bluuebunny/crossref_metadata_2025 huggingface dataset:
Kidney Protection During Surgery on the Thoracoabdominal Aorta: A Systematic Review
Authors: Bennett James Thomas , Shirley Sarah , Murray Patricia , Wilm Bettina , Field Mark
Published: June 2024

Background

Acute kidney injury (AKI) is a common complication of surgery to repair the thoracoabdominal aorta, and is associated with risks of dialysis and early mortality. Renal ischaemia, initiated by clamping of the suprarenal aorta, is a major cause. Consequently, perfusion techniques are commonly used to sustain renal blood flow or facilitate hypothermic kidney preservation during surgery. This systematic review provides a comprehensive assessment of renal and mortality outcomes by perfusion techniques, to evaluate their ability to provide effective kidney protection.

Methods & Results

Searches of PubMed, Web of Science,ClinicalTrials.govand ClinicalTrialsRegister.EU were conducted to identify relevant studies published from 1995 to 2024. Included studies were quality assessed, and data were extracted by perfusion techniques. Outcomes of the highest quality studies were used to synthesise a narrative discussion.

Forty-five studies were included in our analysis, featuring three extracorporeal strategies: Left heart bypass (LHB; n=24), cardiopulmonary bypass with deep hypothermic circulatory arrest (DHCA; n=19), and partial cardiopulmonary bypass (pCPB; n=12). Three categories of selective renal perfusion strategy were identified: Warm blood, cold blood and cold crystalloid. Our analysis identified operative mortality as 0-23.4% following LHB, 2.2-12.5% following DHCA and 0-42.1% following pCPB. The incidence of renal replacement therapy was 0-40.0% following LHB, 0-15.0% following DHCA and 0-22.2% following pCPB.

Conclusions

Strong evidence supports the use of distal aortic perfusion (DAP) with LHB or pCPB, to reduce the risks of dialysis and operative mortality associated with aortic cross clamping. Furthermore, when DAP cannot prevent kidney ischaemia, adjunctive perfusion of the renal arteries with cold histidine-tryptophan-ketoglutarate (HTK) can reduce the risk of AKI. However, no professional guidance on the management of HTK exists, and rates of AKI remain high despite its use. Selective renal perfusion with warm blood is identified as a risk factor for AKI and operative mortality. DHCA is associated with low rates of AKI, warranting further prospective investigation. Finally, intravascular haemolysis and myoglobinaemia are acknowledged as important risk factors that require urgent research to address the problem of AKI.
Estimating young adult uptake of smoking by area across the UK
Authors: Jackson Sarah E. , Tattan-Birch Harry , Hopkinson Nicholas S , Brown Jamie , Shahab Lion , Bunce Laura , Laverty Anthony A , Arnott Deborah
Published: June 2024

Background

There is majority support in parliament and across the United Kingdom (UK) to implement a ‘smokefree generation’ policy which would increase the legal age of sale of tobacco from 18 by one year each year from 2027 onwards, such that people born on or after 1 January 2009 could never legally be sold tobacco. To explore the potential impact this policy could have, we estimated the number of young adults (18–25y) currently taking up smoking each year by area across the UK.

Methods

Using data from the Office for National Statistics (ONS), Annual Population Survey (APS), and Smoking Toolkit Study (STS), we estimated the total number of 18–25-year-olds in the UK taking up smoking each year, based on national estimates of population size (ONS) and the proportion who reported ever having been a regular smoker (STS). We used local data on adult smoking rates (APS) to apportion the national estimated number of young adults taking up smoking to specific areas.

Results

Around 127,500 18–25-year-olds in the UK start smoking regularly each year (349 each day); 105,700 each year (290 each day) in England, 11,500 (32) in Scotland, 6,500 (18) in Wales, and 3,800 (10) in Northern Ireland. Estimates of uptake varied across localities: for example, North East Lincolnshire had the highest proportion of young adults taking up smoking each year (3.96%) and Wokingham had the lowest (0.85%).

Conclusions

Despite reductions in smoking prevalence over recent decades, hundreds of young adults in the UK start smoking every day. Data on rates of uptake among individual local authorities can be used to focus attention locally prior to the introduction of new age of sale laws.
Evaluating the Effectiveness of a Population-Level Health Intervention to Increment HCV Treatment Coverage in Tuscany Region, Italy: An Interrupted Time Series Analysis
Authors: Seghieri Chiara , Ceccarelli Luca , Tortù Costanza , Tavoschi Lara
Published: June 2024

Worldwide, an estimated 71.1 million people are chronically infected with the Hepatitis C virus (HCV). The advent of direct-acting antivirals (DAAs) has made possible the definition of elimination targets by 2030. This study aimed to evaluate the effectiveness of a population-level health intervention to expand access to HCV treatment in the Tuscany Region, Italy.

We used individual-level administrative data from the Tuscany region, collected between January 2015 and December 2022. Data include monthly observations on i) the number of serological tests to detect HCV, ii) the number of PCR tests to detect HCV and, iii) the number of prescriptions of direct-acting antivirals against HCV.

We implemented an Interrupted Time Series (ITS) model, where the primary outcome was the number of monthly prescriptions of direct-acting antivirals, while the number of tests to detect HCV were included as control variables. The analysis was implemented i) in the general population, ii) in specific sub-population groups.

Results show that the health intervention promoted by the Tuscany Regional Health Authority was highly effective in increasing DAAs treatment coverage in the general population, while no significant effects were observed among sub-population groups.

Findings of this study provide evidence to support policies at national and subnational levels to booster HCV screening and simplify access to DAA prescriptions.
A Bayesian Survival Analysis on Long COVID and non Long COVID patients: A Cohort Study Using National COVID Cohort Collaborative (N3C) Data
Authors: Jiang Sihang , Loomba Johanna , Zhou Andrea , Sharma Suchetha , Sengupta Saurav , Liu Jiebei , Brown Donald
Published: June 2024

Since the outbreak of COVID-19 pandemic in 2020, numerous researches and studies have focused on the long-term effects of COVID infection. The Centers for Disease Control (CDC) implemented an additional code into the International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) for reporting ‘Post COVID-19 condition, unspecified (U09.9)’ effective on October 1st 2021, representing that Long COVID is a real illness with potential chronic conditions. The National COVID Cohort Collaborative (N3C) provides researchers with abundant electronic health records (EHR) data by aggregating and harmonizing EHR data across different clinical organizations in the United States, making it convenient to build up a survival analysis on Long COVID patients and non Long COVID patients among large amounts of COVID positive patients.
High confidence and demand for hepatitis E vaccine during an outbreak in Bentiu, South Sudan: A qualitative study
Authors: Koyuncu Aybüke , Asilaza Kinya Vincent , Rumunu John , Wamala Joseph , Gitahi Priscillah , Antier Zelie , Duncker Jetske , Nkemenang Patrick , Gakima Primitive , Haile Melat , Gignoux Etienne , Albela Manuel , Loro Frederick Beden , Biem Duol , Rull Monica , Azman Andrew S , Ciglenecki Iza , Nesbitt Robin
Published: June 2024

Introduction

In 2021 in response to an outbreak of hepatitis E in Bentiu internally displaced persons camp the South Sudanese Ministry of Health with support from Médecins Sans Frontières implemented the first-ever mass reactive vaccination campaign with HEV239 (Hecolin; Innovax, Xiamen, China). As part of an evaluation of the feasibility of hepatitis vaccination as part of an epidemic response, we conducted qualitative research to assess knowledge, attitudes, and practices related to hepatitis E and the hepatitis E vaccine.

Methods

We conducted 8 focus group discussions (FGDs) with community leaders, the general population of vaccine-eligible adults, vaccine-eligible pregnant women (vaccinated and non-vaccinated), and healthcare workers. FGDs were separate by gender and were audio recorded, transcribed, and translated to English by trained research assistants. Two coders used inductive thematic analysis to organize emergent themes.

Results

Data were collected in November 2022. Most individuals had personal experiences with hepatitis E. Hepatitis E was perceived as a dangerous disease, and almost everyone was knowledgeable about transmission pathways. Participants believed children, pregnant women, and the elderly were the highest risk groups. Participants frequently made requests for additional hepatitis E vaccination campaigns and expanded eligibility criteria for vaccination. The primary barriers to vaccination were practical issues related to being away from the camp at the time of the campaign, but participants shared that some in the community were unvaccinated due to fears about injections, social pressure, misinformation about side effects such as infertility, concerns about why some groups were eligible for vaccination and not others (e.g. young children), and a lack of information about the vaccine/vaccination campaigns.

Conclusion

Personal experiences with hepatitis E illness, perceived severity of illness, and confidence in organizations recommending the vaccine were drivers of high demand for hepatitis E vaccines in the first-ever use of the vaccine in an outbreak setting.
Divergent roles of SOX2 in human and mouse germ cell specification related to X-linked gene dosage effects
Authors: He Wenteng , Luo Qing , Zhao Jian , Wang Mengting , Feng Luohua , Zhao Allan , Reda Ahmed , Lindgren Eva , Strukenborg Jan-Bernd , Chen Jiayu , Deng Qiaolin
Published: June 2024

Human primordial germ cell-like cells (hPGCLCs) can be generated from pluripotent stem cells (PSCs) but the differentiation efficiency of female hPSCs is often lower than that of male hPSCs. Moreover, Klinefelter Syndrome (KS), a condition characterized by an extra X-chromosome in males, often presents the failure of germline specification and infertility. In this study, we investigate how X-linked gene dosage affects hPGCLCs specification potential in both healthy and diseased conditions. We reveal that the X-chromosome plays a multifaceted role in modulating hPGCLCs induction. The inhibitory effects on TGF-beta/Activin A and BMP pathways by escape genes IGSF1 and CHRDL1, respectively, are demonstrated by the increased yield of hPGCLCs with knockdown experiments. Importantly, our results identified the intriguing role of SOX2 that is upregulated by the escape geneUSP9Xin hPGCLCs specification, highlighting a species-specific difference from the mouse model. The elevatedUSP9X-SOX2regulatory axis profoundly influences cellular metabolism, mitochondrial morphology, and progenitor competence, thereby affecting hPGCLCs induction. Furthermore, the inability to downregulate SOX2 and upregulate SOX17 in response to BMP signaling impedes downstream gene activation due to motif binding competition. These findings shed novel insights into the hPGC specification by elucidating the differential roles of SOX2 versus SOX17 between mice and humans, influenced by X-linked gene dosage effects. Additionally, our results offer potential applications for improving the induction and survival efficiency of hPGCLCs from hPSCs, facilitating disease modeling and mechanistic studies.

Highlights

Downregulation of three X-linked genes, i.e. IGSF1, CHRDL1 and USP9X, enhanced the differentiation efficiency of hPGCLCs

SOX2 as a downstream of human-specific escape gene USP9X plays a multifacet role against hPGCLCs specification

Failure to timely downregulate SOX2 and upregulate SOX17 interferes downstream gene activation likely due to motif binding competition
Epigenetic memory of Lateral Ganglionic Eminence derived hiPSCs cannot overcome barriers in authentic MSN differentiation
Authors: Bartley O. J. M. , Vinh N. N. , Lelos M.J. , Williams N. M. , Precious S. V. , Rosser A. E.
Published: June 2024

Induced pluripotent stem cells (iPSCs) have previously been shown to retain some of the epigenetic features associated with the tissues from which they were derived, which in turn can help the iPSCs to differentiate towards similar cell fates. Here we investigate whether human iPSCs (hiPSC) derived from the lateral ganglionic eminence (LGE) retain sufficient epigenetic features of their original tissue to enhance their capacity to differentiate into striatal medium spiny neurons (MSN) compared to isogenic controls. We identify a subtle methylation signature within these isogenic hiPSCs, and observe line specific capacities to produce MSN-like cells and their subtypes. We directly compare these cells to authentic LGE derived MSNs and identify large differences in DNA methylation between these populations. Using single cell RNA sequencing, we also find subpopulations that do not reflect the transcriptional profile of authentic MSNs. While we observe some potential epigenetic “benefits” within our LGE derived hiPSC-MSNs (e.g. reduced hypomethylation of off-target pathways), we did not observe an improved propensity to differentiate towards an MSN-like fate. Overall, this work highlights that pluripotent stem cells are unique in their individual capacity for differentiation, that subtle differences between cell lines can have far reaching effects on the final cell product, and that while hPSC-MSNs can model many aspects of MSN development, there are still epigenetic and transcriptional differences that limit the full recapitulation of the authentic LGE-derived MSN phenotype.
Fibrillarin modulates fetal hemoglobin silencing
Authors: Wu Dongliang , Li Qixiang , Qiu Sipei , Guo Chan , Li Feng , Shangguan Wenbing , Li Wenyang , Yang Dongjun , Meng Xingjun , Xing Mengying , Chen Bing , Kong Lingdong , Huang David C. S. , Zhao Quan
Published: June 2024

Decoding the molecular mechanisms underlying human fetal (γ) globin gene silencing impacts therapeutic strategies for β-thalassemia and sickle cell disease. Here, we identified a nucleolar protein, fibrillarin (FBL), which mediates the methylation of glutamine104 in histone H2A and functions as a repressor of the γ-globin gene in cultured erythroid cells, including those from β-thalassemia patients. ConditionalFbldepletion in adult β-YAC transgenic mice or in βIVS-2-654-thalassemic mice reactivated the human γ-globin gene or murine embryonic globin expression, respectively, which corrects hematologic and pathologic defects in β-thalassemic mice. We showed that FBL plays a dual role in activatingBCL11Aexpression and repressing γ-globin gene expression, which is dependent on its histone methyltransferase activity. Our study may provide an alternative strategy for therapeutic targeted treatment of β-hemoglobinopathies.
Structural basis of nucleotide selectivity in pyruvate kinase
Authors: Taguchi Atsushi , Nakashima Ryosuke , Nishino Kunihiko
Published: June 2024

Nucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures ofStreptococcus pneumoniaePYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.
Natural Variation in HIV-1 Entry Kinetics Map to Specific Residues and Reveal an Interdependence Between Attachment and Fusion
Authors: Webb Nicholas E. , Sevareid Colin M. , Sanchez Carolina , Tobin Nicole H. , Aldrovandi Grace M.
Published: June 2024

HIV-1 entry kinetics reflect the fluid motion of the HIV envelope glycoprotein through at least three major structural configurations that drive virus-cell membrane fusion. The lifetime of each state is an important component of potency for inhibitors that target them. We used the time-of-addition inhibitor assay and a novel analytical strategy to define the kinetics of pre-hairpin exposure (using T20) and co-receptor engagement (via. maraviroc), through a characteristic delay metric, across a variety of naturally occurring HIV Env isolates. Among 257 distinct HIV-1 envelope isolates we found a remarkable breadth of T20 and maraviroc delays ranging from as early as 30 seconds to as late as 60 minutes. The most extreme delays were observed among transmission-linked clade C isolates. We identified four single-residue determinants of late T20 and maraviroc delays that are associated with either receptor engagement or gp41 function. Comparison of these delays with T20 sensitivity suggest co-receptor engagement and fusogenic activity in gp41 act cooperatively but sequentially to drive entry. Our findings support current models of entry where co-receptor engagement drives gp41 eclipse and have strong implications for the design of entry inhibitors and antibodies that target transient entry states.

Author Summary.

The first step of HIV-1 infection is entry, where virus-cell membrane fusion is driven by the HIV-1 envelope glycoprotein through a series of conformational changes. Some of the most broadly active entry inhibitors work by binding conformations that exist only transiently during entry. The lifetimes of these states and the kinetics of entry are important elements of inhibitor activity for which little is known. We demonstrate a remarkable range of kinetics among 257 diverse HIV-1 isolates and find that this phenotype is highly flexible, with multiple single-residue determinants. Examination of the kinetics of two conformational landmarks shed light on novel kinetic features that offer new details about the role of co-receptor engagement and provide a framework to explain entry inhibitor synergy.
Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth: a conserved metabolic switch
Authors: Medini Hadar , Mishmar Dan
Published: June 2024

Interactions between mitochondrial and nuclear factors are essential to life. Nevertheless, the importance of coordinated regulation of mitochondrial-nuclear gene expression (CMNGE) to changing physiological conditions is poorly understood, and is limited to certain tissues and certain organisms. We hypothesized that CMNGE is important for development across vertebrates, and hence will be conserved. As a first step, we analyzed >1400 RNA-seq experiments performed during embryo development, neonates and adults across vertebrate evolution. We found conserved sharp elevation after birth of CMNGE, including oxidative phosphorylation (OXPHOS) and mitochondrial ribosome genes, in heart, hindbrain, forebrain and kidney across mammals,Gallus gallusand in the lizardAnolis carolinensis. This was accompanied by elevated expression of TCA cycle enzymes, and reduction in hypoxia response genes, suggesting a conserved cross-tissue metabolic switch after birth/hatching. Analysis of ∼70 known regulators of mitochondrial gene expression revealed consistently elevated expression of PGC-1a and C/EBPB after birth/hatching across organisms and tissues, thus highlighting them as candidate regulators of CMNGE upon transition to the neonate. Analyses ofDanio rerio,Xenopus tropicalisandDrosophila melanogasterrevealed elevated CMNGE prior to hatching, coinciding with the development of motor neurons. Lack of such ancient pattern in mammals and in the chicken suggests that it was lost during radiation of terrestrial vertebrates. Taken together, our results suggest that regulated CMNGE during embryogenesis and after birth, alludes to metabolic switch which is under strong selective constraints and hence essential.
Presynaptic GABAAreceptors control integration of nicotinic input onto dopaminergic axons in the striatum
Authors: Brill-Weil Samuel G. , Kramer Paul F. , Yanez Anthony , Clever Faye H. , Zhang Renshu , Khaliq Zayd M.
Published: June 2024

Axons of dopaminergic neurons express gamma-aminobutyric acid type-A receptors (GABAARs) and nicotinic acetylcholine receptors (nAChRs) which are both independently positioned to shape striatal dopamine release. Using electrophysiology and calcium imaging, we investigated how interactions between GABAARs and nAChRs influence dopaminergic axon excitability. Direct axonal recordings showed that benzodiazepine application suppresses subthreshold axonal input from cholinergic interneurons (CINs). In imaging experiments, we used the first temporal derivative of presynaptic calcium signals to distinguish between direct- and nAChR-evoked activity in dopaminergic axons. We found that GABAAR antagonism with gabazine selectively enhanced nAChR-evoked axonal signals. Acetylcholine release was unchanged in gabazine suggesting that GABAARs located on dopaminergic axons, but not CINs, mediated this enhancement. Unexpectedly, we found that a widely used GABAAR antagonist, picrotoxin, inhibits axonal nAChRs and should be used cautiously for striatal circuit analysis. Overall, we demonstrate that GABAARs on dopaminergic axons regulate integration of nicotinic input to shape presynaptic excitability.
Dopamine increases protein synthesis in hippocampal neurons enabling dopamine-dependent LTP
Authors: Fuchsberger T. , Stockwell I. , Woods M. , Brzosko Z. , Greger I. , Paulsen O.
Published: June 2024

The reward and novelty related neuromodulator dopamine plays an important role in hippocampal long- term memory, which is thought to involve protein synthesis-dependent synaptic plasticity. However, the direct effects of dopamine on protein synthesis, and the functional implications of newly synthesized proteins for synaptic plasticity, have not yet been investigated. We have previously reported that timing- dependent synaptic depression (t-LTD) can be converted into potentiation by dopamine application during synaptic stimulation (Brzosko et al., 2015) or postsynaptic burst activation (Fuchsberger et al., 2022). Here we show that dopamine increases protein synthesis in mouse hippocampal CA1 neurons, enabling dopamine-dependent long-term potentiation (DA-LTP), which is mediated via the Ca2+-sensitive adenylate cyclase (AC) subtypes 1/8, cAMP, and cAMP-dependent protein kinase (PKA). We found that neuronal activity is required for the dopamine-induced increase in protein synthesis. Furthermore, dopamine induced a protein synthesis-dependent increase in the AMPA receptor subunit GluA1, but not GluA2. We found that DA-LTP is absent in GluA1 knock-out mice and that it requires calcium-permeable AMPA receptors. Taken together, our results suggest that dopamine together with neuronal activity controls synthesis of plasticity-related proteins, including GluA1, which enable DA-LTP via a signalling pathway distinct from that of conventional LTP.
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells
Authors: Love Kasey S. , Johnstone Christopher P. , Peterman Emma L. , Gaglione Stephanie , Galloway Kate E.
Published: June 2024

To realize the potential of engineered cells in therapeutic applications, transgenes must be expressed within the window of therapeutic efficacy. Differences in copy number and other sources of extrinsic noise generate variance in transgene expression and limit the performance of synthetic gene circuits. In a therapeutic context, supraphysiological expression of transgenes can compromise engineered phenotypes and lead to toxicity. To ensure a narrow range of transgene expression, we design and characterizeCompactmicroRNA-MediatedAttenuator ofNoise andDosage (ComMAND), a single-transcript, microRNA-based incoherent feedforward loop. We experimentally tune the ComMAND output profile, and we model the system to explore additional tuning strategies. By comparing ComMAND to two-gene implementations, we highlight the precise control afforded by the single-transcript architecture, particularly at relatively low copy numbers. We show that ComMAND tightly regulates transgene expression from lentiviruses and precisely controls expression in primary human T cells, primary rat neurons, primary mouse embryonic fibroblasts, and human induced pluripotent stem cells. Finally, ComMAND effectively sets levels of the clinically relevant transgenes FMRP1 and FXN within a narrow window. Together, ComMAND is a compact tool well-suited to precisely specify expression of therapeutic cargoes.
ThePlasmodium falciparumhistone methyltransferase PfSET10 is dispensable for the regulation of antigenic variation and gene expression in blood stage parasites
Authors: Wyss Matthias , Kanyal Abhishek , Niederwieser Igor , Bartfai Richard , Voss Till S.
Published: June 2024

The malaria parasitePlasmodium falciparumemploys antigenic variation of the virulence factorP. falciparumerythrocyte membrane protein 1 (PfEMP1) to escape adaptive immune responses during blood infection. Antigenic variation of PfEMP1 occurs through epigenetic switches in the mutually exclusive expression of individual members of the multi-copyvargene family.vargenes are located in perinuclear clusters of transcriptionally inactive heterochromatin. Singularvargene activation is linked to locus repositioning into a dedicated zone at the nuclear periphery and deposition of histone 3 lysine 4 di-/trimethylation (H3K4me2/3) and H3K9 acetylation marks in the promoter region. While previous work identified the putative H3K4-specific methyltransferase PfSET10 as an essential enzyme and positive regulator ofvargene expression, a recent study reported conflicting data. Here, we used iterative genome editing to engineer a conditional PfSET10 knockout line tailored to study the function of PfSET10 invargene regulation. We demonstrate that PfSET10 is not required for mutually exclusivevargene expression and switching. We also show that PfSET10 is dispensable not only for asexual parasite proliferation but also for sexual conversion and gametocyte differentiation. Furthermore, comparative RNA-seq experiments revealed that PfSET10 plays no obvious role in regulating gene expression during asexual parasite development and gametocytogenesis. Interestingly, however, PfSET10 shows different subnuclear localization patterns in asexual and sexual stage parasites and female-specific expression in mature gametocytes. In summary, our work confirms in detail that PfSET10 is not involved in regulatingvargene expression and not required for blood stage parasite viability, indicating PfSET10 may be important for life cycle progression in the mosquito vector or during liver stage development.
Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes
Authors: Graham Thomas G.W. , Dugast-Darzacq Claire , Dailey Gina M. , Weng Britney , Darzacq Xavier , Tjian Robert
Published: June 2024

Cells are built from vast networks of competing molecular interactions, most of which have been impossible to monitor in vivo. We recently devised a new strategy, proximity-assisted photoactivation (PAPA), to detect these interactions at single-molecule resolution in live cells. Here we apply PAPA to visualize the network of interactions that regulate the central transcription elongation factor P-TEFb. PAPA between multiple pairs of endogenous proteins, combined with fast single-molecule tracking (fSMT), revealed that inactive P-TEFb within the 7SK ribonucleoprotein complex is largely unbound to chromatin, that this complex dissociates within minutes of treatment with a P-TEFb kinase inhibitor, and that heterogeneous ribonucleoproteins (hnRNPs) bind 7SK concomitant with P-TEFb release. Unlike 7SK-bound P-TEFb, P-TEFb associated with the coactivator BRD4 exhibited increased binding to chromatin. Our results address longstanding questions about a key transcriptional regulator and demonstrate that PAPA-fSMT can probe subunit interactions and exchange within endogenous regulatory complexes in live cells.
The Alzheimer’s disease geneSORL1regulates lysosome function in human microglia
Authors: Mishra Swati , Morshed Nader , Sindhu Sonia , Kinoshita Chizuru , Stevens Beth , Jayadev Suman , Young Jessica E.
Published: June 2024

Abstract

TheSORL1gene encodes the sortilin related receptor protein SORLA, a sorting receptor that regulates endo-lysosomal trafficking of various substrates. Loss of function variants inSORL1are causative for Alzheimer’s disease (AD) and decreased expression of SORLA has been repeatedly observed in human AD brains.SORL1is highly expressed in the central nervous system, including in microglia, the tissue resident immune cells of the brain. Loss of SORLA leads to enlarged lysosomes in hiPSC-derived microglia like cells (hMGLs). However, how SORLA deficiency contributes to lysosomal dysfunction in microglia and how this contributes to AD pathogenesis is not known. In this study, we show that loss of SORLA results in decreased lysosomal degradation and lysosomal enzyme activity due to altered trafficking of lysosomal enzymes in hMGLs. Phagocytic uptake of fibrillar amyloid beta 1-42 and synaptosomes is increased in SORLA deficient hMGLs, but due to reduced lysosomal degradation, these substrates aberrantly accumulate in lysosomes. An alternative mechanism of lysosome clearance, lysosomal exocytosis, is also impaired inSORL1deficient microglia, which may contribute to an altered immune response. Overall, these data suggest that SORLA has an important role in proper trafficking of lysosomal hydrolases in hMGLs, which is critical for microglial function. This further substantiates the microglial endo-lysosomal network as a potential novel pathway through whichSORL1may increase AD risk and contribute to development of AD. Additionally, our findings may inform development of novel lysosome and microglia associated drug targets for AD.
Neural and sensory basis of homing behavior in the invasive cane toad,Rhinella marina
Authors: Shaykevich Daniel A , Pareja-Mejía Daniela , Golde Chloe , Pašukonis Andrius , O'Connell Lauren A
Published: June 2024

The behavioral, sensory, and neural bases of vertebrate navigation are primarily described in mammals and birds. While many studies have explored amphibian navigation, none have characterized brain activity associated with navigation in the wild. To address this knowledge gap, we conducted a study on navigation in the cane toad, Rhinella marina. First, we performed a translocation experiment to describe how invasive cane toads in Hawaiʻi navigate home and observed homing following displacements of up to one kilometer. Next, we tested the effect of olfactory and magnetosensory manipulations on homing, as these senses are most commonly associated with amphibian navigation. We found that neither ablation alone prevents homing, further supporting that toad navigation is multimodal. Finally, we tested the hypothesis that the medial pallium, the amphibian homolog to the hippocampus, is involved in homing. Our comparisons of neural activity revealed evidence supporting a conservation of neural structures associated with navigation across vertebrates consistent with neural models of amphibian spatial cognition from recent laboratory studies. Our work furthers our evolutionary understanding of spatial behavior and cognition in vertebrates and lays a foundation for studying the behavioral, sensory, and neural bases of navigation in an invasive amphibian.
Hepatocyte-derived extracellular vesicles regulate liver regeneration after partial hepatectomy
Authors: McGinn Mina , Rabender Christopher , Mikkelsen Ross , Yakovlev Vasily
Published: June 2024

While significant progress has been made in understanding different aspects of liver regeneration, the molecular mechanisms responsible for the initiation and termination of cell proliferation in the liver after massive loss or injury of liver tissue remain unknown. The loss of liver mass affects tissue-specific mitogenic inhibitors in the blood, which in turn regulate the proliferation of remaining hepatocytes and liver regeneration. Although well described in a number of publications, which inhibitory substances or “sensor molecules” control the regeneration mechanisms to properly maintain liver size remain unknown. Extracellular vesicles (EVs) are nano-sized, membrane-limited structures secreted by cells into the extracellular space. Their proposed role is stable intercellular carriers of proteins and RNAs, mostly micro-RNA, from secreted to recipient cells. Taken up by the recipient cells, EVs can significantly modulate their biological functions. In the present study, usingin vivoandin vitromodels, we demonstrate that hepatocyte proliferation and liver regeneration are regulated by EVs secreted by hepatocytes into the bloodstream. This regulation is carried out through a negative feedback mechanism, which explains the very precise regeneration of liver tissue after massive damage. We also demonstrate that an essential component of this mechanism is RNA carried by hepatocyte-derived EVs. These findings open up a new and unexplored area of biology regarding the mechanisms involved in the homeostasis regulation of various constantly renewing tissues by maintaining the optimal size and correct ratio between differentiating and proliferating cells.
Glycogen homeostasis and mtDNA expression require motor neuron to muscle TGFβ/Activin Signaling inDrosophila
Authors: Bretscher Heidi , O’Connor Michael B.
Published: June 2024

Maintaining metabolic homeostasis requires coordinated nutrient utilization between intracellular organelles and across multiple organ systems. Many organs rely heavily on mitochondria to generate (ATP) from glucose, or stored glycogen. Proteins required for ATP generation are encoded in both nuclear and mitochondrial DNA (mtDNA). We show that motoneuron to muscle signaling by the TGFβ/Activin family member Actβ positively regulates glycogen levels duringDrosophiladevelopment. Remarkably, we find that levels of stored glycogen are unaffected by altering cytoplasmic glucose catabolism. Instead, Actβ loss reduces levels of mtDNA and nuclearly encoded genes required for mtDNA replication, transcription and translation. Direct RNAi mediated knockdown of these same nuclearly encoded mtDNA expression factors also results in decreased glycogen stores. Lastly, we find that expressing an activated form of the type I receptor Baboon in muscle restores both glycogen and mtDNA levels inactβmutants, thereby confirming a direct link between Actβ signaling, glycogen homeostasis and mtDNA expression.

Key Points

The Drosophila TGFβ family member Actβ signals from motor neuron to muscle positively regulating glycogen levels

Actβ positively regulates nuclearly encoded factors required for mtDNA expression

Genes involved in mtDNA expression directly regulate glycogen stores

Expressing an activated receptor in muscle restores glycogen and mtDNA inactβmutants

Abstract Figure
Type I interferon responses contribute to immune protection against mycobacterial infection
Authors: Szydlo-Shein Andrea , Sanz-Magallón Duque de Estrada Blanca , Rosenheim Joshua , Turner Carolin T. , Chandran Aneesh , Tsaliki Evdokia , Lipman Marc C. I. , Kunst Heinke , Pollara Gabriele , Elks Philip M. , Levraud Jean-Pierre , Payne Elspeth M. , Noursadeghi Mahdad , Tomlinson Gillian S.
Published: June 2024

Type I interferon responses have been considered detrimental to host protection in tuberculosis (TB). We provide novel data to challenge this paradigm, derived from transcriptional profiling of human in vivo immune responses to discover associations with radiographic disease severity in pulmonary TB, combined with mechanistic studies to test causality for observed associations using a zebrafish larval mycobacterial infection model. Type I interferon activity in tissue samples from the site of a standardised mycobacterial challenge, the tuberculin skin test, was associated with less severe human TB disease. Abrogation of type I interferon signalling, by CRISPR-mediated mutagenesis ofstat2, led to increased burden and dissemination ofMycobacterium marinuminfection in zebrafish larvae. The mechanism for increased severity of mycobacterial infection in zebrafish involves reduced recruitment of myeloid cells required to restrict bacterial growth. Our data support a clear host protective role for type I interferon responses in mycobacterial infection, with potential applications for risk-stratification of adverse outcomes and development of a host-directed therapy to mitigate against severe disease.
Glymphatic dysfunction in multiple sclerosis and its association with disease pathology and disability
Authors: Bayoumi Ahmed , Hasan Khader M , Yazdani Akram , Lincoln John A
Published: June 2024

Background: MS is a chronic neuroinflammatory and neurodegenerative disease, in which the glymphatic system remains underexplored. The diffusion tensor image analysis along the perivascular space (ALPS) offers a non-invasive method to assess glymphatic function. Objective: To investigate glymphatic function in MS, and its relationship with disease pathology and disability. Methods: This retrospective study involved 118 MS patients, divided based on the Expanded Disability Status Scale (EDSS) into MS-L (EDSS < 3) and MS-H (EDSS ≥ 3). The ALPS index, brain parenchymal fraction (BPF), and lesion load (LL) were measured. Subgroup comparisons, ALPS index correlations with clinical and MRI measures, and logistic regression were performed. Results: Significant differences in the mean ALPS index between MS-H and MS-L (d=-0.71, p-FDR=0.001) were found. The ALPS index correlated significantly with disease duration (rp=-0.29, p-FDR=0.002), and EDSS (rsp=-0.35, p-FDR=0.0002). The ALPS index also showed significant correlations with BPF and LL. The ALPS index and LL were significant predictors of lower disability (ALPS: Odds ratio (OR)=1.77, p=0.04, LL: OR=0.94, p=0.02). Conclusion: Our findings highlight the ALPS index as an imaging biomarker in MS. This suggests the involvement of glymphatic dysfunction in MS pathology and underscores the need for further research to elucidate its role in MS.
“Transcriptomic Profiling Unveils Novel Therapeutic Options for Drug-Resistant Temporal Lobe Epilepsy”
Authors: Sánchez-Jiménez Patricia , Alonso-Guirado Lola , Cerrada-Gálvez Laura , Elizalde-Horcada Marcos , Granero-Cremades Inmaculada , Maietta Paolo , Gómez-Martín Antonio , Abad-Santos Francisco , Torres-Díaz Cristina Virginia , de Toledo Maria , Frade-Porto Natalia , Gonzalez-Tarno Patricia , Pulido Paloma , Ovejero-Benito María C.
Published: June 2024

Background

Epilepsy drug treatments fail in 25-30% of patients, who then develop drug resistance. Temporal lobe epilepsy is the most prevalent subtype associated with drug resistance. Classical drug discovery is a long and extremely costly process with a high rate of failure in clinical trials. Drug repurposing is a more cost- and time-effective strategy. Hence, the main objective of this study is to propose drug candidates for the treatment of drug-resistant temporal lobe epilepsy (DR-TLE) through drug repurposing based on transcriptomic profiling.

Methods

Total RNA-sequencing (RNA-Seq) was performed on 45 formalin-fixed paraffin-embedded (FFPE) hippocampi of DR-TLE patients and 36 FFPE hippocampi of post-mortem biobank donors. RNA-Seq was carried out in an Illumina NovaSeq 6000 platform in 100bp paired-end. Drug repurposing based on transcriptomic analysis top candidates was performed against these databases: Pandrugs2, PharmOmics, DGIdb, ToppGene, L1000CDS2and Connectivity Map.

Results

We found 887 genes differentially expressed between DR-TLE patients and post-mortem controls. We observed 74 potential drug candidates in at least two independent databases. Of these, we selected only the 11 which can cross the blood-brain barrier: cobimetinib, panobinostat, melphalan, rucaparib, alectinib, ponatinib, danazol, carboplatin, vandetanib, erlotinib, and gefitinib. After analyzing their safety and efficacy profile based on previous publications, we provide a list of the top 5 candidates.

Conclusions

We therefore propose erlotinib, danazol, rucaparib, ponatinib, and panobinostat as potential therapies for DR-TLE based on differential RNA-Seq profiling.
The Impact of Instructions on Individual Prioritization Strategies in a Dual-Task Paradigm for Listening Effort
Authors: Kestens Katrien , Lepla Emma , Vandoorne Flore , Ceuleers Dorien , Van Goylen Louise , Keppler Hannah
Published: June 2024

Introduction

This study examined the impact of instructions on the prioritization strategy employed by individuals during a listening effort dual-task paradigm.

Methods

The dual-task paradigm consisted of a primary speech understanding task in different listening conditions and a secondary visual memory task, both performed separately (baseline) and simultaneously (dual-task). Twenty-three normal-hearing participants (mean age: 36.8 years; 14 females) were directed to prioritize the primary speech understanding task in the dual-task condition, whereas another twenty-three (matched for age, gender, and education level) received no specific instructions regarding task priority. Both groups performed the dual-task paradigm twice (mean interval: 14.8 days). Patterns of dual-task interference were assessed by plotting the dual-task effect of the primary and secondary task against each other. Fisher’s exact tests were used to assess whether there was an association between interference patterns and group (non-prioritizing and prioritizing) across all listening conditions and test sessions.

Results

No statistically significant association was found between the pattern of dual-task interference and the group to which the participants belong for any of the listening conditions and test sessions. Descriptive analysis revealed no consistent strategy use within individuals across listening conditions and test sessions, suggesting a lack of a uniform approach regardless of the given instructions.

Conclusion

Providing prioritization instructions was insufficient to ensure that an individual will mainly focus on the primary task and consistently adhere to this strategy across listening conditions and test sessions. These results raised reservations about the current usage of dual-task paradigms for listening effort.
Modulation of Microtubule Dynamics by Monovalent Ions
Authors: Fernandes Simon , Aumeier Charlotte
Published: June 2024

The microtubule cytoskeleton is a dynamic network essential for many cellular processes, influenced by physicochemical factor such as temperature, pH, dimer concentration and ionic environment. In this study, we used in vitro reconstitution assays to examine the effects of four monovalent ions (Na+, K+, Cl-, and Ac-) on microtubule dynamics, uncovering distinct effects for each ion. Na+was found to increase microtubule dynamicity by raising catastrophe frequency, polymerization and depolymerization speeds, ultimately reducing microtubule lifetime by 80 %. Conversely, Ac boosts microtubule nucleation and stabilizes microtubules by increasing rescue frequency and preventing breakages, resulting in longer microtubules with extended lifetimes. Cl-appeared to potentiate the effects of Na+, while K+had minimal impact on microtubule dynamic parameters. These findings demonstrate that Na+and Ac-have opposing effects on microtubule dynamics, with Na+destabilizing and Ac-stabilizing the microtubule structure. This ionic impact is mainly through modulation of tubulin-tubulin interactions rather than affecting the hydrolysis rate. In conclusion, ion identity plays a crucial role in modulating microtubule dynamics. Understanding the ionic environment is essential for microtubule-related research, as it significantly influences microtubule behavior, stability, and interactions with other proteins.

SIGNIFICANCE STATEMENT

The microtubule cytoskeleton is vital for cellular processes and influenced by temperature, pH, dimer concentration, and ionic environment. Understanding how these physicochemical factors regulate microtubule polymerization is crucial for elucidating microtubule dynamics and stability. Our in vitro reconstitution assays reveal that Na+and Ac-ions have opposing effects on microtubule dynamics. Na+increases dynamicity by raising catastrophe frequency and reducing lifetime by 80 %, while Ac-enhances nucleation and stability, resulting in longer microtubules. Cl-potentiates the effects of Na+, and K+has minimal impact. Our findings highlight that ion identity crucially modulates microtubule dynamics, significantly influencing stability and interactions.
CCDC32 stabilizes clathrin-coated pits and drives their invagination
Authors: Yang Ziyan , Yang Changsong , Xu Peiliu , Han Lu , Li Yueping , Peng Linyuan , Wei Xiangying , Schmid Sandra L. , Svitkina Tatyana , Chen Zhiming
Published: June 2024

Clathrin-mediated endocytosis (CME) is essential for maintaining cellular homeostasis. Previous studies have reported more than 50 CME accessory proteins; however, the mechanism driving the invagination of clathrin-coated pits (CCPs) remains elusive. Quantitative live cell imaging reveals that CCDC32, a poorly characterized endocytic accessory protein, regulates CCP stabilization and is required for efficient CCP invagination. CCDC32 interacts with the α-appendage domain (AD) of AP2 via its coiled-coil domain to exert this function. Furthermore, we showed that the clinically observed nonsense mutations in CCDC32, which result in the development of cardio-facio-neuro-developmental syndrome (CFNDS), inhibit CME by abolishing CCDC32-AP2 interactions. Overall, our data demonstrates the function and molecular mechanism of a novel endocytic accessory protein, CCDC32, in CME regulation.

Significance Statement

Clathrin-mediated endocytosis (CME) happens via the initiation, stabilization, and invagination of clathrin-coated pits (CCPs). In this study, we used a combination of quantitative live cell imaging, ultrastructure electron microscopy and biochemical experiments to show that CCDC32, a poorly studied and functional ambiguous protein, acts as an important endocytic accessory protein that regulates CCP stabilization and invagination. Specifically, CCDC32 exerts this function via its interactions with AP2, and the coiled-coil domain of CCDC32 and the α-appendage domain (AD) of AP2 are essential in mediating CCDC32-AP2 interactions. Importantly, we demonstrate that clinically observed loss-of-function mutations in CCDC32 lose AP2 interaction capacity and inhibit CME, resulting in the development of cardio-facio-neuro-developmental syndrome (CFNDS).