bluuebunny/crossref_metadata_2025 huggingface dataset:
Diosmetin alleviates liver inflammation by improving liver sinusoidal endothelial cell dysfunction
Authors: Żurawek Dariusz , Pydyn Natalia , Major Piotr , Szade Krzysztof , Trzos Katarzyna , Kuś Edyta , Pośpiech Ewelina , Małczak Piotr , Radkowiak Dorota , Budzyński Andrzej , Chłopicki Stefan , Jura Jolanta , Kotlinowski Jerzy
Published: October 2023

Background & Aims

Tumor necrosis factor-alpha (TNFα) induces pro-inflammatory activation in liver sinusoidal endothelial cells (LSEC) and liver inflammation. However, knowledge about whether modulating LSEC activation can alleviate liver inflammation is scarce. This study aimed to establish and validate an animal model mimicking LSEC dysfunction observed in patients with elevated plasma levels of TNFα, and explore whether vasoactive flavonoid diosmetin could serve as a therapeutic agent for liver inflammation.

Approach & Results

Genetic deletion of Mcpip1 in myeloid leukocytes (Mcpip1fl/flLysMCre) resulted in the development of systemic and liver inflammation in mice. Symptoms were compared with those in liver samples from obese humans with elevated TNFα. Mice were treated with diosmetin, and its effectiveness in alleviating liver inflammation was evaluated. Elevated TNFα correlated with reduced Mcpip1 expression in peripheral blood mononuclear cells and LSEC dysfunction in obese patients. Mcpip1 knockout in myeloid cells in mice replicated molecular signs observed in human samples. Diosmetin efficiently reduced LSEC activation and liver inflammation in Mcpip1fl/flLysMCremice. Diosmetin’s effects may stem from inhibiting NF-κB-p50 subunit production in TNFα-activated endothelial cells.

Conclusions

Diosmetin treatment efficiently restricted liver inflammation, despite ongoing systemic inflammation, by diminishing LSEC dysfunction. Mcpip1fl/flLysMCremice mimic symptoms of liver inflammation observed in humans and can be useful in studies on new anti-inflammatory therapies for the liver. We show that diosmetin, a vasoactive flavonoid that is successfully used in the clinic to treat chronic venous insufficiency, has also strong anti-inflammatory properties in the liver. This suggests that diosmetin treatment may be tested in humans as a supportive therapy for liver inflammation.

Graphical abstract
PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data
Authors: Maurer Valentin J. , Siggel Marc , Kosinski Jan
Published: October 2023

Cryogenic electron microscopy (cryo-EM) is a key method in structural and cell biology. Analysis of cryo-EM images requires interpretation of noisy, low-resolution densities which relies on identifying the most probable orientation of macromolecules in a target using template matching. Many method-specific template matching software exist for single-particle cryo-EM, cryo-electron tomography (cryo-ET), or fitting atomic structures into averaged 3D maps of macromolecules. Here, we report the Python Template Matching Engine (pyTME), a software engine that consolidates method-specific template matching problems. The underlying library provides highly efficient template-matching implementation and abstract data structures for storing and manipulating input and output data. It scales favorable to large datasets, both with multiple CPUs and GPUs, compared to existing software enabling template matching of even unbinned cryo-ET data in hours, which was previously nearly impossible due to technical restraints. Any hardware-specific optimization needed for dealing with large data is automatically performed to increase ease of use and minimize user intervention. The efficiency and simplicity of pyTME will enable high throughput mining of a variety of cryo-EM and ET datasets in the future.
Brief disruption of activity in a subset of dopaminergic neurons during consolidation impairs long-term memory by fragmenting sleep
Authors: Yan Lin , Wu Litao , Wiggin Timothy D. , Su Xiaojuan , Yan Wei , Li Hailiang , Li Lei , Lu Zhonghua , Li Yuantao , Meng Zhiqiang , Guo Fang , Li Fan , Griffith Leslie C. , Liu Chang
Published: October 2023

Sleep disturbances are associated with poor long-term memory (LTM) formation, yet the underlying cell types and neural circuits involved have not been fully decoded. Dopamine neurons (DANs) are involved in memory processing at multiple stages. Here, using both male and female flies,Drosophila melanogaster, we show that, during the first few hours of memory consolidation, disruption of basal activity of a small subset of protocerebral anterior medial DANs (PAM-DANs), by either brief activation or inhibition of the two dorsal posterior medial (DPM) neurons, impairs 24 h LTM. Interestingly, these brief changes in activity using female flies result in sleep loss and fragmentation, especially at night. Pharmacological rescue of sleep after manipulation restores LTM. A specific subset of PAM-DANs (PAM-α1) that synapse onto DPM neurons specify the microcircuit that links sleep and memory. PAM-DANs, including PAM-α1, form functional synapses onto DPM mainly via multiple dopamine receptor subtypes. This PAM-α1 to DPM microcircuit exhibits a synchronized, transient, post-training increase in activity during the critical memory consolidation window, suggesting an effect of this microcircuit on maintaining the sleep necessary for LTM consolidation. Our results provide a new cellular and circuit basis for the complex relationship between sleep and memory.
Piezo1 Mutant Zebrafish as a Model of Idiopathic Scoliosis
Authors: Ramli  , Aramaki Toshihiro , Watanabe Masakatsu , Kondo Shigeru
Published: October 2023

Scoliosis is a condition where the spine curves sideways, unique to humans due to their upright posture. However, the cause of this disease is not well understood because it’s challenging to find a model for experimentation. This study aimed to create a model for human idiopathic scoliosis by manipulating the function of mechanosensitive channels called Piezo channels in zebrafish. Zebrafish were chosen because they experience similar biomechanical forces to humans, particularly in relation to the role of mechanical force in scoliosis progression. Here we describepiezo1andpiezo2aare involved in bone formation, with a double knockout resulting in congenital systemic malformations. However, an in-frame mutation ofpiezo1led to fully penetrant juvenile-onset scoliosis, bone asymmetry, reduced tissue mineral density, and abnormal intervertebral discs-resembling non-congenital scoliosis symptoms in humans. These findings suggest that functional Piezo channels responding to mechanical forces are crucial for bone formation and maintaining spine integrity, providing insights into skeletal disorders.
Sex determination system turnovers play important roles in the willows speciation
Authors: Xue Zhi-Qing , Applequist Wendy L. , Hörandl Elvira , He Li
Published: October 2023

Almost all species in the genusSalix(willow) are dioecious, but some have male and some female heterogamety, and the chromosomal location of the sex-linked regions (termed SDSs) differs between different species. We first analyzed the SDSs of two species,Salix cardiophyllaandS. interior, whose positions in theSalixphylogeny make them important species for understanding a sex chromosome turnover that has been detected in their relatives, and that changed the system from male to female heterogamety. We show that both species have male heterogamety, with XY-linked regions on chromosome 15 (termed a 15XY system). The sex-linked regions occupy 21.3% and 22.8% of the entire reference chromosome, respectively. By constructing phylogenetic trees of species with known SDSs, we determined the phylogenetic positions of all the species. Reconstruction of SDSs revealed that 15XY system is likely the ancestral of willows. Finally, we tested for both current and ancestral gene flow between different species with the same or different sex-determining systems, as the sex chromosomes can play important roles in reproductive isolation between species. We inferred lower gene flow between species with XY on chromosome 7 (7XY) and ZW on chromosome 15 (15ZW) systems, compared with gene flow either between species with XY on chromosome 15 (15XY) and 15ZW systems or between species with 7XY and 15XY systems. We argue that, although sex chromosomes turnovers in willows may not create complete reproductive barriers, gene flow may be reduced between species with different SDSs.
Lysogeny destabilizes computationally simulated microbiomes
Authors: Gilman R. Tucker , Muldoon Mark R. , Megremis Spyridon , Robertson David L. , Chanishvili Nina , Papadopoulos Nikolaos G.
Published: October 2023

Background

The Anna Karenina Principle predicts that stability in host-associated microbiomes correlates with health in the host. Microbiomes are ecosystems, and classical ecological theory suggests that predators impact ecosystem stability. Phages can act as predators on bacterial species in microbiomes. However, our ability to extrapolate results from existing ecological theory to phages and microbiomes is limited because some phages can stage lysogenic infections, a process with no precise analog in classical ecology. In lysogenic infections, so-called “temperate” phages integrate into the cells of their hosts where they can remain dormant as prophages for many generations. Prophages can later be induced by environmental conditions, whereupon they lyse their host cells and phage progeny are released. It has been suggested that prophages can act as biological timebombs that destabilize microbial ecosystems, but formal theory to support this hypothesis is lacking.

Results

We studied the effects of temperate and virulent phages on diversity and stability in computationally simulated microbiomes. The presence of either phage type in a microbiome increased bacterial diversity. Bacterial populations were more likely to fluctuate over time when there were more temperate phages in the system. When microbiomes were disturbed from their steady states, both phage types affected return times, but in different ways. Bacterial species returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species.

Conclusions

Phages shape the diversity and stability of microbiomes, and temperate and virulent phages impact microbiomes in different ways. A clear understanding of the effects of phage life cycles on microbiome dynamics is needed to predict the role of microbiome composition in host health, and for applications including phage therapy and microbiome transplants. The results we present here provide a theoretical foundation for this body of work.
CSTA: A Biomarker Regulating Esophageal Stricture Epithelial Barrier, Potential Medication Target
Authors: Yang Fang , Hu Yiwei , Shi Zewen , Jin Haozhou , Hu Kefeng , Ye Guoliang , Pang Qian , Hou Ruixia , Tang Keqi , Zhu Yabin
Published: October 2023

Esophageal strictures resulting from ESD/EMR in the esophagus are distressing, with uncertain causes and treatments due to epithelial barrier dysfunction. We explored cystatin A (CSTA) as a novel biomarker for the esophageal epithelial barrier. CSTA regulates the barrier and is influenced by tacrolimus (FK506). Analyzing biopsy samples by proteomics, we identified CSTA as an esophageal epithelial biomarker. Knocking down CSTA reduced responsiveness to triamcinolone acetonide (TA) and lowered expression of proteins related to cell-cell junctions and barrier function during inflammation. These findings suggest that down-regulate CSTA weakens tight junctions and the esophageal barrier, leading to strictures. Notably, FK506 showed promise in rescuing CSTA-knockdown cells by increasing the expression of proteins related to cell-cell junctions and barrier function. This highlights FK506 as a potential therapy for esophageal strictures in patients with CSTA mutations.
Inference and design of antibody specificity: from experiments to models and back
Authors: Fernandez-de-Cossio-Diaz Jorge , Uguzzoni Guido , Ricard Kévin , Anselmi Francesca , Nizak Clément , Pagnani Andrea , Rivoire Olivier
Published: October 2023

Exquisite binding specificity is essential for many protein functions but is difficult to engineer. Many biotechnological or biomedical applications require the discrimination of very similar ligands, which poses the challenge of designing protein sequences with highly specific binding profiles. Current methods for generating specific binders rely onin vitroselection experiments, but these have limitations in terms of library size and control over specificity profiles. We present a multi-stage approach that overcomes these limitations by combining high-throughput sequencing of phage display experiments with machine learning and biophysical modeling. Our models predict the binding profiles of antibodies against multiple ligands and generate antibody sequences with desired specificity profiles. The approach involves the identification of different binding modes, each associated with a particular ligand against which the antibodies are either selected or not. We demonstrate that the model successfully disentangles these modes, even when they are associated with chemically very similar ligands. Additionally, we demonstrate and validate experimentally the computational design of antibodies with customized specificity profiles, either with specific high affinity for a particular target ligand, or with cross-specificity for multiple target ligands. Overall, our results showcase the potential of leveraging a biophysical model learned from selections against multiple ligands to design proteins with tailored specificity, with applications to protein engineering extending beyond the design of antibodies.
Quantifying fluorescence lifetime responsiveness of environment sensitive probes for membrane fluidity measurements
Authors: Ragaller Franziska , Sjule Ellen , Urem Yagmur Balim , Schlegel Jan , El Rojbin , Urbancic Dunja , Urbancic Iztok , Blom Hans , Sezgin Erdinc
Published: October 2023

The structural diversity of different lipid species within the membrane defines its biophysical properties such as membrane fluidity, phase transition, curvature, charge distribution and tension. Environment-sensitive probes, which change their spectral properties in response to their surrounding milieu, have greatly contributed to our understanding of such biophysical properties. To realize the full potential of these probes and to avoid misinterpretation of their spectral responses, a detailed investigation of their fluorescence characteristics in different environments is necessary. Here, we examined fluorescence lifetime of two newly developed membrane order probes, NR12S and NR12A, in response to alterations in their environments such as degree of lipid saturation, cholesterol content, double bond position and configuration and phospholipid headgroup. As comparison, we investigated lifetime sensitivity of the membrane tension probe Flipper in these environments. Applying fluorescence lifetime imaging microscopy (FLIM) in both model membranes and biological membranes, all probes distinguished membrane phases by lifetime, but exhibited different lifetime sensitivities to varying membrane biophysical properties (e.g. cholesterol). While the lifetime of Flipper is particularly sensitive to membrane cholesterol content, NR12S and NR12A lifetime is moderately sensitive to both cholesterol content and lipid acyl chains. Moreover, all probes exhibit longer lifetimes at longer emission wavelengths in membranes of any complexity. This emission-wavelength dependency results in varying lifetime resolution at different spectral regions, highly relevant for FLIM data acquisition. Our data provides valuable insights on how to perform FLIM with these probes and highlights both their potential and limitations.
Synthetic Biodegradable Void-forming Hydrogels forIn Vitro3D Culture of Functional Human Bone Cell Networks
Authors: Zauchner Doris , Müller Monica Zippora , Horrer Marion , Bissig Leana , Zhao Feihu , Lee Sung Sik , Müller Ralph , Qin Xiao-Hua
Published: October 2023

Generating 3D bone cell networksin vitrothat accurately mimic the dynamic process of osteoblast embedding during early bone formation poses a significant challenge. Herein, we report a synthetic biodegradable macroporous hydrogel for efficient formation of 3D networks from human primary cells, analysis of cell-secreted extracellular matrix (ECM) and microfluidic integration. Using polymerization-induced phase separation, matrix metalloproteinase-sensitive polyethylene glycol hydrogels are formed with interconnected porosity in the presence of living cells. The pore size (5-20 μm) and permeability can be fine-tuned by adjusting the concentration and molecular weight of dextran. After encapsulation in these hydrogels, human mesenchymal stem cells and osteoblasts form a 3D cell network within 24 hours. The synthetic nature of this hydrogel enables histological analysis of cell-secreted collagen, a task previously challenging using collagen-derived hydrogels. Moreover, this hydrogel is integrated with a commercial chip, showcasing the potential for microfluidic perfusion cultures. Time-lapsed imaging of fluid flow and fast formation of 3D cell networks is demonstrated on chip. Altogether, this work introduces a versatile synthetic macroporous hydrogel, which can be integrated with microfluidic chip to enable 3D culture of human bone cell networks and analysis of cell-secreted ECM. This hydrogel may facilitate future mechanistic studies on bone development.
Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections
Authors: VanInsberghe David , McBride Dillon S. , DaSilva Juliana , Stark Thomas J. , Lau Max S.Y. , Shepard Samuel S. , Barnes John R. , Bowman Andrew S. , Lowen Anice C. , Koelle Katia
Published: October 2023

Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intra-host single nucleotide variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.
Lipin-1 restrains macrophage lipid synthesis to promote inflammation resolution
Authors: Bamgbose Temitayo T. , Schilke Robert M. , Igiehon Oluwakemi O. , Nkadi Ebubechukwu H. , Custis David , Bharrhan Sushma , Schwarz Benjamin , Bohrnsen Eric , Bosio Catharine M. , Scott Rona S. , Yurdagul Arif , Finck Brian N. , Woolard Matthew D.
Published: October 2023

Macrophages are critical to maintaining and restoring tissue homeostasis during inflammation. The lipid metabolic state of macrophages influences their function, but a deeper understanding of how lipid metabolism is regulated in pro-resolving macrophage responses is needed. Lipin-1 is a phosphatidic acid phosphatase with a transcriptional coregulatory activity (TC) that regulates lipid metabolism. We previously demonstrated that lipin-1 supports pro-resolving macrophage responses, and here, myeloid-associated lipin-1 is required for inflammation resolution, yet how lipin-1-regulated cellular mechanisms promote macrophage pro-resolution responses is unknown. We demonstrated that the loss of lipin-1 in macrophages led to increased free fatty acid, neutral lipid, and ceramide content and increased phosphorylation of acetyl-CoA carboxylase. The inhibition of the first step of lipid synthesis and transport of citrate from the mitochondria in macrophages reduced lipid content and restored efferocytosis and inflammation resolution in lipin-1mKO macrophages and mice. Our findings suggest macrophage-associated lipin-1 restrains lipid synthesis, promoting pro-resolving macrophage function in response to pro-resolving stimuli.

Teaser

Lipin 1 blockade of lipid biosynthesis inducing mitochondrial citrate export promotes efferocytosis and inflammation resolution.
Multilayer network associations between the exposome and childhood brain development
Authors: Simpson-Kent Ivan L. , Gataviņš Mārtiņš M. , Tooley Ursula A. , Boroshok Austin L. , McDermott Cassidy L. , Park Anne T. , Reyes Lourdes Delgado , Bathelt Joe , Tisdall M. Dylan , Mackey Allyson P.
Published: October 2023

Growing up in a high poverty neighborhood is associated with elevated risk for academic challenges and health problems. Here, we take a data-driven approach to exploring how measures of children’s environments relate to the development of their brain structure and function in a community sample of children between the ages of 4 and 10 years. We constructed exposomes including measures of family socioeconomic status, children’s exposure to adversity, and geocoded measures of neighborhood socioeconomic status, crime, and environmental toxins. We connected the exposome to two structural measures (cortical thickness and surface area,n= 170) and two functional measures (participation coefficient and clustering coefficient,n= 130). We found dense connectionswithinexposome and brain layers and sparse connectionsbetweenexposome and brain layers. Lower family income was associated with thinner visual cortex, consistent with the theory that accelerated development is detectable in early-developing regions. Greater neighborhood incidence of high blood lead levels was associated with greater segregation of the default mode network, consistent with evidence that toxins are deposited into the brain along the midline. Our study demonstrates the utility of multilayer network analysis to bridge environmental and neural explanatory levels to better understand the complexity of child development.
Functional effects of TBC1 domain containing kinase deletion in immortalized B cells and plasma cells
Authors: von Beck Troy , Jacob Joshy
Published: October 2023

TBC1 domain containing kinase (TBCK) is a ubiquitous protein pseudokinase highly expressed in neurons and glial cells. Mutations in TBCK disrupt nervous system function and cause a characteristic syndrome of intellectual disability and hypotonia with various other comorbidities occurring in non-nervous tissues. Previous studies have shown a vacuolation defect present in B cells from individuals with TBCK mutations, but it is unclear if this affects plasma cell differentiation or humoral immunity. Recent research has revealed that TBCK is part of the FERRY complex involved in mRNA transport and is implicated in regulating mTORC1 signaling, autophagy, and cellular processes like cell proliferation and migration. Yet, the exact role of TBCK in these processes is still not fully understood. In this study, TBCK knockout cell lines were generated to investigate its impact on B cells and plasma cells. TBCK knockout plasma cells showed reduced immunoglobulin secretion after one week in culture, suggesting a possible defect in recycling cell components or energy usage. However, more experiments are needed to confirm this observation.
Comprehensive Assessment of Blood-Brain Barrier Opening and Sterile Inflammatory Response: Unraveling the Therapeutic Window
Authors: Martinez Payton , Song Jane J. , Garay Francis G. , Song Kang-Ho , Mufford Toni , Steiner Jenna , DeSisto John , Ellens Nicholas , Serkova Natalie J. , Green Adam L. , Borden Mark
Published: October 2023

Microbubbles (MBs) combined with focused ultrasound (FUS) have emerged as a promising noninvasive technique to permeabilize the blood-brain barrier (BBB) for drug delivery to the brain. However, the safety and biological consequences of BBB opening remain incompletely understood. This study investigates the effects of varying microbubble volume doses (MVD) and ultrasound mechanical indices (MI) on BBB opening and the sterile inflammatory response (SIR) using high-resolution ultra-high field MRI-guided FUS in mouse brains. The results demonstrate that both MVD and MI significantly influence the extent of BBB opening, with higher doses and mechanical indices leading to increased permeability. Moreover, RNA sequencing reveals upregulated inflammatory pathways and immune cell infiltration after BBB opening, suggesting the presence and extent of SIR. Gene set enrichment analysis identifies 12 gene sets associated with inflammatory responses that are upregulated at higher doses of MVD or MI. A therapeutic window is established between significant BBB opening and the onset of SIR, providing operating regimes for avoiding each three classes of increasing damage from stimulation of the NFκB pathway via TNFL signaling to apoptosis. This study contributes to the optimization and standardization of BBB opening parameters for safe and effective drug delivery to the brain and sheds light on the underlying molecular mechanisms of the sterile inflammatory response.

Significance Statement

The significance of this study lies in its comprehensive investigation of microbubble-facilitated focused ultrasound for blood-brain barrier (BBB) opening. By systematically exploring various combinations of microbubble volume doses and ultrasound mechanical indices, the study reveals their direct impact on the extent of BBB permeability and the induction of sterile inflammatory response (SIR). The establishment of a therapeutic window between significant BBB opening and the onset of SIR provides critical insights for safe and targeted drug delivery to the brain. These findings advance our understanding of the biological consequences of BBB opening and contribute to optimizing parameters for clinical applications, thus minimizing potential health risks, and maximizing the therapeutic potential of this technique.
Accurate Automated Segmentation of Autophagic Bodies in Yeast Vacuoles Using Cellpose 2.0
Authors: Marron Emily C. , Backues Jonathan , Ross Andrew M. , Backues Steven K.
Published: October 2023

Segmenting autophagic bodies in yeast TEM images is a key technique for measuring changes in autophagosome size and number in order to better understand autophagy. Manual segmentation of these images can be very time consuming, particularly since hundreds of images are needed for accurate measurements. Here we describe a validated Cellpose 2.0 model that can segment these images with accuracy comparable to that of human experts. This model can be used for fully automated segmentation, eliminating the need for manual body outlining, or for model-assisted segmentation, which allows human oversight but is still five times as fast as the current manual method. The model and instructions for its use are presented here for the autophagy community.
Neutrophil Extracellular Traps have DNAzyme activity that drives bactericidal potential
Authors: Ku Ti-Hsuan , Ram-Mohan Nikhil , Zudock Elizabeth J , Abe Ryuichiro , Yang Samuel
Published: October 2023

The mechanisms of bacterial killing by neutrophil extracellular traps (NETs) are unclear. DNA, the largest component of NETs is believed to merely be a scaffold with minimal antimicrobial activity through the charge of the backbone. Here, we report that NETs DNA is beyond a scaffold and produces hydroxyl free radicals through the spatially concentrated G-quadruplex/hemin DNAzyme complexes, driving bactericidal effects. Immunofluorescence staining showed colocalization of G-quadruplex and hemin in extruded NETs DNA, and Amplex UltraRed assay portrayed its peroxidase activity. Proximity labeling of bacteria revealed localized concentration of radicals resulting from NETs bacterial trapping.Ex vivobactericidal assays revealed that G-quadruplex/hemin DNAzyme is the primary driver of bactericidal activity in NETs. NETs are DNAzymes that may have important biological consequences.

One-Sentence Summary

G-quadruplex/hemin DNAzymes may be major contributors to biological consequences of neutrophil extracellular traps.
Platelet proteo-transcriptomic profiling validates mediators of thrombosis and proteostasis in patients with myeloproliferative neoplasms
Authors: Kelliher Sarah , Gamba Sara , Weiss Luisa , Shen Zhu , Marchetti Marina , Schieppati Francesca , Scaife Caitriona , Madden Stephen , Bennett Kathleen , Fortune Anne , Maung Su , Fay Michael , Áinle Fionnuala Ní , Maguire Patricia , Falanga Anna , Kevane Barry , Krishnan Anandi
Published: October 2023

Patients with chronic Myeloproliferative Neoplasms (MPN) including polycythemia vera (PV) and essential thrombocythemia (ET) exhibit unique clinical features, such as a tendency toward thrombosis and hemorrhage, and risk of disease progression to secondary bone marrow fibrosis and/or acute leukemia. Although an increase in blood cell lineage counts (quantitative features) contribute to these morbid sequelae, the significant qualitative abnormalities of myeloid cells that contribute to vascular risk are not well understood. Here, we address this critical knowledge gap via a comprehensive and untargeted profiling of the platelet proteome in a large (n= 140) cohort of patients (from two independent sites) with an established diagnosis of PV and ET (and complement prior work on the MPN platelet transcriptome from a third site). We discover distinct MPN platelet protein expression and confirm key molecular impairments associated with proteostasis and thrombosis mechanisms of potential relevance to MPN pathology. Specifically, we validate expression of high-priority candidate markers from the platelet transcriptome at the platelet proteome (e.g.,calreticulin (CALR), Fc gamma receptor (FcγRIIA)and galectin-1 (LGALS1)pointing to their likely significance in the proinflammatory, prothrombotic and profibrotic phenotypes in patients with MPN. Together, our proteo-transcriptomic study identifies the peripherally-derived platelet molecular profile as a potential window into MPN pathophysiology and demonstrates the value of integrative multi-omic approaches in gaining a better understanding of the complex molecular dynamics of disease.

Highlights

MPN patient platelet proteome identifies key pathobiological mediators of thrombosis and proteostasis. The MPN platelet proteomic profile validates our prior findings from the platelet transcriptome.
Selective Removal of 7KC by a Novel Atherosclerosis Therapeutic Candidate Reverts Foam Cells to a Macrophage-like Phenotype
Authors: Bhargava Prerna , Dinh Darren , Teramayi Fadzai , Silberg Ana , Petler Noa , Anderson Amelia M. , Clemens Daniel M. , O’Connor Matthew S.
Published: October 2023

The removal of the toxic oxidized cholesterol, 7-ketocholesterol (7KC), from cells through the administration of therapeutics has the potential to treat atherosclerosis and various other pathologies. While cholesterol is a necessary building block for homeostasis, oxidation of cholesterol can lead to the formation of toxic oxysterols involved in various pathologies, the most prominent of which is 7KC, which is formed through the non-enzymatic oxidation of cholesterol. Oxidized LDL (oxLDL) particles, highly implicated in heart disease, contain high levels of 7KC, and molecular 7KC is implicated in the pathogenesis of numerous diseases, including multiple sclerosis, hypercholesterolemia, sickle cell anemia, and multiple age related diseases. Of particular interest is the role of 7KC in the progression of atherosclerosis, with several studies associating elevated levels of 7KC with the etiology of the disease or in the transition of macrophages to foam cells. This research aims to elucidate the molecular mechanisms of UDP-003, a novel therapeutic, in mitigating the harmful effects of 7KC in mouse and human monocyte and macrophage cell lines. Experimental evidence demonstrates that administration of UDP-003 can reverse the foam cell phenotype, rejuvenating these cells by returning phagocytic function and decreasing both reactive oxygen species (ROS) and intracellular lipid droplet accumulation. Furthermore, our data suggests that the targeted removal of 7KC from foam cells with UDP-003 can potentially prevent and reverse atherosclerotic plaque formation. UDP-003 has the potential to be the first disease-modifying therapeutic approach to treating atherosclerotic disease.
Effect of homotypicvs. heterotypic interactions on the cellular uptake of extracellular vesicles
Authors: Jhaveri Jhanvi R. , Khare Purva , Pinky Paromita Paul , Kamte Yashika S. , Chandwani Manisha N. , Milosevic Jadranka , Abraham Nevil , Dave Kandarp M. , Zheng Si-yang , O’Donnell Lauren , Manickam Devika S
Published: October 2023

Extracellular vehicles (EVs) are an emerging class of drug carriers and are primarily reported to be internalized into recipient cells via a combination of endocytic routes such as clathrin-mediated, caveolae-mediated and macropinocytosis pathways. In this work, (1) we investigated potential effects of homotypicvs. heterotypic interactions by studying the cellular uptake of homologous EVs (EV donor cells and recipient cells of the same type)vs. heterologous EVs (EV donor cells and recipient cells of different types) and (2) determined the route of EV internalization into low pinocytic/hard-to-deliver cell models such as brain endothelial cells (BECs). We used BECs and macrophages as low-pinocytic and phagocytic cell models, respectively, to study the effect of homotypicvs. heterotypic interactions on EV uptake in the recipient cells. Homotypic interactions led to a greater extent of uptake into the recipient BECs compared to heterotypic interactions. However, we did not see a complete reduction in EV uptake into recipient BECs when endocytic pathways were blocked using pharmacological inhibitors. Our results suggest that EVs primarily use membrane fusion to enter low-pinocytic recipient BECs instead of relying on endocytosis.Lipophilic PKH67 dye-labeled EVsbut not intravesicular esterase-activated calcein ester-labeled EVs severely reduced particle uptake into BECs while phagocytic macrophages internalized both types of EV-labeled particles to comparable extents. Our results also highlight the importance of carefully choosing labeling dye chemistry to study EV uptake, especially in the case of low pinocytic cells such as BECs.

Graphical abstract
A novel genetic fluorescent reporter to visualize mitochondrial nucleoids
Authors: Deng Jingti , Swift Lucy , Zaman Mashiat , Shahhosseini Fatemeh , Sharma Abhishek , Bureik Daniela , Padovani Francesco , Benedikt Alissa , Jaiswal Amit , Brideau Craig , Grewal Savraj , Schmoller Kurt M. , Colarusso Pina , Shutt Timothy E.
Published: October 2023

Mitochondria have their own genome (mtDNA), which is present in hundreds of copies per cell and organized into nucleoid structures that are distributed throughout the dynamic mitochondrial network. Beyond encoding essential protein subunits for oxidative phosphorylation, mtDNA can also serve as a signalling molecule when it is present into the cytosol. Despite the importance of this genome, there are still many unknowns with respect to its regulation. To study mtDNA dynamics in living cells, we have developed a genetic fluorescent reporter, mt-HI-NESS, which is based on the HI-NESS reporter that uses the bacterial H-NS DNA binding domain. Here, we describe how this reporter can be used to image mtDNA nucleoids for live cell imaging without affecting the replication or expression of the mtDNA. In addition to demonstrating the adaptability of the mt-HI-NESS reporter for multiple fluorescent proteins, we also emphasize important factors to consider during the optimization and application of this reporter.
Borrowing Transcriptional Kinases to Activate Apoptosis
Authors: Sarott Roman , Gourisankar Sai , Karim Basel , Nettles Sabin , Yang Haopeng , Dwyer Brendan G. , Simanauskaite Juste M. , Tse Jason , Abuzaid Hind , Krokhotin Andrey , Zhang Tinghu , Hinshaw Stephen M. , Green Michael R. , Crabtree Gerald R. , Gray Nathanael S.
Published: October 2023

Protein kinases are disease drivers whose therapeutic targeting traditionally centers on inhibition of enzymatic activity. Here chemically induced proximity is leveraged to convert kinase inhibitors into context-specific activators of therapeutic genes. Bivalent molecules that link ligands of the transcription factor B-cell lymphoma 6 (BCL6) to ATP-competitive inhibitors of cyclin-dependent kinases (CDKs) were developed to re-localize CDK to BCL6-bound loci on chromatin and direct phosphorylation of RNA Pol II. The resulting BCL6-target proapoptotic gene expression translated into killing of diffuse large B-cell lymphoma (DLBCL) cells at 72 h with EC50s of 0.9 – 10 nM and highly specific ablation of the BCL6-regulated germinal center response in mice. The molecules exhibited 10,000-fold lower cytotoxicity in normal lymphocytes and are well tolerated in mice. Genomic and proteomic evidence corroborated a gain-of-function mechanism where, instead of global enzyme inhibition, a fraction of total kinase activity is borrowed and re-localized to BCL6-bound loci. The strategy demonstrates how kinase inhibitors can be used to context-specifically activate transcription, accessing new therapeutic space.
Brain enlargement with rostral bias in larvae from a spontaneously occurring female variant line ofXenopus; role of aberrant embryonic Wnt/β-catenin signaling
Authors: Hongo Ikuko , Yamaguchi Chihiro , Okamoto Harumasa
Published: October 2023

Increased brain size and its rostral bias are hallmarks of vertebrate evolution, but the underlying developmental and genetic basis remains poorly understood. To provide clues to understanding vertebrate brain evolution, we investigated the developmental mechanisms of brain enlargement observed in the offspring of a previously unrecognized, spontaneously occurring female variant line ofXenopusthat appears to reflect a genetic variation. Brain enlargement in larvae from this line showed a pronounced rostral bias that could be traced back to the neural plate, the primordium of the brain. At the gastrula stage, the Spemann organizer, which is known to induce the neural plate from the adjacent dorsal ectoderm and give it the initial rostrocaudal patterning, was expanded from dorsal to ventral in a large proportion of the offspring of variant females. Consistently,siamoisexpression, which is required for Spemann organizer formation, was expanded laterally from dorsal to ventral at the blastula stage in variant offspring. This implies that the active region of the Wnt/β-catenin signaling pathway was similarly expanded in advance on the dorsal side, assiamoisis a target gene of this pathway. Notably, the earliest detectable change in variant offspring was in fertilized eggs, in which maternalwnt11bmRNA, a candidate dorsalizing factor that activates Wnt/β-catenin signaling, had a wider distribution in the vegetal cortical cytoplasm. Since lateral spreading ofwnt11bmRNA, and possibly that of other potential maternal dorsalizing factors in these eggs, is expected to facilitate lateral expansion of the active region of the Wnt/β-catenin pathway during subsequent embryonic stages, we concluded that aberrant Wnt/β-catenin signaling could cause rostral-biased brain enlargement via expansion ofsiamoisexpression and consequent expansion of the Spemann organizer inXenopus. Our studies of spontaneously occurring variations in brain development inXenopuswould help uncover genetic mutations that drive analogous morphogenetic variations during vertebrate brain evolution.
Plasma-based antigen persistence in the post-acute phase of SARS-CoV-2 infection
Authors: Peluso Michael J. , Swank Zoe N. , Goldberg Sarah A. , Lu Scott , Dalhuisen Thomas , Borberg Ella , Senussi Yasmeen , Luna Michael A. , Chang Song Celina , Clark Alexus , Zamora Andhy , Lew Megan , Viswanathan Badri , Huang Beatrice , Anglin Khamal , Hoh Rebecca , Hsue Priscila Y. , Durstenfeld Matthew S. , Spinelli Matthew A. , Glidden David V. , Henrich Timothy J. , Kelly J. Daniel , Deeks Steven G. , Walt David R. , Martin Jeffrey N.
Published: October 2023

BACKGROUND

Persistent symptoms among some persons who develop COVID-19 has led to the hypothesis that SARS-CoV-2 may, in some form or location, persist for long periods following acute infection. Several studies have shown data in this regard but are limited by non-representative and small study populations, short duration since acute infection, and lack of a true-negative comparator group to assess assay specificity.

METHODS

We evaluated adults with RNA-confirmed COVID-19 at multiple time points following acute infection (pandemic-era participants) and adults with specimens collected prior to 2020 (pre-pandemic era). Using once-thawed plasma, we employed the Simoa® (Quanterix) single molecule array detection platform to measure SARS-CoV-2 spike, S1, and nucleocapsid antigens.

RESULTS

Compared to 250 pre-pandemic participants who had 2% assay positivity, detection of any SARS-CoV-2 antigen was significantly more frequent among 171 pandemic-era participants at three different time periods in the post-acute phase of infection. The absolute difference in SARS-CoV-2 plasma antigen prevalence was +11% (95% CI: +5.0% to +16%) at 3.0-6.0 months post-onset of COVID-19; +8.7% (95% CI: +3.1% to +14%) at 6.1 to 10.0 months; and +5.4% (95% CI: +0.42% to +10%) at 10.1-14.1 months. Hospitalization for acute COVID-19 and, among the non-hospitalized, worse self-reported health during acute COVID-19 were associated with greater post-acute phase antigen detection.

CONCLUSIONS

Compared to uninfected persons, there is an excess prevalence of SARS-CoV-2 antigenemia in SARS-CoV-2-infected individuals up to 14 months after acute COVID-19. These findings motivate an urgent research agenda regarding the short-term and long-term clinical manifestations of this viral persistence.
Children’s Residential Proximity, Spousal Presence and Modifiable Risk Factors for Dementia among Older Adults with Cognitive Impairment
Authors: Lin Zhuoer , Yin Xuecheng , Levy Becca R. , Yuan Yue , Chen Xi
Published: October 2023

Background

Cognitive impairment in older adults poses considerable challenges, and the role of family support becomes increasingly crucial. This study aims to examine the impact of children’s residential proximity and spousal presence on the key modifiable risk factors for dementia among older adults with cognitive impairment.

Methods

Utilizing the Health and Retirement Study (HRS) data from 1995 to 2018, we analyzed 14,731 participants (35,840 person-waves) aged 50 and older with cognitive impairment. Family support was characterized based on the presence of a spouse and residential proximity to children. Smoking, depressive symptoms and social isolation were included as the key modifiable risk factors for dementia identified in later life. Using mixed-effects logistic regressions, associations between access to family support and the modifiable risk factors were determined, adjusting for various socio-demographic and health-related factors.

Results

Significant associations were found between access to family support and modifiable risk factors for dementia. Cognitively impaired older adults with less available family support, characterized by distant-residing children and the absence of a spouse, had significantly higher risks of smoking, depressive symptoms, and social isolation. Moreover, we revealed a consistent gradient in the prevalence of the risk factors based on the degree of family support. Relative to older adults with a spouse and co-resident children, those without a spouse and with all children residing further than 10 miles displayed the highest risks of smoking, depressive symptoms, and social isolation.

Conclusion

Access to family support, particularly from spouses and proximate children, plays a protective role against key modifiable risk factors for dementia in older adults with cognitive impairment. The findings highlight the need for bolstering family and social support systems to enhance the well-being of this vulnerable population.
A parametric bootstrap approach for computing confidence intervals for genetic correlations with application to genetically-determined protein-protein networks
Authors: Tsai Yi-Ting , Hrytsenko Yana , Elgart Michael , Tahir Usman , Chen Zsu-Zsu , Wilson James G , Gerszten Robert , Sofer Tamar
Published: October 2023

Genetic correlation refers to the correlation between genetic determinants of a pair of traits. When using individual-level data, it is typically estimated based on a bivariate model specification where the correlation between the two variables is identifiable and can be estimated from a covariance model that incorporates the genetic relationship between individuals, e.g., using a pre-specified kinship matrix. Inference relying on asymptotic normality of the genetic correlation parameter estimates may be inaccurate when the sample size is low, when the genetic correlation is close to the boundary of the parameter space, and when the heritability of at least one of the traits is low. We address this problem by developing a parametric bootstrap procedure to construct confidence intervals for genetic correlation estimates. The procedure simulates paired traits under a range of heritability and genetic correlation parameters, and it uses the population structure encapsulated by the kinship matrix. Heritabilities and genetic correlations are estimated using the close-form, method of moment, Haseman-Elston regression estimators. The proposed parametric bootstrap procedure is especially useful when genetic correlations are computed on pairs of thousands of traits measured on the same exact set of individuals. We demonstrate the parametric bootstrap approach on a proteomics dataset from the Jackson Heart Study.
Estimating the maximum risk of measles outbreaks due to heterogeneous fall in immunization rates
Authors: Wu Nicholas , Moon Sifat Afroj , Falk Ami , Marathe Achla , Vullikanti Anil
Published: October 2023

Immunization rates for childhoold vaccines, such as MMR, have seen a reduction over the recent years; this fall has only been accentuated after the COVID-19 pandemic. However, there is limited data on where the rates have reduced, and prior work has shown that heterogeneity in the drop in immunization rates has a significant impact on the risk of an outbreak. An important question from a public health perspective is: what is the maximum size of an outbreak in a region, when limited information is available on the fall in immunization rates within the region?

This turns out to be a very hard computational problem. We develop a Bayesian optimization based approach for estimating the maximum outbreak size, and use it on a measles model for the state of Virginia. Our results show that the maximum outbreak size is several orders of magnitude higher than estimated in a baseline which assumes homogeneous fall. Even for a 5% reduction in the statewide immunzation rate, the expected outbreak size can be very high. The maximum outbreak size depends crucially on the importation location, i.e., where the disease starts, and importation in an urban region leads to a significantly higher outbreak. The outbreak size remains high even if the drop in immunization is bounded in health service areas in the state.