bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems-level investigation of mucopolysaccharidosis IIIA identifies deficient synaptic activity as a key driver of disease progression
Authors: Douek Alon M , Salavaty Abbas , Kreuder Florian , Stamatis Sebastian-Alexander , Steele Joel R , Hanchapola Iresha , Shah Anup D , Schittenhelm Ralf B , Ramialison Mirana , Currie Peter D , Kaslin Jan 
Published: October 2022

AbstractMucopolysaccharidoses are lysosomal storage diseases that collectively represent a major cause of lethal, treatment-refractory childhood dementias 1–7 Clinically-useful interventions are hampered due to an incomplete understanding of their neuropathological origins. Using the zebrafish sgsh model of mucopolysaccharidosis IIIA 8 (MPS IIIA, Sanfilippo syndrome A), we conducted several ‘omics-based analyses, and developed and benchmarked a novel bioinformatic feature classification and ranking model for high-throughput datasets – ExIR – to prioritise important features in the progression of neurological manifestations of the disease. We find that the massive endolysosomal burden resulting from increased lysosomal storage of heparan sulfate and other secondarily accumulating substrates, such as sphingolipids, induces abnormal microtubule organisation and vesicle trafficking in neurons. This results in a gradual impairment of synaptic vesicle localisation at the presynaptic terminal and consequently impaired neuronal activity. Importantly, the endolysosomal phenotype in MPS IIIA zebrafish well-precedes the onset of neural pathology, though the larval MPS IIIA brain was found to be more susceptible to perturbation than wild type siblings. Collectively, these analyses demonstrate the presence of a progressive ‘functional neurodegenerative’ phenotype underpinning neurological disease in MPS IIIA. Our findings provide direct mechanistic evidence linking the well-described lysosomal storage basis for MPS IIIA to its disproportionately severe neural clinical involvement, enabling development and refinement of future therapeutic interventions for this currently untreatable disorder.HighlightsMPS IIIA represents one of the most common causes of broadly fatal childhood dementia, but the mechanisms underlying disease progression are poorly understood.The first systems-level analyses of disease state and progression in the CNS of an MPS IIIA animal model were performed.Experimental data-based Integrative Ranking (ExIR) was developed to provide unbiased prioritisation and classification of biological data as drivers, biomarkers and mediators of biological processes from high-throughput data at a systems level.Application of ExIR to a transcriptomic and proteomic analyses of a zebrafish model of MPS IIIA implies progressive deficiencies in synaptic activity as a key driver of disease progression correlating with progressive neuronal endolysosomal burden and secondary storage diseases.A novel unifying explanation of pathobiology and progression of MPS IIIA facilitates identification of clinically targetable features and may be generalised to other neuronopathic storage disorders.
Inhibition of CHK2 dependent DNA damage response suppresses Zika virus infection through a STING dependent mechanism
Authors: Ma Huailiang , Li Chunfeng , Wang Yanli , Valore Erika V. , Trisal Meera , Hui Harold Sai-yin , Hakimpour Paul , Bowen James R. , Mak Tak W , Suthar Mehul S. , Pulendran Bali 
Published: October 2022

ABSTRACTZika virus (ZIKV) is a mosquito-borne flavivirus that causes neurological disorders and microcephaly. Recent research has shown that ZIKV causes cell cycle arrest and DNA damage response in neuronal progenitor cells that potentially leads to congenital neurodevelopmental defects. However, the specific role of regulators that control DNA damage response to ZIKV infection and the related mechanisms remain largely unknown. Here through bothin vitroandin vivostudies, we observe that ZIKV induces DNA damage response in both human cell line and mouse embryo. When CHK2 dependent DNA damage response pathway is inhibited by a small molecule inhibitor or genetic deletion, ZIKV production is reduced and the embryonic developmental defects are rescued. Furthermore, we demonstrate that in ZIKV infectedChk2-/-mice, the reduced viral load correlates with elevated antiviral innate immune response which is found to be dependent on the STING signaling pathway. Collectively, our study reveals a specific role of CHK2 for ZIKV infection and pathogenesis, demonstrating a mechanism that inhibition of the CHK2 axis suppresses ZIKV infection through the STING-dependent antiviral pathway, thus providing a new therapeutic strategy against ZIKV. These findings also suggest the intriguing possibility that ZIKV evolved to orchestrate DNA damage response factors to create a beneficial environment for its infection in the host cells.
Raman microspectroscopy reveals unsaturation heterogeneity at the lipid droplet level and validates anin vitromodel of bone marrow adipocyte subtypes
Authors: Tratwal Josefine , Falgayrac Guillaume , During Alexandrine , Bertheaume Nicolas , Bataclan Charles , Tavakol Daniel N. , Campos Vasco , Duponchel Ludovic , Daley George Q. , Penel Guillaume , Chauveau Christophe , Naveiras Olaia 
Published: October 2022

AbstractBone marrow adipocytes (BMAds) constitute the most abundant stromal component of adult human bone marrow. Two subtypes of BMAds have been described, the more labile regulated adipocytes (rBMAds) and the more stable constitutive adipocytes (cBMAds), which develop earlier and are more resilient to environmental and metabolic disruptions.In vivo, rBMAds are enriched in saturated fatty acids, contain smaller lipid droplets (LDs) and more readily provide hematopoietic support than their cBMAd counterparts. Mouse models have been used for BMAds research, but isolation of primary BMAds presents many challenges, and thusin vitromodels remain the current standard to study nuances of adipocyte differentiation. Noin vitromodel has yet been described for the study of rBMAds/cBMAds.Here, we present anin vitromodel of BM adipogenesis with differential rBMAd and cBMAd-like characteristics. We used OP9 BM stromal cells derived from a (C57BL/6xC3H)F2-op/op mouse, which have been extensively characterized as feeder layer for hematopoiesis research. We observed similar canonical adipogenesis transcriptional signatures for spontaneously-differentiated (sOP9) and induced (iOP9) cultures, while fatty acid composition and desaturase expression ofScd1andFads2differed at the population level. To resolve differences at the single adipocyte level we tested Raman microspectroscopy and show it constitutes a high-resolution method for studying adipogenesisin vitroin a label-free manner, with resolution to individual LDs. We found sOP9 adipocytes have lower unsaturation ratios, smaller LDs and higher hematopoietic support than iOP9 adipocytes, thus functionally resembling rBMAds, while iOP9 more closely resembled cBMAds. Validation in human primary samples confirmed a higher unsaturation ratio for lipids extracted from stable cBMAd-rich sites (femoral head upon hip-replacement surgery) versus labile rBMAds (iliac crest after chemotherapy). As a result, the 16:1/16:0 fatty acid unsaturation ratio, which was already shown to discriminate BMAd subtypes in rabbit and rat marrow, was validated to discriminate cBMAds from rBMAd in both the OP9 modelin vitrosystem and in human samples. We expect our model will be useful for cBMAd and rBMAd studies, particularly where isolation of primary BMAds is a limiting step.
Atypical peripheral actin band formation via overactivation of RhoA and Non-muscle myosin II in Mitofusin 2 deficient cells
Authors: Wang Yueyang , Troughton Lee D. , Xu Fan , Chatterjee Aritra , Zhao Han , Cifuentes Laura P. , Wagner Ryan B. , Chen Jingjuan , Kuang Shihuan , Suter Daniel M. , Yuan Chongli , Chan Deva , Huang Fang , Oakes Patrick W. , Deng Qing 
Published: October 2022

AbstractCell spreading and migration play central roles in many physiological and pathophysiological processes. We have previously shown that MFN2 regulates the migration of human neutrophillike cells via suppressing Rac activation. Here, we show that in mouse embryonic fibroblasts, MFN2 suppresses RhoA activation and supports cell polarization. After the initial spreading period, the wild-type cells polarize and migrate, whereas the Mfn2-/- cells maintain a circular shape. Increased cytosolic Ca2+ resulting from the loss of Mfn2 is directly responsible for this phenotype, which can be rescued by expressing an artificial tether to bring mitochondria and ER to close vicinity. Elevated cytosolic Ca2+ activates Ca2+/calmodulin-dependent protein kinase II, RhoA, and Myosin light-chain kinase, causing an over-activation of non-muscle myosin II and a formation of a prominent F-actin ring at the cell periphery and increased cell contractility. The formation of the peripheral actin band alters cell physics and is dependent on substrate rigidity.Our results provide a novel molecular basis to understand how MFN2 regulates distinct signaling pathways in different cells and tissue environments, which is instrumental in understanding and treating MFN2-related diseases.
Ni(II) binding affinity and specificity of solute binding proteins: the importance of the double His motif and variable loop revealed by structural and mutational studies
Authors: Diep Patrick , Stogios Peter J. , Evdokimova Elena , Savchenko Alexei , Mahadevan Radhakrishnan , Yakunin Alexander F. 
Published: October 2022

AbstractExtracytoplasmic solute binding proteins (SBPs) are molecular shuttles involved in the cellular uptake of various small molecules and metal ions including Ni(II). Our previous study with the Ni(II) binding proteins (NiBPs) CjNikZ from Campylobacter jejuni and CcNikZ-II from Clostridium carboxidivorans demonstrated they were able to bind Ni(II) at low micromolar affinity without the need for additional chelators. Here, we determined the crystal structure of apo CcNikZ-II, which revealed a Ni(II) binding site comprised of the highly conserved double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Alanine scanning mutagenesis of the CcNikZ-II Ni(II) binding site identified Glu60 and His511 as essential for high affinity binding to Ni(II). Phylogenetic analysis of >4000 SBP sequences demonstrated the presence of two clusters of proteins containing the HH-prong with CcNikZ-II and CjNikZ. To provide insights into the role of the double His-prong and v-loop sequence in Ni(II) binding of NiBPs, nine purified CcNikZ-II homologues containing the HH-prong and v-loop were screened using an automated screening workflow. Metal binding assays with purified homologous NiBPs revealed high Ni(II) binding affinity without requirement for chelators indicating that the double His prong represents a signature motif for the presence of Ni(II) binding activity in SBPs. The engineered CcNikZ-II variants with the wild type v-loop (TEDKYT) replaced with v-loops from NiBPs with higher affinity showed up to an order of magnitude higher affinity for Ni(II). In addition, the v-loop appears to play a role in metal ion specificity as purified wild type and engineered NiBPs with different v-loop sequences showed distinct metal profiles. This work paves way for metalloprotein engineering of NiBPs towards biocatalytic and metal recovery applications.
The Ketogenic Diet Metabolite β-Hydroxybutyrate Promotes Mitochondrial Elongation via Deacetylation and Improves Autism-like Behavior in Zebrafish
Authors: Uddin Golam M. , Lacroix Rachel , Zaman Mashiat , Khatib Iman Al , Rho Jong M. , Kurrasch Deborah M. , Shutt Timothy E. 
Published: October 2022

AbstractThe ketogenic diet (KD) is clinically beneficial and has therapeutic potential access a growing list of neurological disorders, including autism spectrum disorder (ASD). However, the underlying mechanisms mediating the benefits of the KD, which can also have undesirable side effects, remain undefined. To this end, improvements in mitochondrial morphology and function correlate with improved ASD behaviours in response to the KD, though how the KD influences mitochondrial morphology, and whether this is sufficient to improve behaviour remains unknown. Here, we investigate how beta-hydroxybutyrate (βHB), a key metabolite produced by the KD regulates mitochondrial morphology, and whether this pathway could be exploited to improve ASD behaviours. We found that β-oxidation of ΒHB promotes mitochondrial elongation by increasing NAD+ levels, which in turn activates SIRT deacetylases that act on key regulators of both mitochondrial fusion and fission. Our data suggest that increasing NAD+ levels with its precursor, nicotinamide nucleotide (NMN), is sufficient to promote mitochondrial hyperfusion. Finally, both ΒHB and NMN improve locomotor behaviour in the shank3+/- zebrafish model of ASD. Together, our findings elucidate a mechanism by which the ketogenic diet promotes mitochondrial elongation. Moreover, manipulation of this pathway may provide a novel avenue for the treatment of neurological disorders such as ASD, one which may obviate potential complications of the KD in clinical practice.
Arterial cells support the development of human hematopoietic progenitors in vitro via secretion of IGFBP2
Authors: Petazzi Paolo , Ventura Telma , Luongo Francesca Paola , May Alisha , Taylor Helen Alice , Romanò Nicola , Forrester Lesley M. , Menéndez Pablo , Fidanza Antonella 
Published: October 2022

AbstractHematopoietic stem and progenitor cells develop from the hemogenic endothelium located in various sites during development, including the dorsal aorta from where Hematopoietic Stem Cells (HSCs) emerge. This process has proven especially challenging to recapitulate in vitro from pluripotent stem cells and further studies are needed to pinpoint the missing stimuli in vitro. Here, we compared iPSC-derived endothelial cells and in vivo HSC-primed hemogenic endothelium and identified 9 transcription factors expressed at significantly lower levels in cells generated in vitro. Using a novel DOX-inducible CRISPR activation system we induced the expression of those genes during in vitro differentiation. To study the phenotypical changes induced by the activation of target genes, we employed single cell RNA sequencing in combination with engineered gRNA that are detectable within the sequencing pipeline. Our data showed a significant expansion of arterial-fated endothelial cells associated with a higher in vitro progenitor activity. The expanded arterial cluster was marked by high expression of IGFBP2 and it was distinct from the hemogenic cluster that showed increased cell cycle progression. We demonstrated that the addition of IGFBP2 to differentiating PSCs resulted in a higher number of functional progenitors, identifying the supporting role of arterial cells play to the emergence of blood progenitors via IGFBP2 paracrine signalling.
Relevance of the viral Spike protein/cellular Estrogen Receptor-α interaction for endothelial-based coagulopathy induced by SARS-CoV-2
Authors: Barbieri Silvia , Cattani Franca , Sandrini Leonardo , Grillo Magda Maria , Talarico Carmine , Iaconis Daniela , Lione Lucia , Salvatori Erika , Amadio Patrizia , Garoffolo Gloria , Maffei Mariano , Galli Francesca , Beccari Andrea Rosario , Marra Emanuele , Zoppi Marica , Michaelides Michael , Roscilli Giuseppe , Aurisicchio Luigi , Bertini Riccardo , Allegretti Marcello , Pesce Maurizio 
Published: October 2022

AbstractSevere coagulopathy has been observed at the level of the microcirculation in several organs including lungs, heart and kidneys in patients with COVID-19, and in a minority of subjects receiving the SARS-CoV-2 vaccine. Various mechanisms have been implicated in these effects, including increases in circulating neutrophil extracellular traps, excessive inflammation, and endothelial dysfunction. Even if a correlation between infection by SARS-CoV-2 and upregulation of coagulation cascade components has been established in the lung, no direct proofs have been yet provided about the transcriptional machinery controlling the expression of these factors. Recent results obtained by us reported a novel transcriptional function of the SARS-CoV-2 Spike (S) viral protein involving a direct protein-protein interaction with the human Estrogen Receptor-α (ERα). Given the implications of ERα in the control of key effectors in the coagulation cascade, we hypothesized that S-protein might increase the pro-coagulation activity of endothelial cells via the transcriptional activity of the ERα, thus justifying the enhanced risk of thrombosis. To assess this, we tested the effects of S-protein on the expression of Tissue Factor (TF) and the overall procoagulation activity in a human endothelial cell line and confirmed this finding by overexpressing S-protein by gene transfer in mice. We then designed and tested two-point mutations in the S2 S-protein sequence that abolished the pro-coagulation function of S-protein in vitro and in vivo, without compromising its immunogenicity. In addition to reveal a new potential transcriptional function of S-protein, these results inspire the design of new vaccines with lower risk of thrombogenesis. Indeed, while the benefit/risk ratio remains overwhelming in favor of COVID-19 vaccination, our results shed light on the causal mechanisms of some rare anti-SARS-CoV-2 vaccine adverse events, and are thus essential for current and future vaccination and booster campaigns.
A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8
Authors: Rodriguez-Rodriguez Bruno A. , Ciabattoni Grace O. , Duerr Ralf , Valero-Jimenez Ana M , Yeung Stephen T. , Crosse Keaton M. , Schinlever Austin R. , Bernard-Raichon Lucie , Rodriguez-Galvan Joaquin J. , McGrath Marisa E. , Vashee Sanjay , Xue Yong , Loomis Cynthia , Khanna Kamal M. , Cadwell Kenneth , Desvignes Ludovic , Frieman Matthew F. , Ortigoza Mila B , Dittmann Meike 
Published: October 2022

AbstractSmall animal models have been a challenge for the study of SARS-CoV-2 transmission, with most investigators using golden hamsters or ferrets1, 2. Mice have the advantages of low cost, wide availability, less regulatory and husbandry challenges, and the existence of a versatile reagent and genetic toolbox. However, adult mice do not robustly transmit SARS-CoV-23. Here we establish a model based on neonatal mice that allows for transmission of clinical SARS-CoV-2 isolates. We characterize tropism, respiratory tract replication and transmission of ancestral WA-1 compared to variants Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Omicron BA.1 and Omicron BQ.1.1. We identify inter-variant differences in timing and magnitude of infectious particle shedding from index mice, both of which shape transmission to contact mice. Furthermore, we characterize two recombinant SARS-CoV-2 lacking either the ORF6 or ORF8 host antagonists. The removal of ORF8 shifts viral replication towards the lower respiratory tract, resulting in significantly delayed and reduced transmission in our model. Our results demonstrate the potential of our neonatal mouse model to characterize viral and host determinants of SARS-CoV-2 transmission, while revealing for the first time a role for an accessory protein in this context.
Equivalent excitability through different sodium channels and implications for the analgesic efficacy of selective drugs
Authors: Xie Yu-Feng , Yang Jane , Ratté Stéphanie , Prescott Steven A. 
Published: October 2022

ABSTRACTNociceptive sensory neurons convey pain-related signals to the CNS using action potentials. Loss-of-function mutations in the voltage-gated sodium channel NaV1.7 cause insensitivity to pain (presumably by reducing nociceptor excitability) but efforts to treat pain by inhibiting NaV1.7 pharmacologically have largely failed. This may reflect the variable contribution of NaV1.7 to nociceptor excitability. Contrary to claims that NaV1.7 is necessary for nociceptors to initiate action potentials, we show that nociceptors can achieve equivalent excitability using different combinations of NaV1.3, NaV1.7, and NaV1.8. Selectively blocking one of those NaVsubtypes reduces nociceptor excitability only if the other two subtypes are weakly expressed. For example, excitability relies on NaV1.8 in acutely dissociated nociceptors but responsibility shifts to NaV1.7 and NaV1.3 by the fourth day in culture. A similar shift in NaVdependence occurs in vivo after inflammation, impacting ability of the NaV1.7-selective inhibitor PF-05089771 to reduce pain in behavioral tests. Flexible use of different NaVsubtypes exemplifies degeneracy – equivalent function using different components – and compromises the reliable modulation of nociceptor excitability by subtype-selective inhibitors. Identifying the dominant NaVsubtype to predict drug efficacy is not trivial. Degeneracy at the cellular level must be considered when choosing drug targets at the molecular level.SIGNIFICANCE STATEMENTNociceptors can achieve equivalent excitability using different sodium channel subtypes. The analgesic efficacy of subtype-selective drugs hinges on which subtype controls excitability. This contingency likely contributes to poor clinical outcomes.
Broad Brain Networks Support Curiosity-Motivated Incidental Learning Of Naturalistic Dynamic Stimuli With And Without Monetary Incentives
Authors: Meliss Stefanie , van Reekum Carien , Murayama Kou 
Published: October 2022

AbstractCuriosity – the intrinsic desire to know – is a concept central to the human mind and knowledge acquisition. Experimental studies on information-seeking have found that curiosity facilitates memory encoding and exhibits similar reward,ng properties as extrinsic rewards/incentives by eliciting a dopaminergic response. However, it is not clear whether these findings hold with more naturalistic dynamic stimuli and how the joint effect of curiosity and extrinsic incentive manifests in learning and neural activation patterns. Herein, we presented participants with videos of magic tricks across two behavioural (N1 = 77, N2 = 78) and one fMRI study (N = 50) and asked them to rate subjective feelings of curiosity, while also performing a judgement task that was incentivised for the half of participants. Incidental memory for the magic trick was tested a week later. The integrated results showed that both curiosity and availability of extrinsic incentives enhanced encoding but did not interact with each other. However, exploratory analyses showed that curiosity and monetary incentives were associated with recollection and familiarity differently, suggesting the involvement of different encoding mechanisms. Analysis of the fMRI data using the intersubject synchronisation framework showed that, while the effects of curiosity on memory were located in the hippocampus and dopaminergic brain areas, neither the effects of curiosity nor incentives themselves were found in the often-implicated reward network, but instead were associated with cortical areas involved in processing uncertainly and attention. These results suggest that curiosity recruits broader brain networks than what was implicated in the previous literature when investigated with dynamic stimuli.