Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.

Type V and type VI CRISPR-Cas systems have been shown to cleave nonspecific single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) in trans, but this has not been observed in type II CRISPR-Cas systems using single guide RNA. We show here that the type II CRISPR-Cas9 systems directed by CRISPR RNA and trans-activating CRISPR RNA dual RNAs show RuvC domain-dependent trans-cleavage activity for both ssDNA and ssRNA substrates. Cas9 possesses sequence preferences for trans-cleavage substrates, preferring to cleave T- or C-rich ssDNA substrates. We find that the trans-cleavage activity of Cas9 can be activated by target ssDNA, double-stranded DNA and ssRNA. The crystal structure of Cas9 in complex with guide RNA and target RNA provides a structural basis for the binding of target RNA to activate Cas9. Based on the trans-cleavage activity of Cas9 and nucleic acid amplification technology, we develop the nucleic acid detection platforms DNA-activated Cas9 detection and RNA-activated Cas9 detection, which are capable of detecting DNA and RNA samples with high sensitivity and specificity.

Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery.

Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length Saccharomyces cerevisiae and Cyberlindnera jadinii Las1-Grc3 complexes, and C. jadinii Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis.

Weakly supervised video-based cardiac detection for hypertensive cardiomyopathy.

INTRODUCTION: Parameters, such as left ventricular ejection fraction, peak strain dispersion, global longitudinal strain, etc. are influential and clinically interpretable for detection of cardiac disease, while manual detection requires laborious steps and expertise. In this study, we evaluated a video-based deep learning method that merely depends on echocardiographic videos from four apical chamber views of hypertensive cardiomyopathy detection. METHODS: One hundred eighty-five hypertensive cardiomyopathy (HTCM) patients and 112 healthy normal controls (N) were enrolled in this diagnostic study. We collected 297 de-identified subjects' echo videos for training and testing of an end-to-end video-based pipeline of snippet proposal, snippet feature extraction by a three-dimensional (3-D) convolutional neural network (CNN), a weakly-supervised temporally correlated feature ensemble, and a final classification module. The snippet proposal step requires a preliminarily trained end-systole and end-diastole timing detection model to produce snippets that begin at end-diastole, and involve contraction and dilatation for a complete cardiac cycle. A domain adversarial neural network was introduced to systematically address the appearance variability of echo videos in terms of noise, blur, transducer depth, contrast, etc. to improve the generalization of deep learning algorithms. In contrast to previous image-based cardiac disease detection architectures, video-based approaches integrate spatial and temporal information better with a more powerful 3D convolutional operator. RESULTS: Our proposed model achieved accuracy (ACC) of 92%, area under receiver operating characteristic (ROC) curve (AUC) of 0.90, sensitivity(SEN) of 97%, and specificity (SPE) of 84% with respect to subjects for hypertensive cardiomyopathy detection in the test data set, and outperformed the corresponding 3D CNN (vanilla I3D: ACC (0.90), AUC (0.89), SEN (0.94), and SPE (0.84)). On the whole, the video-based methods remarkably appeared superior to the image-based methods, while few evaluation metrics of image-based methods exhibited to be more compelling (sensitivity of 93% and negative predictive value of 100% for the image-based methods (ES/ED and random)). CONCLUSION: The results supported the possibility of using end-to-end video-based deep learning method for the automated diagnosis of hypertensive cardiomyopathy in the field of echocardiography to augment and assist clinicians. TRIAL REGISTRATION: Current Controlled Trials ChiCTR1900025325, Aug, 24, 2019. Retrospectively registered.

Phellopterin attenuates ovarian cancer proliferation and chemoresistance by inhibiting the PU.1/CLEC5A/PI3K-AKT feedback loop.

Ovarian cancer is known as the second leading cause of gynecologic cancer-associated deaths in women worldwide. Developing new and effective compounds to alleviate chemoresistance is an urgent priority in ovarian cancer. Here, we aimed to reveal the biological function and underlying mechanisms of phellopterin, a naturally sourced ingredient of Angelica dahurica, in ovarian cancer progression as well as evaluate the therapeutic potential of phellopterin in ovarian cancer patients. In this investigation, we found that phellopterin mitigated DNA replication and induced cell cycle arrest, apoptosis, and DNA damage, attenuating cell proliferation and chemoresistance of ovarian cancer. Interestingly, bioinformatics analyses of data from our RNA sequencing and The Cancer Genome Atlas ovarian cancer dataset suggested that phellopterin presented anti-cancer activities in ovarian cancer cells by modulating signals affecting ovarian cancer progression and identified phellopterin as a potential compound in improving ovarian cancer patients' prognosis. In addition, the C-Type Lectin Domain Containing 5A (CLEC5A) was demonstrated as a downstream effector of phellopterin and involved in a positive PU.1/CLEC5A/PI3K-AKT feedback loop. Interestingly, phellopterin might inactivate the positive feedback circuit to suppress ovarian cancer progression. Collectively, our investigation revealed that phellopterin mitigated ovarian cancer proliferation and chemoresistance through suppressing the PU.1/CLEC5A/PI3K-AKT feedback loop, and predicted phellopterin as a new and effective cytotoxic drug and CLEC5A as a potential target for the treatment of ovarian cancer.

Electrochemically Exfoliated Graphene Oxide for Simple Fabrication of Cocaine Aptasensors.

Transducers made from graphene-type materials are widely used in sensing applications. However, utilization of graphene oxide obtained from electrochemical exfoliation of graphite (EGO) has remained relatively unexplored. In this study, electrochemical cocaine aptasensors based on large-size EGO flakes were investigated. In particular, the influence of the following parameters on the sensor performance was examined: (i) aptamer's terminal group (-NH2 vs -OH), (ii) functionalization of EGO with the aptamer via physical adsorption and covalent immobilization, and (iii) intrinsic electrochemical properties of EGO such as the electrochemical surface area (ESA) and standard rate constant of electron transfer (k0). The results demonstrate that EGO-based electrochemical aptasensors fabricated by physical adsorption with an NH2-modified aptamer have very good reproducibility, shelf-life stability, and high sensitivity for detecting cocaine with a detection limit of 50 nM. Their performance is comparable to that of the aptasensors prepared using the covalent immobilization. Additionally, it is shown that EGO materials with high ESA and k0 can enhance the sensing performance. The fast (less than 10 min) and strong adsorption of the NH2-modified cocaine aptamer on the surface of large EGO flakes makes the fabrication of the sensing platform simple and rapid. This simple approach has the potential to simplify the fabrication of sensors.

One-Step Synthesis of Aminobenzoic Acid Functionalized Graphene Oxide by Electrochemical Exfoliation of Graphite for Oxygen Reduction to Hydrogen Peroxide and Supercapacitors.

Graphene-based materials have attracted considerable attention as promising electrocatalysts for the oxygen reduction reaction (ORR) and as electrode materials for supercapacitors. In this work, electrochemical exfoliation of graphite in the presence of 4-aminebenzoic acid (4-ABA) is used as a one-step method to prepare graphene oxide materials (EGO) functionalized with aminobenzoic acid (EGO-ABA). The EGO and EGO-ABAs materials were characterized by FT-IR spectroscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, X-ray diffraction and scanning electron microscopy. It was found that the EGO-ABA materials have smaller flake size and higher density of oxygenated functional groups compared to bare EGO. The electrochemical studies showed that the EGO-ABA catalysts have higher activity for the ORR to H2O2 in alkaline medium compared to EGO due to their higher density of oxygenated functional groups. However, bare EGO has a higher selectivity for the 2-electron process (81%) compared to the EGO-ABA (between 64 and 72%) which was related to a lower content of carbonyl groups. The specific capacitance of the EGO-ABA materials was higher than that of EGO, with an increase by a factor of 3 for the materials prepared from exfoliation in 5 mM 4-ABA/0.1 M H2SO4. This electrode material also showed a remarkable cycling capability with a loss of only 19.4% after 5000 cycles at 50 mVs-1.

Structural basis for MTA1c-mediated DNA N6-adenine methylation.

DNA N6-adenine methylation (6 mA) has recently been found to play a crucial role in epigenetic regulation in eukaryotes. MTA1c, a newly discovered 6 mA methyltransferase complex in ciliates, is composed of MTA1, MTA9, p1 and p2 subunits and specifically methylates ApT dinucleotides, yet its mechanism of action remains unknown. Here, we report the structures of Tetrahymena thermophila MTA1 (TthMTA1), Paramecium tetraurelia MTA9 (PteMTA9)-TthMTA1 binary complex, as well as the structures of TthMTA1-p1-p2 and TthMTA1-p2 complexes in apo, S-adenosyl methionine-bound and S-adenosyl homocysteine-bound states. We show that MTA1 is the catalytically active subunit, p1 and p2 are involved in the formation of substrate DNA-binding channel, and MTA9 plays a structural role in the stabilization of substrate binding. We identify that MTA1 is a cofactor-dependent catalytically active subunit, which exhibits stable SAM-binding activity only after assembly with p2. Our structures and corresponding functional studies provide a more detailed mechanistic understanding of 6 mA methylation.

MOF-derived ultrasmall CoSe2 nanoparticles encapsulated by an N-doped carbon matrix and their superior lithium/sodium storage properties.

Ultrasmall CoSe2 nanoparticles encapsulated by an N-doped carbon matrix were prepared by selenizing a novel Co-metal organic framework precursor. The excellent electrochemical performance may be due to the synergistic effect of the N-doped carbon matrix and the ultrasmall CoSe2.

The biomarkers and potential pathogenesis of lung cancer related cerebral hemorrhage.

Cerebral hemorrhage is one of the common complications in patients with lung cancer (LC). Although cancer related cerebral hemorrhage was aware, the pathogenesis and biomarkers of lung cancer related cerebral hemorrhage (LCRCH) remained not well known. The aim of this study was to investigate the pathogenesis and plasma biomarkers of LCRCH.A retrospective review was conducted on acute cerebral hemorrhage patients with active LC who was admitted to the hospital between January 2007 and December 2017. A total of 56 patients with LCRCH (active LC patients with acute cerebral hemorrhage but without conventional vascular risks) was recruited. Meanwhile, 112 patients with active LC alone and gender, age, and subtype of cancer cell matched were recruited as control group.In LCRCH patients, most of the hemorrhagic lesions were located in lobes. And most of them with adenocarcinoma were in medium to terminal stage with poor prognosis short-term. Moreover, LCRCH patients had a lengthened prothrombin time (PT), elevated plasma carcinoembryonic antigen (CEA), cancer antigen 125 (CA125) and cancer antigen 199 (CA199) levels and decreased platelet (PLT) level than did the patients with LC. Multivariate logistic regression analysis showed that lengthened PT, elevated plasm CEA, and CA199 levels were independent risk factors for LCRCH.It was suggested that lengthened PT, elevated plasm CEA and CA199 levels associated with the pathogenesis of LCRCH, and that the Index derived from independent risks should be serve as a specific biomarker of LCRCH.

NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.

The exosome functions in the degradation of diverse RNA species, yet how it is negatively regulated remains largely unknown. Here, we show that NRDE2 forms a 1:1 complex with MTR4, a nuclear exosome cofactor critical for exosome recruitment, via a conserved MTR4-interacting domain (MID). Unexpectedly, NRDE2 mainly localizes in nuclear speckles, where it inhibits MTR4 recruitment and RNA degradation, and thereby ensures efficient mRNA nuclear export. Structural and biochemical data revealed that NRDE2 interacts with MTR4's key residues, locks MTR4 in a closed conformation, and inhibits MTR4 interaction with the exosome as well as proteins important for MTR4 recruitment, such as the cap-binding complex (CBC) and ZFC3H1. Functionally, MID deletion results in the loss of self-renewal of mouse embryonic stem cells. Together, our data pinpoint NRDE2 as a nuclear exosome negative regulator that ensures mRNA stability and nuclear export.

Single particle ICP-MS-based absolute and relative quantification of E. coli O157 16S rRNA using sandwich hybridization capture.

Herein, a novel 16S rRNA detection platform was achieved by combining a sandwich hybridization reaction, a single-molecule magnetic capture, and single particle-inductively coupled plasma mass spectrometry amplification. The assay was developed for the direct detection of RNA from dangerous human pathogens and enabled absolute and high-precision quantification of a target with a detection limit of 10 fM.

Crystal structure of EGFR T790M/C797S/V948R in complex with EAI045.

Lung cancer is the leading cause of cancer deaths. Epidermal growth factor receptor (EGFR) kinase domain mutations are a common cause of non-small cell lung cancers (NSCLCs), a major subtype of lung cancers. Patients harboring most of these mutations respond well to the anti-EGFR tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib initially, but soon develop resistance to them in about half of the cases due to the emergence of the gatekeeper mutation T790M. The third-generation TKIs such as AZD9291, HM61713, CO-1686 and WZ4002 can overcome T790M through covalent binding to the EGFR kinase through Cys 797, but ultimately lose their efficacy upon emergence of the C797S mutation that abolishes the covalent bonding. Therefore to develop new TKIs to overcome EGFR drug-resistant mutants harboring T790M/C797S is urgently demanded. EAI001 and EAI045 are a new type of EGFR TKIs that bind to EGFR reversibly and not relying on Cys 797. EAI045 in combination with cetuximab is effective in mouse models of lung cancer driven by EGFR L858R/T790M and L858R/T790M/C797S. Here we report the crystal structure of EGFR T790M/C797S/V948R in complex with EAI045, and compare it to EGFR T790M/V948R in complex with EAI001. The complex structure reveals why EAI045 binds tighter to EGFR than does EAI001, and why EAI001 and EAI045 prefer binding to EGFR T790M. The knowledge may facilitate future drug development studies targeting this very important cancer target.

Biomarkers of gastric cancer-related ischemic stroke and its underlying pathogenesis.

This study aimed to investigate the biomarkers and underlying pathogenesis of ischemic stroke in patients with gastric cancer (GC).Patients with active gastric cancer who had experienced acute ischemic stroke without conventional vascular risk factors (gastric cancer-related stroke [GCS] group) and visited The First Affiliated Hospital of Guangxi Medical University and First Affiliated Hospital of Sun Yat-sen University from January 2003 to December 2016 were retrospectively enrolled. The patients' clinical features and laboratory findings were compared with those of age-, sex-, and disease progression-matched patients with GC without ischemic stroke (GC group) who had been admitted to the same hospital during the same period (GCS:GC ratio = 1:2).Among the 9166 patients diagnosed with GC, 70 had experienced a cerebral infarction and were enrolled in this study. Among them, 53 (75.71%) harbored multiple lesions in multiple vascular territories. Notably, patients in the GCS group exhibited significant increases in the D-dimer and cancer antigen 125 (CA125) levels and platelet-to-neutrophil ratio (PNR), compared to their counterparts in the GC group. A multiple logistic regression analysis identified all 3 factors as independent risk factors for cerebral infarction in patients with GC (D-dimer, odds ratio [OR] = 1.006 per 1 ng/mL increase, 95% confidence interval [CI], 1.004-1.009, P = .000; CA125, OR = 1.016 per 1 U/mL increase, 95% CI, 1.005-1.027, P = .005; PNR, OR = 1.025 per 1 point increase, 95% CI: 1.003-1.048, P = .023).Elevated plasma D-dimer and CA125 levels and an increased PNR might affect the occurrence of GC-related ischemic stroke and could therefore serve as potential biomarkers.

FOXO1 inhibition potentiates endothelial angiogenic functions in diabetes via suppression of ROCK1/Drp1-mediated mitochondrial fission.

Diabetes-induced endothelial cell (EC) dysfunction and neovascularization impairment constitute vascular complications with limited treatment regimens. Transcription factor FOXO1 is a key angiogenic regulator and plays a pathologic role in progression of diabetes. The present study was designed to determine the involvement of FOXO1 in impaired EC function and post-ischemic neovascularization in diabetes and investigate underlying mechanisms. We found that FOXO1-selective inhibitor AS1842856 improved blood flow recovery and capillary density in ischemic hindlimb, and rescued the delay of wound closure with a concomitant augmentation of mean perfusion rate in diabetic mice. In vitro, treatment with AS1842856 or FOXO1 siRNA abrogated high glucose-induced apoptosis and ameliorated capillary tube formation in human umbilical vein endothelial cells (HUVECs). FOXO1 inhibition relieved alterations in mitochondrial networks and significantly suppressed the overproduction of mitochondrial reactive oxygen species (mtROS) induced by high glucose in ECs. Expression of dynamin-related protein-1 (Drp1) and phosphorylation at Ser616, a protein required for mitochondrial fission, were enhanced by hyperglycemia, which could be neutralized by FOXO1 inhibition. Moreover, the transcription of Rho-associated coiled-coil containing protein kinase 1 (ROCK1), which phosphorylates Drp1 at Ser616, was shown by luciferase assay to be directly regulated by FOXO1. These findings suggested that FOXO1 is critical to preserve mitochondrial quantity and function in ECs, and FOXO1 may serve as a therapeutic target for microvascular complications of diabetes.

BEAMing LAMP: single-molecule capture and on-bead isothermal amplification for digital detection of hepatitis C virus in plasma.

A novel dNAD platform (BEAMing LAMP) by combining emulsion micro-reactors, single-molecule magnetic capture and on-bead loop-mediated isothermal amplification has been developed for DNA detection, which enables absolute and high-precision quantification of a target with a detection limit of 300 copies.

Phase I, Randomized, Double-blind, Placebo-controlled, Single-dose, and Multiple-dose Studies of Erenumab in Healthy Subjects and Patients With Migraine.

Monoclonal antibodies (mAbs) targeting calcitonin gene-related peptide (CGRP) signaling are being explored as prophylactic treatments for migraine. Erenumab (AMG 334) is the first potent, selective, and competitive human mAb antagonist of the CGRP receptor. We report the data from two phase I studies assessing the safety, pharmacokinetics (PK), and pharmacodynamics of single and multiple administrations of erenumab in healthy subjects and patients with migraine. The results indicate that the PK profile of erenumab is nonlinear from 1 mg to 70 mg and the linear portion of the clearance from 70 mg to 210 mg is consistent with other human immunoglobulin G2 antibodies. Single doses of erenumab resulted in >75% inhibition of capsaicin-induced dermal blood flow, with no apparent dose-dependency for erenumab ≥21 mg. Erenumab was generally well tolerated, with an acceptable safety profile, supporting further clinical development of erenumab for migraine prevention.

Enzyme-free, signal-amplified nucleic acid circuits for biosensing and bioimaging analysis.

Enzyme-free, signal-amplified nucleic acid circuits utilize programmed assembly reactions between nucleic acid substrates to transduce a chemical input into an amplified detection signal. These circuits have shown great potential for developing biosensors for high-sensitivity and high-selectivity detection of varying targets including nucleic acids, small molecules and proteins in vitro and for high-contrast in situ visualization and imaging of these targets in tissues and living cells. We review the background of the enzyme-free, signal-amplified nucleic acid circuits, including their mechanism, significance, types and development. We also review current applications of these circuits for biosensors and bioimaging.

Pharmacokinetic-Pharmacodynamic Relationship of Erenumab (AMG 334) and Capsaicin-Induced Dermal Blood Flow in Healthy and Migraine Subjects.

PURPOSE: Capsaicin-induced dermal blood flow (CIDBF) is a validated biomarker used to evaluate the target engagement of potential calcitonin gene-related peptide-blocking therapeutics for migraine. To characterize the pharmacokinetics (PK) and quantify the inhibitory effects of erenumab (AMG 334) on CIDBF, CIDBF data were pooled from a single- and a multiple-dose study in healthy and migraine subjects. METHODS: Repeated capsaicin challenges and DBF measurements were performed and serum erenumab concentrations determined. A population analysis was conducted using a nonlinear mixed-effects modeling approach. Effects of body weight, gender, and age on model parameters were evaluated. RESULTS: Two-compartment target-mediated drug disposition (TMDD) model assuming binding of erenumab in the central compartment best described the nonlinear PK of erenumab. Subcutaneous absorption half-life was 1.6 days and bioavailability was 74%. Erenumab produced a maximum inhibition of 89% (95% confidence interval: 87-91%). Erenumab concentrations required for 50% and 99% of maximum inhibition were 255 ng/mL and 1134 ng/mL, respectively. Increased body weight was associated with increased erenumab clearance but had no effect on the inhibitory effect on CIDBF. CONCLUSIONS: Our results show that erenumab pharmacokinetics was best characterized by a TMDD model and resulted in potent inhibition of CIDBF.

A survey of renal impairment pharmacokinetic studies for new oncology drug approvals in the USA from 2010 to early 2015: a focus on development strategies and future directions.

The US Food and Drug Administration (FDA) issued a guidance document in 2010 on pharmacokinetic (PK) studies in renal impairment (RI) on the basis of observations that substances such as uremic toxins might result in altered drug metabolism and excretion. No specific recommendations for oncology drugs were included. We surveyed the publicly available FDA review documents of 29 small molecule oncology drugs approved between 2010 and the first quarter of 2015. The objectives were as follows: (i) summarize the impact of RI on PK at the time of the initial new drug application; (ii) identify limitations of the guidance; and (iii) outline an integrated approach to study the impact of RI on these drugs. Our survey indicates that the current FDA guidance does not appear to provide clear strategic or decision pathways for RI studies in terms of small molecule oncology drugs. The FDA review documents indicate an individualized approach to the review because of the complex pharmacologic nature of these drugs and patient populations. Overall, the strategy for carrying out a RI study during clinical development or as a postmarketing study requires integration with the totality of data, including mass balance, absolute bioavailability, drug-drug interaction, hepatic dysfunction, population PK, exposure-response analysis, the therapeutic window for best guidance, and determination of the optimal doses for special oncology populations.

Facile Synthesis of Nanoporous Pt-Y alloy with Enhanced Electrocatalytic Activity and Durability.

Recently, Pt-Y alloy has displayed an excellent electrocatalytic activity for oxygen reduction reaction (ORR), and is regarded as a promising cathode catalyst for fuel cells. However, the bulk production of nanoscaled Pt-Y alloy with outstanding catalytic performance remains a great challenge. Here, we address the challenge through a simple dealloying method to synthesize nanoporous Pt-Y alloy (NP-PtY) with a typical ligament size of ~5 nm. By combining the intrinsic superior electrocatalytic activity of Pt-Y alloy with the special nanoporous structure, the NP-PtY bimetallic catalyst presents higher activity for ORR and ethanol oxidation reaction, and better electrocatalytic stability than the commercial Pt/C catalyst and nanoporous Pt alloy. The as-made NP-PtY holds great application potential as a promising electrocatalyst in proton exchange membrane fuel cells due to the advantages of facile preparation and excellent catalytic performance.