bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases
Authors: Weisburd Ben , Dolzhenko Egor , Bennett Mark F. , Danzi Matt C. , English Adam , Hiatt Laurel , Tanudisastro Hope , Kurtas Nehir Edibe , Jam Helyaneh Ziaei , Brand Harrison , Sedlazeck Fritz J. , Gymrek Melissa , Dashnow Harriet , Eberle Michael A. , Rehm Heidi L. 
Published: October 2024

AbstractTandem repeat (TR) catalogs are important components of repeat genotyping studies as they define the genomic coordinates and expected motifs of all TR loci being analyzed. In recent years, genome-wide studies have used catalogs ranging in size from fewer than 200,000 to over 7 million loci. Where these catalogs overlapped, they often disagreed on locus boundaries, hindering the comparison and reuse of results across studies. Now, with multiple groups developing public databases of TR variation in large population cohorts, there is a risk that, without sufficient consensus in the choice of locus definitions, the use of divergent repeat catalogs will lead to confusion, fragmentation, and incompatibility across future resources.In this paper, we compare existing TR catalogs and discuss desirable features of a comprehensive genome-wide catalog. We then present a new, richly annotated catalog designed for large-scale analyses and population databases. Our catalog stratifies TRs into two groups: 1) isolated TRs suitable for repeat copy number analysis using short read or long read data and 2) so-called variation clusters that contain TRs within wider polymorphic regions that are best studied through sequence-level analysis. To define variation clusters, we present a novel algorithm that leverages long-read HiFi sequencing data to group repeats with surrounding polymorphisms. We show that the human genome contains at least 25,000 complex variation clusters, most of which span over 120 bp and contain five or more TRs. Resolving the sequence of entire variation clusters instead of individually genotyping constituent TRs leads to a more accurate analysis of these regions and enables us to profile variation that would have been missed otherwise.
Suppression of NRF2-dependent cancer growth by a covalent allosteric molecular glue
Authors: Roy Nilotpal , Wyseure Tine , Lo I-Chung , Metzger Justine , Eissler Christie L. , Bernard Steffen M. , Bok Ilah , Snead Aaron N. , Parker Albert , Green Jason C. , Inloes Jordon , Jacinto Sarah R. , Kuenzi Brent , Horning Benjamin D. , Ibrahim Noah , Grabow Stephanie , Panda Harit , Bhatt Dhaval P. , Saeidi Soma , Zolkind Paul , Rush Zoe , Negri Kathleen , Williams Heather N. , Walton Eric , Pastuszka Martha K. , Sigler John J. , Tran Eileen , Hee Kenneth , McLaughlin Joseph , Ambrus-Aikelin Géza , Pollock Jonathan , Abraham Robert T. , Kinsella Todd M. , Simon Gabriel M. , Major Michael B. , Weinstein David S. , Patricelli Matthew P. 
Published: October 2024

AbstractThe NRF2 transcription factor is constitutively active in cancer where it functions to maintain oxidative homeostasis and reprogram cellular metabolism. NRF2-active tumors exhibit NRF2-dependency and resistance to chemo/radiotherapy. Here we characterize VVD-065, a first-in-class NRF2 inhibitor that acts via an unprecedented allosteric molecular glue mechanism. In the absence of stress or mutation, NRF2 is rapidly degraded by the KEAP1-CUL3 ubiquitin-ligase complex. VVD-065 specifically and covalently engages C151 on KEAP1, which in turn promotes KEAP1-CUL3 complex formation, leading to enhancement of NRF2 degradation. Previously reported C151-directed compounds decrease KEAP1-CUL3 interactions and stabilize NRF2, thus establishing KEAP1_C151 as a tunable regulator of the KEAP1-CUL3 complex and NRF2 stability. VVD-065 inhibited NRF2-dependent tumor growth and sensitized cancers to chemo/radiotherapy, supporting an open Phase I clinical trial (NCT05954312).
Human gray matter microstructure mapped using Neurite Exchange Imaging (NEXI) on a clinical scanner
Authors: Uhl Quentin , Pavan Tommaso , Feiweier Thorsten , Piredda Gian Franco , Jelescu Ileana 
Published: October 2024

AbstractBiophysical models of diffusion in gray matter (GM) can provide unique information about microstructure of the human brain, in health and disease. Therefore, their compatibility with clinical settings is key. Neurite Exchange Imaging (NEXI) is a two-compartment model of GM microstructure that accounts for inter-compartment exchange, whose parameter estimation requires multi-shell multi-diffusion time data. In this work, we report the first estimates of NEXI in human cortex obtained on a clinical MRI scanner. To do that, we establish an acquisition protocol and fitting routine compatible with clinical scanners.The model signal equation can be expressed either in the narrow-pulse approximation, NEXINPA, or accounting for the actual width of the diffusion gradient pulses, NEXIWP. While NEXINPAenables a faster analytical fit and is a valid approximation for data acquired on high-performance gradient systems (preclinical and Connectom scanners), on which NEXI was first implemented, NEXIWPhas significant relevance for data acquired on clinical scanners with longer gradient pulses. We establish that, in the context of broad pulses, NEXIWPestimates were more comparable to previous literature values.Furthermore, we evaluate the repeatability of NEXI estimates in the human cortex on a clinical MRI scanner and show intra-subject variability to be lower than inter-subject variability, which is promising for characterizing healthy and patient cohorts.Finally, we analyze the relationship of NEXI parameters on the cortical surface to the Myelin Water Fraction (MWF), estimated using an established multicomponent T2relaxation technique. Indeed, although it is present in small quantities in the cortex, myelin can be expected to decrease permeability. We confirm a strong correlation between the exchange time (tex) estimates and the MWF, although the spatial correspondence between the two is brain-region specific and other drivers oftexthan myelin density are likely at play.
Temperature-induced membrane trafficking drives antibody delivery to the brain
Authors: Du Fusheng , Wan Qi , Glebov Oleg O. 
Published: October 2024

AbstractDespite quotidian occurrence of fever and hyperthermia, cell biological mechanisms underlying their effects remain unclear. Neurological complications of severe (>40°C) fever have been associated with increased blood-brain barrier (BBB) permeability due to structural disruption, while little is known about brain physiology of moderate fever. Here, we show that a temperature increase to 39-40°C increased fluid-phase uptake in PC12 cells and primary neurons. Uptake of selective cargoes showed that clathrin-mediated endocytosis and macropinocytosis were induced in a translation-dependent manner, consistent with a role for heat shock response. Exocytic recycling was also increased by hyperthermia, suggesting a comprehensive boost of membrane trafficking. Mild (<39°C) whole-body hyperthermiain vivotriggered fluid-phase uptake in various organs, notably enabling brain accumulation of an intravenously injected antibody that was blocked by dynamin inhibition. Taken together, our findings show that fever systemically regulates membrane trafficking, reveal dynamin-dependent endocytosis as a cell biological mechanism for temperature control of BBB permeability, and demonstrate a clinical potential of mild hyperthermia for facilitating brain delivery of biologic drugs.HighlightsTemperature increase of 2-3°C upregulates endocytosis and exocytosisTemperature-induced upregulation of membrane trafficking requires protein translation and dynamin functionMild whole-body hyperthermia enhances fluid-phase endocytosis across the bodyMild hyperthermia enables delivery of an exogenous antibody from the bloodstream into the brain through a dynamin-dependent pathway
Structural Basis for the Improved RNA-Clamping of Amidino-Rocaglates to eIF4A1
Authors: Conley James F. , Brown Lauren E. , McNeely James H. , Pelletier Jerry , Porco John A. , Allen Karen N. 
Published: October 2024

AbstractEukaryotic Initiation Factor 4A-1 (eIF4A1) is an ATP-dependent RNA helicase that unwinds 5’-UTR mRNA secondary structures to facilitate cap-dependent translation initiation. Rocaglates, a class of natural products typified by rocaglamide A (RocA), possess anti-neoplastic and anti-infectious activity mediated by their interaction with eIF4A1. Rocaglates inhibit cap-dependent translation initiation by “clamping” eIF4A1 onto polypurine RNA, impeding ribosome scanning. A novel class of rocaglate derivatives, amidino-rocaglates (ADRs) which feature an amidine ring fused to the rocaglate core, are particularly effective at promoting eIF4A1-RNA-clamping compared to other rocaglate congeners. Herein, we present the X-ray crystal structure of an ADR in complex with eIF4A1, the nonhydrolyzable ATP ground-state mimic adenylyl-imidodiphosphate (AMPPNP), and poly r(AG)5RNA refined to 1.69 Å resolution. The binding pose and interactions of the ADR with eIF4A1 do not differ substantially from those of RocA, prompting investigation of the basis for enhanced target engagement. Computational modeling suggests that the rigidified ADR scaffold is inherently preorganized in an eIF4A1-RNA-binding-competent conformation, thereby avoiding entropic penalties associated with RocA binding. This study illustrates how conformational rigidification of the rocaglate scaffold can be leveraged to improve potency for the development of rocaglates as potential anticancer and anti-infectious agents.Abstract Figure
Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution
Authors: Borthakur Kaushik , Sisk Thomas R. , Panei Francesco P. , Bonomi Massimiliano , Robustelli Paul 
Published: October 2024

AbstractDetermining accurate atomic resolution conformational ensembles of intrinsically disordered proteins (IDPs) is extremely challenging. Molecular dynamics (MD) simulations provide atomistic conformational ensembles of IDPs, but their accuracy is highly dependent on the quality of physical models, or force fields, used. Here, we demonstrate how to determine accurate atomic resolution conformational ensembles of IDPs by integrating all-atom MD simulations with experimental data from nuclear magnetic resonance (NMR) spectroscopy and small-angle x-ray scattering (SAXS) with a simple, robust and fully automated maximum entropy reweighting procedure. We demonstrate that when this approach is applied with sufficient experimental data, IDP ensembles derived from different MD force fields converge to highly similar conformational distributions. The maximum entropy reweighting procedure presented here facilitates the integration of MD simulations with extensive experimental datasets and enables the calculation of accurate, force-field independent atomic resolution conformational ensembles of IDPs.
Siglec-F Deficiency Prevents Fibrosis After Bleomycin-Induced Acute Lung Injury
Authors: Orlov Marika , Rangarajan Sunad , Jaramillo Ana M. , Ye Qihua , Hara Naoko , Ngo Kenny , NeeDell James C. , Harder Anna Q. , Jia Fan , Vestal Brian , Blumhagen Rachel Z. , Tu Ting-Hui , McClendon Jazalle , McCubbrey Alexandra L. , Smith Bradford J. , Schwartz David A. , Janssen William J. , Evans Christopher M. 
Published: October 2024

AbstractInjury to the lungs causes acute inflammation that can lead to pathological lung fibrosis. Airspace macrophages (AMs) are critical for repair of injured tissue, but they can contribute fibrosis through mechanisms that are incompletely understood. Siglecs are expressed by immune cells. In mice, Siglec-F is chiefly expressed AMs where it is considered inflammosuppressive. We hypothesized that its deletion would worsen lung injury and fibrosis in response to intratracheal bleomycin challenge. We evaluated Siglec-F expression and function in mice challenged with bleomycin on days 7, 14, and 21 post-challenge (2.5 U/kg). AMs were the predominant inflammatory cells at all timepoints, and they included resident (RAM) and recruited (RecAM) subsets. Siglec-F deficiency prevented fibrosis than in Siglecf−/− mouse lungs, as evident from biochemical and histologic readouts. We performed RNAseq on pooled RAMs and RecAMs from wild type and Siglec-F deficient mice. Lung fibrosis 21 d after bleomycin challenge was associated with differentially expressed genes (DEGs) related to cholesterol synthesis and metabolism. In AMs from healthy lung lavage fluid and idiopathic pulmonary fibrosis patient tissues, the human paralogs Siglec-7 and Siglec-9 were expressed. Findings here identify novel mechanisms that control protective and detrimental functions of AMs after lung injury.
Transport and InsP8 activation mechanisms of the human inorganic phosphate exporter XPR1
Authors: Zhu Qinyu , Yaggi Madeleine F. , Jork Nikolaus , Jessen Henning J. , Diver Melinda M. 
Published: October 2024

SummaryInorganic phosphate (Pi) has essential metabolic and structural roles in living organisms. The Pi exporter, XPR1/SLC53A1, is critical for maintaining cellular Pi homeostasis. When intercellular Pi is high, cells synthesize inositol pyrophosphate (1,5-InsP8) – a signaling molecule that is required for XPR1 function. Inactivating mutations of XPR1 lead to brain calcifications causing neurological symptoms that include migraine, movements disorders, psychosis, and dementia. Distinct cryo-electron microscopy structures of dimeric XPR1 and functional characterization define the substrate translocation pathway and delineate how binding of InsP8initiates the transport cycle. InsP8binding rigidifies the intracellular SPX domains with InsP8acting as a bridge between dimers and the SPX and transmembrane domains. When locked in this state, the C-terminal tail is sequestered revealing the entrance to the transport pathway, thus explaining the obligate roles of the SPX domain and InsP8. Together, these findings advance our understanding of XPR1 transport activity and expand opportunities for rationalizing disease mechanisms and therapeutic intervention.
Stretch-induced recruitment of myosin into transversal actin rings stabilizes axonal large cargo transport
Authors: Rahman Nizhum , Oelz Dietmar B. 
Published: October 2024

AbstractWe study the axonal transport of large cargo vesicles and its feedback with contractile transversal actomyosin rings in axons through modelling and simulation. To this end, we simulate a mathematical model that integrates forces generated by the molecular motors and forces exerted by transversal actin rings. Our results predict that cargo vesicles exhibit bidirectional movement along with pauses in agreement with observations. It has been observed that during predominantly retrograde axonal cargo transport, blebbistatin treatment prolongs the periods spent by the cargo in anterograde transport. Our simulations show that this can be explained by mechanotransductive stretch-induced recruitment of myosin motors into transversal actin rings. These findings offer valuable insights into the complex dynamics of axonal cargo transport and propose potential avenues for further experimental research.
Comprehensive sequencing of the lung neuroimmune landscape in response to asthmatic induction
Authors: McSwiggin Hayden , Wang Rui , Magalhães Rubens Daniel Miserani , Zhu Fengli , Doherty Taylor A. , Yan Wei , Jendzjowsky Nicholas 
Published: October 2024

AbstractEvidence demonstrates that sensory neurons respond to pathogenic/allergic infiltration and mediate immune responses, forming an integral part of host defense that become hypersensitized during allergy. Our objective was to investigate how asthmatic induction alters the pulmonary neuroimmune transcriptome. We hypothesized that asthmatic induction would upregulate genes in the vagal ganglia (nodose/jugular ganglia), which would be associated with asthmatic immunity, and that these would be clustered, primarily in nodose neurons. Furthermore, lungs would increase transcripts associated with nerve activation, and these would be centered in neural and neuroendocrine-like cells. Bulk RNA-seq revealed that genes related to allergen sensing were increased in asthmatic ganglia nodose/jugular ganglia compared to control ganglia. These genes were associated with nodose clusters as shown by single-nucleus RNA sequencing, and a distinct caudal-to-rostral spatial arrangement was presented as delineated by spatial transcriptomics. The distinct clusters closely match previous identification of nodose neuron clusters. Correspondingly, the lung transcriptome was altered with asthmatic induction such that transcripts associated with neural excitation were upregulated. The spatial distribution of these transcripts was revealed by spatial transcriptomics to illustrate that these were expressed in neuroendocrine-like cells/club cells, and neurons. These results show that the neuroimmune transcriptome is altered in response to asthmatic induction in a cell cluster and spatially distinct manner.Significance statementThis study provides a comprehensive transcriptomic map of the neuroimmune alterations in response to asthmatic induction.
Cross-species protection suggestsEntamoeba histolyticatrogocytosis enables complement resistance through the transfer of negative regulators of complement activation
Authors: Ruyechan Maura C. , Huang Wesley , Ralston Katherine S. 
Published: October 2024

ABSTRACTEntamoeba histolyticais a major cause of diarrheal disease.E. histolyticatrophozoites (“amoebae”) can invade the intestine and disseminate via the bloodstream, resisting complement lysis through unknown mechanisms. Amoebae kill human cells by performing trogocytosis. After performing trogocytosis, amoebae display human proteins on their own surface and are resistant to lysis by human serum. In this study we sought to further evaluate the mechanism by which amoebae resist complement. To test if complement is responsible for lysis of amoebae, C3-depleted serum was compared to replete serum, and C3 was required for lysis. Amoebae were allowed to perform trogocytosis of human cells and exposed to mouse serum. Although they had performed trogocytosis on a different species than the source of the serum, they were protected from lysis. To test if the protection from lysis by mouse serum was due to the functional interchangeability of human and mouse complement pathway proteins, human CD46 or CD55 (negative regulators of complement activation) were exogenously expressed. Amoebae that expressed human CD46 or CD55 were protected from lysis by mouse serum, indicating that display of human proteins was sufficient to inhibit mouse complement activation. Finally, amoebae were allowed to perform trogocytosis of a cell type in which the complement pathway is not conserved, and they did not become resistant to lysis. Overall, these findings are consistent with the model that trogocytosis enables amoebic acquisition and display of host proteins, including negative regulators of the complement pathway, that provide protection from complement lysis. Since other microbes can perform trogocytosis, this novel mechanism for complement resistance might apply to other infections.
Gut Bacteria Encode Reductases that Biotransform Steroid Hormones
Authors: Arp Gabriela , Jiang Angela , Dufault-Thompson Keith , Levy Sophia , Zhong Aoshu , Wassan Jyotsna Talreja , Grant Maggie , Li Yue , Hall Brantley , Jiang Xiaofang 
Published: October 2024

AbstractThe metabolism of steroids by the gut microbiome affects hormone homeostasis, impacting host development, mental health, and reproductive functions. In this study, we identify the Δ4-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ5-4isomerase, and Δ6-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, We show that 5β-reductase and Δ6-3-ketosteroid reductase have evolved to specialize in converting diverse 3-keto steroid hormones into their 5β- and Δ6-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ5-4isomerase is fused with 5β-reductase in multiple species, streamlining the multi-step conversion of pregnenolone, a steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations, being enriched in females over males. These findings provide the molecular basis for studying microbial steroid metabolism in the gut, offering insights into its potential impact on hormonal health in hosts, especially in the context of women’s health.
Human and Mouse Models for Kabuki Syndrome Reveal Increase in Inhibitory Synapse Development
Authors: Knopp James , Weaver Alexander , Miller Sean , Nomura Toshihiro , Whitlark Ava , Swantkowski Jack , Noble Alexandra , Nam Sandy , Hutson Katharyn , Bergqvist-Patzke Jenny , Contractor Anis , Patzke Christopher 
Published: October 2024

ABSTRACTIntellectual disability, affecting 2-3% of the general population, often coincides with neurodevelopmental disorders and is frequently caused by mutations that impair synaptic function. Kabuki syndrome (KS), a rare multisystem disorder associated with developmental delay and intellectual disability, results from mutations in eitherKMT2D(KS type 1) orKDM6A(KS type 2), which encode a chromatin-modifying methyltransferase and demethylase, respectively. However, the mechanisms contributing to intellectual disability in KS remain poorly understood. Here, we generated human iPS cells carrying a conditional Cre/lox-dependentKMT2DorKDM6Aloss-of-function mutation, used for directed differentiation into inhibitory or excitatory neurons. Analysis of Cre-mediated induction of KS type 1 and KS type 2 in inhibitory neurons unexpectedly revealed an increase in GABAergic synapse development. Mutant excitatory neurons, however, displayed a reduction in synapse development and impaired information transfer within neural networks. We confirmed these findings in hippocampal neuronsin vitroandin vivousing a mouse model for KS type 1. Synapse numbers and synaptic transmission in acute brain slices were shifted to increased inhibition/excitation ratio. Thus, our results, using purely inhibitory or purely excitatory human neurons with conditional deletion ofKMT2DorKDM6A,and mouse withKmt2ddeletion, reveal a novel disease mechanism of KS and provide a mechanistic explanation for intellectual disability observed in individuals affected by KS highlighting imbalanced excitation to inhibition in neural circuits.
Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase
Authors: Baytshtok Vladimir , DiMattia Michael A. , Lima Christopher D. 
Published: October 2024

AbstractThe human nucleoporin RanBP2/Nup358 interacts with SUMO1-modified RanGAP1 and the SUMO E2 Ubc9 at the nuclear pore complex (NPC) to promote export and disassembly of exportin Crm1/Ran(GTP)/cargo complexes. In mitosis, RanBP2/SUMO1-RanGAP1/Ubc9 remains intact after NPC disassembly and is recruited to kinetochores and mitotic spindles by Crm1 where it contributes to mitotic progression. Interestingly, RanBP2 binds SUMO1-RanGAP1/Ubc9 via motifs that also catalyze SUMO E3 ligase activity. Here, we resolve cryo-EM structures of a RanBP2 C-terminal fragment in complex with Crm1, SUMO1-RanGAP1/Ubc9, and two molecules of Ran(GTP). These structures reveal several unanticipated interactions with Crm1 including a nuclear export signal (NES) for RanGAP1, the deletion of which mislocalizes RanGAP1 and the Ran GTPase in cells. Our structural and biochemical results support models in which RanBP2 E3 ligase activity is dependent on Crm1, the RanGAP1 NES and Ran GTPase cycling.