bluuebunny/crossref_metadata_2025_split huggingface dataset:
The lysosomal V-ATPase B1 subunit in renal proximal tubule is linked to nephropathic cystinosis
Authors: Jamalpoor Amer , van Eerde Albertien M , Lilien Marc R , van Gelder Charlotte AGH , Zaal Esther A , Valentijn Floris A , Broekhuizen Roel , Zielhuis Eva , Egido Julia E , Altelaar Maarten , Berkers Celia R , Masereeuw Rosalinde , Janssen Manoe J 
Published: July 2020

AbstractVariants in ATP6V1B1, the gene encoding the B1 subunit of the vacuolar H+-ATPase lead to distal renal tubular acidosis and hearing loss of variable degree. Apart from metabolic acidosis, a 23-month-old girl with pathogenic ATP6V1B1 variants presented with increased granulocyte cystine levels, and symptoms of renal Fanconi syndrome, indicating an unknown link to proximal tubulopathy and cystinosis, a disorder of the proximal tubule caused by variants in the CTNS gene. Here, we demonstrated that ATP6V1B1 is expressed in proximal tubules of human kidney tissue, though to a lesser extent than in distal tubules. Further, we used CRISPR/Cas9 technology to selectively knockout ATP6V1B1 or CTNS in human renal proximal tubule cells and performed a full metabolomic and proteomic analysis to compare their phenotype to isogenic control cells. In line with the clinical data, the loss of ATP6V1B1 disrupted the chemiosmotic coupling between the lysosomal V ATPase B1 subunit and cystinosin and resulted in intralysosomal accumulation of cystine and autophagy activation in renal proximal tubule cells. In conclusion, we identified ATP6V1B1 as a central player in renal proximal tubule cells, regulating lysosomal cystine transport and autophagy, and its absence can lead to proximal tubule dysfunction.
Kinetochore individualization in meiosis I is required for centromeric cohesin removal in meiosis II
Authors: Gryaznova Yulia , Keating Leonor , Touati Sandra A. , Cladière Damien , Yakoubi Warif El , Buffin Eulalie , Wassmann Katja 
Published: July 2020

AbstractPartitioning of the genome in meiosis occurs through two highly specialized cell divisions, named meiosis I and II. Step-wise cohesin removal is required for chromosome segregation in meiosis I, and sister chromatid segregation in meiosis II. In meiosis I, mono-oriented sister kinetochores appear as fused together when examined by high resolution confocal microscopy, whereas they are clearly separated in meiosis II, when attachments are bipolar. It has been proposed that bipolar tension applied by the spindle is responsible for the physical separation of sister kinetochores, removal of cohesin protection and chromatid separation in meiosis II. We show here that this is not the case, and initial separation of sister kinetochores occurs already in anaphase I, when attachments are still monopolar, and independently of pericentromeric Sgo2 removal. This kinetochore individualization occurs also independently of spindle forces applied on sister kinetochores, but importantly, depends on cleavage activity of Separase. Crucially, without kinetochore individualization by Separase in meiosis I, oocytes separate bivalents into chromosomes and not sister chromatids in meiosis II, showing that whether centromeric cohesin is removed or not is determined by the kinetochore structure prior to meiosis II.
Myeloid lncRNALOUPMediates Opposing Regulatory Effects of RUNX1 and RUNX1-ETO in t(8;21) AML
Authors: Trinh Bon Q. , Ummarino Simone , Ebralidze Alexander K. , van der Kouwe Emiel , Bassal Mahmoud A. , Nguyen Tuan M. , Coffey Rory , Tenen Danielle E. , Fabiani Emiliano , Gurnari Carmelo , Wu Chan-Shuo , Angarica Vladimir Espinosa , Zhang Yanzhou , Ying Li , Yang Henry , Heller Gerwin , Chen Sisi , Zhang Hong , Thurm Abby R. , Marchi Francisco , Levantini Elena , Staber Philipp B. , Zhang Pu , Voso Maria Teresa , Pandolfi Pier Paolo , Ruscio Annalisa Di , Tenen Daniel G. 
Published: July 2020

ABSTRACTThe mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. Here we investigate whether RNAs coordinate with transcription factors to drive myeloid gene transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent RNA- and DNA-interactions with the broadly expressed transcription factor RUNX1, we identified the long noncoding RNALOUP. This myeloid-specific and polyadenylated lncRNA induces myeloid differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master regulatorPU.1. Mechanistically,LOUPrecruits RUNX1 to both thePU.1enhancer and the promoter, leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia, wherein RUNX1 is fused to ETO, the resulting oncogenic fusion protein RUNX1-ETO limits chromatin accessibility at theLOUPlocus, causing inhibition ofLOUPandPU.1expression. These findings highlight the important role of the interplay between cell type-specific RNAs and transcription factors as well as their oncogenic derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of transcription factors represent alternative targets for therapeutic development.KEY POINTSlncRNALOUPcoordinates with RUNX1 to inducesPU.1long-range transcription, conferring myeloid differentiation and inhibiting cell growth.RUNX1-ETO limits chromatin accessibility at theLOUPlocus, causing inhibition ofLOUPandPU.1expression in t(8;21) AML.
The Ran GTPase Gradient Protects the Nucleolus from Aging-Associated Morphological Changes
Authors: Remlein Bartlomiej , Paschal Bryce M. 
Published: July 2020

ABSTRACTIn the context of its regulatory function for nucleocytoplasmic transport, the Ran GTPase undergoes cycles of nuclear import, GTP loading, nuclear export, and GTP hydrolysis. These reactions give rise to a nuclear:cytoplasmic (N:C) Ran gradient. In Hutchinson-Gilford Progeria Syndrome, disruption of the Ran gradient suppresses nuclear import of high molecular mass complexes by reducing the nuclear concentration of Ran. Here, we report that cells undergoing senescence, as a consequence of passage number, chemical induction, and altered nuclear lamina structure, all display a Ran gradient disruption quantitatively similar to that observed in Progeria patient cells. We found that the Ran gradient is critical for maintenance of nucleolar structure, as its disruption increases the size and decreases the average number of nucleoli per cell. Nucleolar number and size are biomarkers of longevity in diverse organisms, thus the nuclear level of Ran may be important for the nucleolar morphology in aging. The contribution of the Ran gradient includes regulating import of nucleolin and nucleophosmin, nucleolar proteins that assemble into high molecular mass complexes. The steepness of the Ran gradient is highly dependent on nuclear heterochromatin, which is reduced by passage number and chemical induction of senescence in cultured cells, and is known to decline during normal aging. Our data suggest that the Ran gradient senses nuclear heterochromatin, and through its function as a transport regulator, helps maintain the protein composition and structure of the nucleolus.
Synapsin-caveolin-1 mitigates cognitive deficits and neurodegeneration in Alzheimer’s disease mice
Authors: Wang Shanshan , Leem Joseph S. , Podvin Sonia , Hook Vivian , Kleschevnikov Natalia , Savchenko Paul , Dhanani Mehul , Zhou Kimberly , Kelly Isabella C. , Zhang Tong , Miyanohara Atsushi , Kleschevnikov Alexander , Wagner Steve L. , Trojanowski John Q. , Roth David M. , Patel Hemal H. , Patel Piyush M. , Head Brian P. 
Published: July 2020

ABSTRACTAD presents with severe neurodegeneration which leads to cognitive deficits and dementia. Identifying the molecular signals that attenuate neurodegeneration in AD may be exploited as therapeutic targets. This study revealed that transgenic AD mice (PSAPP) exhibit decreased caveolin-1 (Cav-1), a membrane/lipid raft (MLR) scaffolding protein that organizes synaptic signaling components. Subcellularly, Cav-1 and full length (fl)-TrkB were significantly decreased in MLRs. We thus developed an in vivo gene therapy that re-expresses neuronal-targeted Cav-1 using the synapsin promoter (SynCav1). While AD mice showed significant learning and memory deficits at 9 and 11 months, AD mice that received hippocampalSynCav1(AD-SynCav1) maintained normal learning and memory at 9 and 11 months respectively. Furthermore, AD-SynCav1mice showed preserved hippocampal MLR-localized fl-TrkB, synaptic ultrastructure, dendritic arborization and axonal myelin content, all of which occurred independent of reducing amyloid deposit and astrogliosis. Thus,SynCav1demonstrates translational potential to treat AD by delaying neurodegeneration.SummaryTransgenic PSAPP mice exhibit decreased hippocampal expression of the membrane lipid raft (MLR) scaffolding protein caveolin-1. Synapsin-promoted re-expression of Cav-1 (termedSynCav1) mitigated neuropathology and cognitive deficits.SynCav1gene therapy has the potential to treat AD and other forms of neurodegeneration.
Regulation of trehalase activity by multi-site phosphorylation and 14-3-3 interaction
Authors: Dengler Lisa , Örd Mihkel , Schwab Lucca M. , Loog Mart , Ewald Jennifer C. 
Published: July 2020

AbstractProtein phosphorylation enables a rapid adjustment of cellular activities to diverse intracellular and environmental stimuli. Many phosphoproteins are targeted on more than one site, which allows the integration of multiple signals and the implementation of complex responses. However, the hierarchy and interplay between multiple phospho-sites are often unknown. Here, we study multi-site phosphorylation using the yeast trehalase Nth1 and its activator, the 14-3-3 protein Bmh1, as a model. Nth1 is known to be phosphorylated by the metabolic kinase PKA on four serine residues and by the cell cycle kinase CDK on one residue. However, how these five phospho-sites adjust Nth1 activity remains unclear. Using a novel reporter construct, we investigated the contribution of the individual sites for the regulation of the trehalase and its 14-3-3 interactor. In contrast to the constitutively phosphorylated S20 and S83, the weaker sites S21 and S60 are only phosphorylated by increased PKA activity. For binding Bmh1, S83 functions as the high-affinity “gatekeeper” site, but successful binding of the Bmh1 dimer and thus Nth1 activation requires S60 as a secondary site. Under nutrient-poor conditions with low PKA activity, S60 is not efficiently phosphorylated and the cell cycle dependent phosphorylation of S66 by Cdk1 contributes to Nth1 activity, likely by providing an alternative Bmh1 binding site. Additionally, the PKA sites S20 and S21 modulate the dephosphorylation of Nth1 on downstream Bmh1 sites. In summary, our results expand our molecular understanding of Nth1 regulation and provide a new aspect of the interaction of 14-3-3 proteins with their targets.
Separation and quantification of 2-Keto-3-deoxy-gluconate (KDG) a major metabolite in pectin and alginate degradation pathways
Authors: Martis B Shiny , Droux Michel , Deboudard Florelle , Nasser William , Meyer Sam , Reverchon Sylvie 
Published: July 2020

AbstractA rapid and sensitive High Performance Liquid Chromatography (HPLC) method with photometric and fluorescence detection is developed for routine analysis of 2-Keto-3-deoxy-gluconate (KDG), a catabolite product of pectin and alginate. These polysaccharides are primary-based compounds for biofuel production and for generation of high-value-added products. HPLC is performed, after derivatization of the 2-oxo-acid groups of the metabolite with o-phenylenediamine (oPD), using a linear gradient of trifluoroacetic acid and acetonitrile. Quantification is accomplished with an internal standard method. The gradient is optimized to distinguish KDG from its close structural analogues such as 5-keto-4-deoxyuronate (DKI) and 2,5-diketo-3-deoxygluconate (DKII). The proposed method is simple, highly sensitive and accurate for time course analysis of pectin or alginate degradation.HighlightsA fluorescent based-HPLC method report the quantification of KDG, a metabolite originating from alginate and from pectin degradation pathways, using derivatization with o-phenylenediamine (oPD)
Surface-associated antigen induces B-cell permeabilization and lysosome exocytosis facilitating antigen uptake and presentation to T-cells
Authors: Maeda Fernando Y. , van Haaren Jurriaan J. H. , Langley David B. , Christ Daniel , Andrews Norma W. , Song Wenxia 
Published: July 2020

AbstractB-cell receptor (BCR)-mediated antigen internalization and presentation are essential for humoral memory immune responses. Antigen encountered by B-cells is often tightly associated with the surface of pathogens and/or antigen-presenting cells. Internalization of such antigens requires myosin-mediated traction forces and extracellular release of lysosomal enzymes, but the mechanism triggering lysosomal exocytosis is unknown. Here we show that BCR-mediated recognition of antigen tethered to beads, to planar lipid-bilayers or expressed on cell surfaces causes localized plasma membrane (PM) permeabilization, a process that requires BCR signaling and non-muscle myosin II activity. B-cell permeabilization triggers PM repair responses involving lysosomal exocytosis, and B-cells permeabilized by surface-associated antigen internalize more antigen than cells that remain intact. Higher affinity antigens cause more B-cell permeabilization and lysosomal exocytosis and are more efficiently presented to T-cells. Thus, PM permeabilization by surface-associated antigen triggers a lysosome-mediated B-cell resealing response, providing the extracellular hydrolases that facilitate antigen internalization and presentation.
Mtg16-dependent repression of E protein activity is required for early lymphopoiesis
Authors: Acharya Pankaj , Sampathi Shilpa , Flaherty David K. , Matlock Brittany K. , Williams Christopher S. , Hiebert Scott W. , Stengel Kristy R. 
Published: July 2020

AbstractThe ETO/MTG family of transcriptional co-repressors play a key role in adult stem cell functions in various tissues. These factors are commonly found in complex with E proteins such as E2A, HEB, and Lyl1 as well as PRDM14 and BTB/POZ domain factors. Structural studies identified a region in the first domain of MTGs that is conserved in theDrosophilahomologue Nervy (Nervy Homology Domain-1, or NHR1) that is essential for ETO/MTG8 to inhibit E protein-dependent transcription. The Cancer Genome Atlas (TCGA) identified cancer associated single nucleotide variants (SNVs) near the MTG16:E protein contact site. We tested these SNVs using sensitive yeast two-hybrid association assays, which suggested that only P209T significantly affected E protein binding. We then used CRISPR-Cas9 and homology directed DNA repair to insert P209T and a known inactivating mutation, F210A, into NHR1 ofMtg16in the germ line of mice. These mice developed normally, but in competitive bone marrow transplantation assays, the F210A-containing stem cells failed to contribute to lymphopoiesis, while P209T mutant cells were reduced in mature T cell populations. High content fluorescent activated analytical flow cytometry assays identified a defect in the multi-potent progenitor to common lymphoid progenitor transition during lymphopoiesis. These data indicate that the cancer associated changes are likely benign polymorphisms, and the MTG:E protein association is required for lymphopoiesis, but less important for myelopoiesis and stem cell functions.
Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts
Authors: Elitzur Shir Bahiri , Cohen-Kupiec Rachel , Yacobi Dana , Fine Larissa , Apt Boaz , Diament Alon , Tuller Tamir 
Published: July 2020

AbstractThe well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between ribosomal RNA (rRNA) and mRNA. However, little is currently known about the contribution of such interactions to the rest of the translation process and to the way bacterial transcript evolve. We used novel computational analyses and modelling of 823 bacterial genomes coupled with experiments to demonstrate that rRNA-mRNA interactions are diverse and regulate not only initiation, but all translation steps from pre-initiation to termination across the many bacterial phyla that have the Shine-Dalgarno sequence. As these interactions dictate translation efficiency, they serve as a driving evolutionary force for shaping transcripts in bacteria. We observed selection for strong rRNA-mRNA interactions in regions where such interactions are likely to enhance initiation, regulate early elongation and ensure the fidelity of translation termination. We discovered selection against strong interactions and for intermediate interactions in coding regions and present evidence that these interactions maximize elongation efficiency while also enhancing initiation by ‘guiding’ free ribosomal units to the start codon.ImportancePrevious research has reported the significant influence of rRNA-mRNA interactions mainly in the initiation phase of translation. The results reported in this paper suggest that, in addition to the rRNA-mRNA interactions near the start codon that trigger initiation in bacteria, rRNA-mRNA interactions affect all sub-stages of the translation process (pre-initiation, initiation, elongation, termination). In addition, these interactions affect the way evolutionary forces shape the bacterial transcripts while considering trade-offs between the effects of different interactions across different transcript regions on translation efficacy and efficiency. Due to the centrality of the translation process, these findings are relevant to all biomedical disciplines.
Screening of Botanical Drugs Against Lassa Virus Entry
Authors: Liu Yang , Guo Jiao , Cao Junyuan , Zhang Guangshun , Jia Xiaoying , Wang Peilin , Xiao Gengfu , Wang Wei 
Published: July 2020

AbstractLassa virus (LASV) belongs to the Old WorldMammarenavirusgenus (familyArenaviridae) and is classified as a category A biological threat agent. At present, there are no approved drugs or vaccines specific for LASV. In this study, high-throughput screening of a botanical drug library was performed against LASV entry using a pseudotype virus bearing the LASV envelope glycoprotein (GPC). Two hit compounds, bergamottin and casticin, were identified as LASV entry inhibitors in the micromolar range. A mechanistic study revealed that casticin inhibited LASV entry by blocking low pH-induced membrane fusion. Adaptive mutant analyses demonstrated that the F446L mutation, located in the transmembrane domain of GP2, conferred resistance to casticin. Furthermore, casticin extended its antiviral spectrum to the New World (NW) pathogenic mammarenaviruses, and mutation of the conserved F446 conferred NW resistance to casticin. Unlike casticin, bergamottin has little effect on LASV GPC-mediated membrane fusion, while it inhibited LASV entry by blocking endocytic trafficking. Our study shows that both bergamottin and casticin are candidates for LASV therapy, indicating that the conserved F446 plays important roles in drug resistance in mammarenaviruses.IMPORTANCECurrently, there is no approved therapy to treat Lassa fever (LASF); we aimed to find candidates for LASF therapy. Herein, we screened a botanical drug library and identified two compounds, bergamottin and casticin, that inhibited LASV entry via different mechanisms.
β-Coronaviruses use lysosomal organelles for cellular egress
Authors: Ghosh S , Dellibovi-Ragheb TA , Pak E , Qiu Q , Fisher M , Takvorian PM , Bleck C , Hsu V , Fehr AR , Perlman S , Achar SR , Straus MR , Whittaker GR , de Haan CAM , Altan-Bonnet G , Altan-Bonnet N 
Published: July 2020

Abstractβ-Coronaviruses are a family of positive-strand enveloped RNA viruses that include the severe acute respiratory syndrome-CoV2 (SARS-CoV2). While much is known regarding their cellular entry and replication pathways, their mode of egress remains uncertain; however, this is assumed to be via the biosynthetic secretory pathway by analogy to other enveloped viruses. Using imaging methodologies in combination with virus-specific reporters, we demonstrate that β-Coronaviruses utilize lysosomal trafficking for egress from cells. This pathway is regulated by the Arf-like small GTPase Arl8b; thus, virus egress is insensitive to inhibitors of the biosynthetic secretory pathway. Coronavirus infection results in lysosome deacidification, inactivation of lysosomal degradation and disruption of antigen presentation pathways. This coronavirus-induced exploitation of lysosomes provides insights into the cellular and immunological abnormalities observed in patients and suggests new therapeutic modalities.
High neutralizing potency of swine glyco-humanized polyclonal antibodies against SARS-CoV-2
Authors: Vanhove Bernard , Duvaux Odile , Rousse Juliette , Royer Pierre-Joseph , Evanno Gwénaëlle , Ciron Carine , Lheriteau Elsa , Vacher Laurent , Gervois Nadine , Oger Romain , Jacques Yannick , Conchon Sophie , Salama Apolline , Duchi Roberto , Lagutina Irina , Perota Andrea , Delahaut Philippe , Ledure Matthieu , Paulus Melody , So Ray T. , Mok Chris Ka-Pun , Bruzzone Roberto , Bouillet Marc , Brouard Sophie , Cozzi Emanuele , Galli Cesare , Blanchard Dominique , Bach Jean-Marie , Soulillou Jean-Paul 
Published: July 2020

AbstractPerfusion of convalescent plasma (CP) has demonstrated a potential to improve the pneumonia induced by SARS-CoV-2, but procurement and standardization of CP are barriers to its wide usage. Many monoclonal antibodies (mAbs) have been developed but appear insufficient to neutralize SARS-CoV-2 unless two or three of them are being combined. Therefore, heterologous polyclonal antibodies of animal origin, that have been used for decades to fight against infectious agents might represent a highly efficient alternative to the use of CP or mAbs in COVID-19 by targeting multiple antigen epitopes. However, conventional heterologous polyclonal antibodies trigger human natural xenogeneic antibody responses particularly directed against animal-type carbohydrate epitopes, mainly the N-glycolyl form of the neuraminic acid (Neu5Gc) and the Gal α1,3-galactose (αGal), ultimately forming immune complexes and potentially leading to serum sickness or allergy. To circumvent these drawbacks, we engineered animals lacking the genes coding for the cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) and α1,3-galactosyl-transferase (GGTA1) enzymes to produce glyco-humanized polyclonal antibodies (GH-pAb) lacking Neu5Gc and α-Gal epitopes. We found that pig IgG Fc domains fail to interact with human Fc receptors and thereby should confer the safety advantage to avoiding macrophage dependent exacerbated inflammatory responses, a drawback possibly associated with antibody responses against SARS-CoV-2 or to avoiding a possible antibody-dependent enhancement (ADE). Therefore, we immunized CMAH/GGTA1 double knockout (DKO) pigs with the SARS-CoV-2 spike receptor-binding domain (RBD) to elicit neutralizing antibodies. Animals rapidly developed a hyperimmune response with anti-SARS-CoV-2 end-titers binding dilutions over one to a million and end-titers neutralizing dilutions of 1:10,000. The IgG fraction purified and formulated following clinical Good Manufacturing Practices, named XAV-19, neutralized Spike/angiotensin converting enzyme-2 (ACE-2) interaction at a concentration < 1μg/mL and inhibited infection of human cells by SARS-CoV-2 in cytopathic assays. These data and the accumulating safety advantages of using glyco-humanized swine antibodies in humans warranted clinical assessment of XAV-19 to fight against COVID-19.