bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harmine enhances the activity of the HIV-1 latency-reversing agents ingenol A and SAHA
Authors: Taylor Jared P. , Armitage Lucas H. , Aldridge Daniel L. , Cash Melanie N. , Wallet Mark A. 
Published: February 2020

AbstractInfection of HIV-1 remains incurable because long-lived, latently-infected cells persist during prolonged antiretroviral therapy. Attempts to pharmacologically reactivate and purge the latent reservoir with latency reactivating agents (LRAs) such as protein kinase C (PKC) agonists (e.g. ingenol A) or histone deacetylase (HDAC) inhibitors (e.g. SAHA) have shown promising but incomplete efficacy. Using the J-Lat T cell model of HIV latency, we found that the plant-derived compound harmine enhanced the efficacy of existing PKC agonist LRAs in reactivating latently-infected cells. Treatment with harmine increased not only the number of reactivated cells but also increased HIV transcription and protein expression on a per-cell basis. Importantly, we observed an additive effect when harmine was used in combination with ingenol A and the HDAC inhibitor SAHA. An investigation into the mechanism revealed that harmine, when used with LRAs, increased the availability of transcription factors needed for viral reactivation such as NFκB, MAPK p38, and ERK1/2. We also found that harmine treatment resulted in reduced expression of HEXIM1, a negative regulator of transcriptional elongation. Despite harmine’s reported inhibitory effects on DYRK1A and consequent enhancement of NFAT signaling, the HIV reactivating effects of harmine occurred independent of DYRK1A and NFAT. Harmine increases the efficacy of LRAs by increasing the availability of HIV-1 transcription factors and decreasing expression of HEXIM1. Combination therapies with harmine and LRAs could benefit patients by achieving deeper reactivation of the latent pool of HIV provirus.
Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer
Authors: Romanens Lou , Chaskar Prasad , Tille Jean-Christophe , Ryser Stephan , Liaudet Nicolas , Hu-Heimgartner Ketty , Heimgartner Killian , Kaya Gurkan , Tsantoulis Petros , Labidi-Galy S. Intidhar 
Published: February 2020

AbstractTumor samples are conserved in clinical practice in formalin-fixed paraffin-embedded (FFPE) blocks. Formalin fixation chemically alters nucleic acids, rendering transcriptomic analysis challenging. RNA-sequencing is usually performed on tumor bulk, without distinction of cell subtypes or location. Here we describe the development of a robust method for RNA extraction and exome-capture RNA-sequencing of laser-capture microdissected tumor cells (TC) and stromal immune cells (TIL) based on their morphology. We applied this method on 7 tumor samples (surgical or core needle biopsy) of triple-negative breast cancer (TNBC) stored in FFPE blocks over 3-10 years. Unsupervised clustering and principal component analysis showed a clear separation between gene-expression profile of TIL and TC. TIL were enriched in markers of B cells (CD79B, PAX5 and BLNK) and T cells (CD2, CD3D and CD8B) whereas tumor cells expressed epithelial markers (EPCAM, MUC1andKRT8). Microenvironment cell populations-counter (MCP)-counter deconvolution showed an enrichment in adaptive immune cell signatures in microdissected TIL. Transcripts of immune checkpoints were differentially expressed in TIL and TC. We further validated our results by qRT-PCR and multispectral immunohistochemistry. In conclusion, we showed that combining laser-capture microdissection and RNA-sequencing on archived FFPE blocks is feasible and allows spatial transcriptional characterization of tumor microenvironment.
Single-molecule imaging of telomerase RNA reveals a Recruitment – Retention model for telomere elongation
Authors: Laprade Hadrien , Querido Emmanuelle , Smith Michael J. , Guérit David , Crimmins Hannah , Conomos Dimitri , Pourret Emilie , Chartrand Pascal , Sfeir Agnel 
Published: February 2020

AbstractExtension of telomeres is a critical step in the immortalization of cancer cells. This complex reaction requires proper spatio-temporal coordination of telomerase and telomeres, and remains poorly understood at the cellular level. To understand how cancer cells execute this process, we combined CRISPR genome editing and MS2 RNA-tagging to image single-molecules of telomerase RNA (hTR). Real-time dynamics and photoactivation experiments of hTR in Cajal bodies (CBs) reveal that hTERT controls the exit of hTR from CBs. Single-molecule tracking of hTR at telomeres shows that TPP1-mediated recruitment results in short telomere-telomerase scanning interactions, then base-pairing between hTR and telomere ssDNA promotes long interactions required for stable telomerase retention. Interestingly, POT1 OB-fold mutations that result in abnormally long telomeres in cancers act by enhancing this retention step. In summary, single-molecule imaging unveils the life-cycle of telomerase RNA and provides a framework to understand how cancer-associated mutations mechanistically drive defects in telomere homeostasis.
TheE. coliNudL enzyme is a Nudix hydrolase that cleaves CoA and its derivatives
Authors: Spangler Joseph Rankin , Huang Faqing 
Published: February 2020

AbstractThe process of bacterial coenzyme A (CoA) degradation has remained unknown despite the otherwise detailed characterization of the CoA synthesis pathway over 30 years ago. Numerous enzymes capable of CoA degradation have been identified in other domains of life that belong to the Nudix superfamily of hydrolases, but the molecule responsible for this process in the model bacterial system ofE. coli remains a mystery. We report here thatE. coli contains two such Nudix enzymes capable of CoA degradation into 4’-phosphopantetheine and 3’,5’-adenosine monophosphate. TheE. coli enzymes NudC and NudL were cloned in various promoter-fusion constructs in order to purify them as soluble active enzymes and characterize their ability to catalyze the phosphohydrolysis of CoA. NudC, an enzyme known to hydrolyze NADH as its principal substrate, demonstrated the ability to hydrolyze CoA, among other coenzymes, at comparable rates to eukaryotic Nudix hydrolases. NudL, a previously uncharacterized enzyme, demonstrated the ability to cleave only CoA and CoA-related molecules at a rate orders of magnitude slower than its eukaryotic orthologs. NudC and NudL therefore represent a previously uncharacterized pathway of CoA degradation in the highly studiedE. coli system. While the two enzymes display some substrate overlap, their respective activities imply that NudC may play a role as a general coenzyme hydrolase, while NudL specifically targets CoA. These data further suggest a role for these enzymes in the regulation of bacterial CoA-RNA.
Phosphorylation of Elovl5 changes its substrate preference to synthesize Mead acid in response to essential fatty acid deficiency
Authors: Hayashi Yuri , Yamano Misato , Kono Nozomu , Arai Hiroyuki , Fujiwara Yoko , Ichi Ikuyo 
Published: February 2020

ABSTRACTPolyunsaturated fatty acids (PUFAs) of the n-6 and n-3 series cannot be synthesized in mammals and therefore are called essential fatty acids (EFAs). Mead acid (20:3n-9) is an unusual n-9 PUFA, endogenously synthesized from oleic acid (18:1n-9) in an EFA-deficient state. Although Elovl5, a fatty acid elongase, has long been known to selectively elongate C18 and C20 PUFAs, it can use 18:1n-9 as a substrate for the synthesis of Mead acid under C20 PUFA-deficient, but not-sufficient, conditions. We found, by an in vitro enzyme assay, that the microsomal fraction obtained from PUFA-deficient, but not -sufficient, cells showed significant Elovl5 activity toward 18:1n-9, with no effect on its constitutive activity toward 18:3n-6, implying that Elovl5 acquires the activity toward 18:1n-9 under the PUFA-deficient conditions at the enzyme level. Further biochemical analysis revealed that Elovl5 was phosphorylated in the C20 PUFA-supplemented cells, and that treatment with an inhibitor of glycogen synthase kinase 3 (GSK3) completely abolished the phosphorylation of Elovl5 and retained the Elovl5 activity toward 18:1n-9, even in the presence of C20 PUFA. Finally, mutation of putative phosphorylation sites (T281A/S283A/S285A) on Elovl5 did not decrease the activity of Elovl5 toward 18:1n-9 by supplementation with C20 PUFA, suggesting that the phosphorylation of Elovl5 contributed to a change in substrate preference. Thus, by changing its substrate specificity in an EFA-deficient state, Elovl5 is able to regulate the synthesis of Mead acid to maintain levels of long-chain PUFAs.
Unification of Environmental Metabolomics with Metacommunity Ecology
Authors: Danczak Robert E. , Chu Rosalie K. , Fansler Sarah J. , Goldman Amy E. , Graham Emily B. , Tfaily Malak M. , Toyoda Jason , Stegen James C. 
Published: February 2020

AbstractEnvironmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis ‘meta-metabolome ecology’ and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed α-diversity and β-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and βNTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.
Myeloid cell mPGES-1 mediates inflammatory pain hypersensitivity in mice
Authors: Chen Lihong , Yang Guangrui , Cormode David P. , Saigal Ashmita , Madhavan Shravanthi , Mazaleuskaya Liudmila L. , Grant Gregory R. , FitzGerald Garret A. , Grosser Tilo 
Published: February 2020

AbstractNonsteroidal anti-inflammatory drugs (NSAIDs) relieve inflammatory pain by predominant suppression of cyclooxygenase-2 derived prostaglandin (PG) E2. Innate immune cells contribute to inflammatory pain hypersensitivity and may be an attractive target for novel non-addictive approaches to pain management. We studied the contribution of PGE2produced by myeloid cell microsomal prostaglandin E synthase -1 (mPGES-1) to peripheral inflammation and hyperalgesia in mice. Selective deletion of mPGES-1 in myeloid cells by crossing LysM-Cre mice with mPGES-1flox/flox mice (Mac-mPGES-1-KO) resulted in significantly reduced mechanical and thermal hyperalgesia in complete Freund’s adjuvant (CFA)-evoked hind paw inflammation, zymosan-induced peri-articular inflammation and collagen II antibody-induced arthritis models. Systemic COX-2 inhibition or myeloid cell specific COX-2 deletion (by crossing LysM-Cre with COX-2 flox/flox mice) recapitulated reduction of CFA-induced inflammation and hyperalgesia. In contrast, deletion of mPGES-1 in neurons and glial cells by crossing mPGES-1flox/flox mice with Nestin-Cre mice had no detectable effect on inflammatory pain hypersensitivity. While macrophage recruitment was unaltered, tissue concentrations of PGE2, IL-1β and TNFα were significantly reduced in Mac-mPGES-1-KO paw tissues following CFA induction. Our results demonstrate that myeloid cell mPGES-1 is the dominant source of PGE2in inflammatory pain hypersensitivity. Targeting myeloid cell mPGES-1 may afford a novel approach to inflammatory pain therapy.
Predicting commercially available antiviral drugs that may act on the novel coronavirus (2019-nCoV), Wuhan, China through a drug-target interaction deep learning model
Authors: Beck Bo Ram , Shin Bonggun , Choi Yoonjung , Park Sungsoo , Kang Keunsoo 
Published: February 2020

AbstractThe infection of a novel coronavirus found in Wuhan of China (2019-nCoV) is rapidly spreading, and the incidence rate is increasing worldwide. Due to the lack of effective treatment options for 2019-nCoV, various strategies are being tested in China, including drug repurposing. In this study, we used our pretrained deep learning-based drug-target interaction model called Molecule Transformer-Drug Target Interaction (MT-DTI) to identify commercially available drugs that could act on viral proteins of 2019-nCoV. The result showed that atazanavir, an antiretroviral medication used to treat and prevent the human immunodeficiency virus (HIV), is the best chemical compound, showing a inhibitory potency withKdof 94.94 nM against the 2019-nCoV 3C-like proteinase, followed by efavirenz (199.17 nM), ritonavir (204.05 nM), and dolutegravir (336.91 nM). Interestingly, lopinavir, ritonavir, and darunavir are all designed to target viral proteinases. However, in our prediction, they may also bind to the replication complex components of 2019-nCoV with an inhibitory potency withKd< 1000 nM. In addition, we also found that several antiviral agents, such as Kaletra, could be used for the treatment of 2019-nCoV, although there is no real-world evidence supporting the prediction. Overall, we suggest that the list of antiviral drugs identified by the MT-DTI model should be considered, when establishing effective treatment strategies for 2019-nCoV.
Selective augmentation of intestinal immunity by CD22-dependent SHP-1 control of β7integrin expression
Authors: Ballet Romain , Brandl Carolin , Feng Ningguo , Berri Jeremy , Cheng Julian , Ocón Borja , Sheikh Amin Alborzian Deh , Marki Alex , Abram Clare L. , Lowell Clifford A. , Tsubata Takeshi , Greenberg Harry B. , Macauley Matthew S. , Ley Klaus , Nitschke Lars , Butcher Eugene C. 
Published: February 2020

AbstractThe regulation of integrin expression and function controls interactions of immune cells and targets their trafficking locally and systemically. We show here that the tyrosine phosphatase SHP-1 is required for lymphocyte surface expression of the intestinal immune response-associated integrin β7, but not for β1or β2integrins.Viable motheatenmice deficient for SHP-1 have less β7on T cells and lack β7on B cells. SHP-1 function is targeted in B cells by the B cell specific lectin CD22 (Siglec-2), suggesting a potential role for CD22 in β7expression. CD22-deficiency on B cells phenocopies the effects of SHP-1 haplodeficiency. Mechanistically, we show that SHP-1 suppresses β7endocytosis: internalization of β7but not β1integrin is accelerated in SHP-1+/−and CD22−/−B cells. Moreover, mutations in CD22 cytoplasmic SHP1-binding ITIM sequences reduce α4β7comparably, and loss of CD22 lectin activity has an intermediate effect suggesting a model in which the CD22 ITIM sequences recruit SHP-1 to control β7expression. Integrin α4β7selectively contributes to cell interactions in intestinal immunity. Consistent with this, CD22 deficient and SHP-1+/−B cells display reduced β7-dependent homing to gut associated Peyer’s patches (PP); and CD22-deficiency impairs intestinal but not systemic antibody responses and delays clearance of the gut pathogen rotavirus. The results define a novel role for SHP-1 in the differential control of leukocyte integrins and an unexpected integrin β7-specific role for CD22-SHP-1 interplay in mucosal immunity.
The ECF sigma factor PvdS regulates the type I-F CRISPR-Cas system inPseudomonas aeruginosa
Authors: Ahator Stephen Dela , Jianhe Wang , Zhang Lian-Hui 
Published: February 2020

AbstractDuring infection, successful colonization of bacteria requires a fine-tuned supply of iron acquired via iron transport systems. However, the transport systems serve as phage attachment sites and entry portals for foreign nucleic acid. Most bacteria possess the CRISPR-Cas system, which targets and destroys foreign nucleic acids and prevents deleterious effects of horizontal gene transfer. To understand the regulation of the CRISPR-Cas system, we performed genome-wide random transposon mutagenesis which led to the identification of the Extracytoplasmic Function (ECF) Sigma factor, PvdS as a regulator of the Type I-F CRISPR-Cas system inP. aeruginosa. We show that under iron-depleted conditions PvdS induces the expression of the type I-F CRISPR-Cas system. This regulatory mechanism involves direct interaction of PvdS with specific binding sites in the promoter region ofcas1. Furthermore, activation of the CRISPR-Cas system under iron-depleted conditions increases horizontal gene transfer (HGT) interference and adaptation. The PvdS activation of the CRISPR-Cas system under iron limitation highlights the versatility of theP. aeruginosain multitasking its regulatory machinery to integrate multiple stress factors.ImportanceP. aeruginosainfects a wide range of host organisms and adapts to various environmental stress factors such as iron limitation due to its elaborate regulatory system.P aeruginosapossesses the type I-F CRISPR-Cas system as a defense mechanism against phages infection and HGT. This work highlights the ability ofP. aeruginosato multitask its iron regulatory system to control the CRISPR-Cas system under a physiologically relevant stress factor such as iron limitation where the bacteria are vulnerable to phage infection. It also adds to the knowledge of the regulation of the CRISPR-Cas system in bacteria and presents a possible target that could prevent the emergence of phage resistance via the CRISPR-Cas system during the development of phage therapy.
IL4-driven microglia modulate stress resilience through BDNF-dependent neurogenesis
Authors: Zhang Jinqiang , Rong Peijing , Zhang Lijuan , He Hui , Zhou Tao , Fan Yonghua , Mo Li , Zhao Qiuying , Han Yue , Li Shaoyuan , Wang Yifei , Yan Wan , Chen Huafu , You Zili 
Published: February 2020

AbstractAdult neurogenesis in the dentate gyrus of the hippocampus is regulated by specific groups of microglia and is functionally implicated in behavioral responses to stress. However, the role of microglia in modulating hippocampal neurogenesis in stress responses remains poorly understood. Here we investigated the effects of IL4-driven Arg1+microglia in the restoration of hippocampal neurogenesis and conferment of stress resilience. We found that low IL4 levels in the hippocampus of mice was associated with greater stress vulnerability and, conversely, overexpression of IL4 in the hippocampus induced a large number of Arg1+microglia and ameliorated stress-induced depressive-like behaviors. Knockdown of microglial IL4 receptors in the hippocampus of mice exacerbated the stress-induced inflammatory response and abolished the antidepressant effects of IL4 overexpression. Enhancement or inhibition of IL4 signaling in hippocampal microglia modulated neurogenesis, and blockade of neurogenesis abolished the resilience to stress-induced depression. We further show that IL4-activated microglia is associated with upregulation of BDNF levels and neurogenesis. Taken together, our findings suggest that IL4-driven microglia in the hippocampus trigger BDNF-dependent neurogenesis in response to chronic stress, helping protect against depressive-like symptoms. These findings identify the modulation of a specific microglial phenotype as a treatment strategy for mood disorders.In BriefZhang et al. show that IL4-induced Arg1+microglia restore hippocampal neurogenesis and promote resilience against stress in mice by increasing BDNF levels. Targeting microglia with immunomodulatory factors may be a strategy for treating mood disorders.HighlightsVulnerability to stress in mice is associated with reduced IL4 signaling in the hippocampusBrain-derived IL4 promotes adult hippocampal neurogenesis and stress resistance by driving Arg1+microgliaIL4-driven Arg1+microglia enhance hippocampal neurogenesis via a BDNF-dependent pathway
G-baToN: a versatile reporter system for cancer cell-stromal cell interactions
Authors: Tang Rui , Murray Christopher W. , Linde Ian , Kramer Nicholas J. , Lyu Zhonglin , Tsai Min K. , Chen Leo , Cai Hongchen , Gitler Aaron D. , Engleman Edgar , Lee Wonjae , Winslow Monte M. 
Published: February 2020

ABSTRACTCell-cell interactions influence all aspects of development, homeostasis, and disease. In cancer, interactions between cancer cells and stromal cells play a major role in nearly every step of carcinogenesis. Thus, the ability to record cell-cell interactions would facilitate mechanistic delineation of the role of cancer microenvironment. Here, we describe GFP-based Touching Nexus (G-baToN) which relies upon nanobody-directed fluorescent protein transfer to enable sensitive and specific labeling of cells after cell-cell interactions. G-baToN is a generalizable system that enables physical contact-based labeling between various cell types, including diverse cancer-stromal cell pairs. A suite of orthogonal baToN tools enables reciprocal cell-cell labeling, interaction-dependent cargo transfer, and the identification of higher-order cell-cell interactions across a wide range of cell types. The ability to track physically interacting cells with these simple and sensitive systems will greatly accelerate our understanding of the outputs of cell-cell interactions in cancer as well as across many biological processes.
Large-scale Dynamics of Perceptual Decision Information across Human Cortex
Authors: Wilming Niklas , Murphy Peter R , Meyniel Florent , Donner Tobias H 
Published: February 2020

AbstractPerceptual decisions entail the accumulation of sensory evidence for a particular choice towards an action plan. An influential framework holds that sensory cortical areas encode the instantaneous sensory evidence and downstream, action-related regions accumulate this evidence. The large-scale distribution of this computation across the cerebral cortex has remained largely elusive. We developed a regionally-specific magnetoencephalography decoding approach to exhaustively map the dynamics of stimulus- and choice-specific signals across the human cortical surface during a visual decision. Comparison with the evidence accumulation dynamics inferred from behavior enabled us to disentangle stimulus-dependent and endogenous components of choice-predictive activity across the visual cortical hierarchy. The endogenous component was present in primary visual cortex, expressed in a low (< 20 Hz) frequency-band, and its time course tracked, with delay, the build-up of choice-predictive activity in (pre-)motor regions. Our results are consistent with choice-specific cortical feedback signaling in a specific frequency channel during decision formation.