synergizes with the anti-VEGFR2 antibody DC101 to flat-line tumor growth. In the MC-38, CT-26 and 4T-1 syngeneic tumor models, Imprime synergizes with both anti-PD-1 and PD-L1 checkpoint inhibitor antibodies to repress tumor growth and/or to eradicate cancer lesions. In situ imaging of these preclinical tumor tissues repeatedly shows that Imprime instigates a re-orientation of the immune microenvironment, promoting an M1 state (e.g. increased iNOS2, decreased Arginase 1), as well as the influx of myeloid cells and, in the syngenic models, CD8 T cells. In clinical trials in &gt; 400 total patients to date, Imprime has been safely administered by IV infusion (4mg/kg over 2 hours) and has repeatedly shown evidence for efficacy in combination with tumor targeting or anti-angiogenic antibodies. Studies with checkpoint inhibitor antibodies are slated to begin summer of 2016. We now provide the first evidence in healthy human volunteers that Imprime (IV- 4mg/kg, 2 hours) drives the same innate immune activation events evident in the preclinical studies (e.g. chemokine and cytokine release, PD-L1 and CD86 upregulation) verifying that the clinical dose activates the innate immune system. Together, these preclinical and clinical studies provide evidence that the novel PAMP, Imprime PGG, can be safely administered systemically and can drive the critical innate immune activation necessary to spark the anti-cancer immunity cycle.

Citation Format: N Bose, K Gorden, A Chan, A Jonas Bykowski, N Ottoson, D Walsh, X Qiu, B Harrison, T Kangas, K Fraser, R Fulton, S Leonardo, M Uhlik, J Graff. Innate immune modulation: The novel immunotherapeutic Imprime PGG triggers the anti-cancer immunity cycle in concert with tumor-targeting, anti-angiogenic and checkpoint inhibitor antibodies. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr B29.

Ebola virus infection induces autoimmunity against dsDNA and HSP60

Ebola virus (EBOV) survivors are affected by a variety of serious illnesses of unknown origin for years after viral clearance from the circulation. Identifying the causes of these persistent illnesses is paramount to develop appropriate therapeutic protocols. In this study, using mouse and non-human primates which survived EBOV challenge, ELISA, western blot, mass spectrometry and flow cytometry were used to screen for autoantibodies, identify their main targets, investigate the mechanism behind their induction and monitor autoantibodies accumulation in various tissues. In infected mice and NHP, polyclonal B cell activation and autoantigens secretion induced autoantibodies against dsDNA and heat shock protein 60 as well as antibody accumulation in tissues associated with long-term clinical manifestations in humans. Finally, the presence of these autoantibodies was confirmed in human EBOV survivors. Overall, this study supports the concept that autoimmunity is a causative parameter that contributes to the various illnesses observed in EBOV survivors.

Identification and expression patterns of Halloween genes encoding cytochrome P450s involved in ecdysteroid biosynthesis in the cotton bollworm Helicoverpa armigera

20-Hydroxyecdysone (20E) is a key hormone which regulates growth, development and reproduction in insects. Although cytochrome P450 enzymes (P450s) participating in the ecdysteroid biosynthesis of 20E have been characterized in a few model insects, no work has been published on the molecular entity of their orthologs in the cotton bollworm Helicoverpa armigera, a major pest insect in agriculture worldwide. In this study, four cytochrome P450 homologs, namely HarmCYP302A1, HarmCYP306A1, HarmCYP314A1 and HarmCYP315A1 from H. armigera, were identified and evolutional conservation of these Halloween genes were revealed among lepidopteran. Expression analyses showed that HarmCYP302A1 and HarmCYP315A1 were predominantly expressed in larval prothoracic glands, whereas this predominance was not always observed for HarmCYP306A1 and CYP314A1. The expression patterns of Halloween genes indicate that the fat bodies may play an important role in the conversion of ecdysone into 20E in larval-larval molt and in larval-pupal metamorphosis, and raise the possibility that HarmCYP315A1 plays a role in tissue-specific regulation in the steroid biosynthesis in H. armigera. These findings represent the first identification and expression characterization of four steriodogenic P450 genes and provide the groundwork for future functional and evolutionary study of steroid biosynthesis in this agriculturally important pest.

Single-cell mRNA quantification and differential analysis with Census

Single-cell gene expression studies promise to unveil rare cell types and cryptic states in development and disease through a stunningly high-resolution view of gene regulation. However, measurements from single-cell RNA-Seq are highly variable, frustrating efforts to assay how expression differs between cells. We introduce Census, an algorithm available through our single-cell analysis toolkit Monocle 2, which converts relative RNA-Seq expression levels into relative transcript counts without the need for experimental spike-in controls. We show that analyzing changes in relative transcript counts leads to dramatic improvements in accuracy compared to normalized read counts and enables new statistical tests for identifying developmentally regulated genes. We explore the power of Census through reanalysis of single-cell studies in several developmental and disease contexts. Census counts can be analyzed with widely used regression techniques to reveal changes in cell fate-dependent gene expression, splicing patterns, and allelic imbalances, demonstrating that Census enables robust single-cell analysis at multiple layers of gene regulation.