bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapaprotin is Activated by an Endopeptidase to Disassemble 26S Proteasome
Authors: Peng Hanjing , Guo Zufeng , Wang Wei Li , Yin Deyao , Zou Shitao , Thomas Asbell , Ullman Brett R , Maya Thakar , Zhang Feiran , Hong Sam Y. , Rao A.V. Subba , Wang Kunyu , Zhang Shuwen , Li Xuemei , Margolis Seth Shatkin , Matsui William H. , Gocke Christian B. , Mao Youdong , Liu Jun O.
Published: February 2025

The 19S regulatory particle (RP) associates with the 20S core particle (CP) to form the 26S proteasome, an evolutionarily conserved holoenzyme that plays key roles in both physiological and pathological processes. Proteasome inhibitors that target the catalytic subunits within the 20S have proven to be valuable research tools and therapeutics for various cancers. Herein we report the discovery of rapaprotin, a 26S proteasome assembly inhibitor from our natural product-inspired hybrid macrocycle rapafucin library. Rapaprotin induces apoptosis in both myeloma and leukemia cell lines. Genome-wide CRISPR-Cas9 screen identified a cytosolic enzyme, prolyl endopeptidase (PREP) that is required for the pro-apoptotic activity of rapaprotin. Further mechanistic studies revealed that rapaprotin acts as a molecular transformer, changing from an inactive cyclic form into an active linear form, rapaprotin-L，upon PREP cleavage, to block 26S proteasome activity. Time-resolved cryogenic electron microscopy (cryo-EM) revealed that rapaprotin-L induces dissociation of the 19S RP from the 26S holoenzyme，which was verified in cells. Furthermore, rapaprotin exhibits a marked synergistic effect with FDA-approved proteasome inhibitors and resensitizes drug-resistant multiple myeloma cells from patients to bortezomib. Taken together, these results suggest that rapaprotin is a new chemical tool to probe the dynamics of the 26S proteasome assembly and a promising anticancer drug lead.
DNA origami vaccines program antigen-focused germinal centers
Authors: Romanov Anna , Knappe Grant A , Ronsard Larance , Suh Heikyung , Omer Marjan , Chapman Asheley P. , Lewis Vanessa , Spivakovsky Katie , Canales Josue , Reizis Boris , Tingle Ryan , Cottrell Christopher , Schiffner Torben , Lingwood Daniel , Bathe Mark , Irvine Darrell J
Published: February 2025

Recruitment and expansion of rare precursor B cells in germinal centers (GCs) is a central goal of vaccination to generate broadly neutralizing antibodies (bnAbs) against challenging pathogens such as HIV. Multivalent immunogen display is a well-established method to enhance vaccine-induced B cell responses, typically accomplished by using natural or engineered protein scaffolds. However, these scaffolds themselves are targets of antibody responses, with the potential to generate competitor scaffold-specific B cells that could theoretically limit expansion and maturation of on-target B cells in the GC response. Here, we rationally designed T-independent, DNA-origami based virus-like particles (VLPs) with optimal antigenic display of the germline targeting HIV Env immunogen, eOD-GT8, and appropriate T cell help to achieve a potent GC response. In preclinical mouse models, these DNA-VLPs expanded significantly higher frequencies of epitope-specific GC B cells compared with a state-of-the-art clinical protein nanoparticle. Optimized DNA-VLPs primed germinal centers focused on the target antigen and rapidly expanded subdominant broadly neutralizing antibody precursor B cells for HIV with a single immunization. Thus, avoiding scaffold-specific responses augments priming of bnAb precursor B cells, and DNA-VLPs are a promising platform for promoting B cell responses towards challenging subdominant epitopes.
HIV-Induced Sialoglycans on Infected Cells Promote Immune Evasion from Myeloid Cell-Mediated Killing
Authors: Singh Shalini , Islam S M Shamsul , Liu Rui , Adeniji Opeyemi S. , Giron Leila B , Saini Pratima , Danesh Ali , Denton Paul W , Jones Brad , Xiao Han , Abdel-Mohsen Mohamed
Published: February 2025

Sialic acid-containing glycans (sialoglycans) on pathological cells interact with Siglecs, glyco-immune checkpoint receptors expressed on myeloid cells such as monocytes and neutrophils. This interaction suppresses the cytotoxic functions of these immune cells. We show that HIV infection reprograms the glycosylation machinery of infected cells to increase the expression of specific sialoglycan ligands for Siglecs-3, -7, and -9. These ligands engage Siglecs on myeloid cells, impairing their ability to target HIV-infected cells. Selective disruption of these interactions using 10-1074-Sia, an HIV-specific antibody conjugated to sialidase, an enzyme that removes sialic acids, significantly enhances monocyte- and neutrophil-mediated killing of HIV-infected cells in autologous assays. Treatment with 10-1074-Sia in humanized mice infected with HIV reduces viral load and decreases inflammation. These findings reveal a novel immune evasion mechanism exploited by HIV to evade myeloid cell immune surveillance and highlight the potential of targeting sialoglycan-Siglec interactions to improve immune clearance of HIV-infected cells.
A cross-week analysis of urinary extracellular vesicles after respiratory tract exposure intervention identifies systemic signaling changes — a pilot study of isocyanate-exposed workers
Authors: Sohal Ikjot Singh , Pal Anoop K , Lepine Jack , Liu Pengyuan , Wisnewski Adam V , Redlich Carrie A , Bello Dhimiter
Published: February 2025

Extracellular vesicles (EVs) from various biofluids have demonstrated potential as prognostic and diagnostic biomarkers in several diseases. However, their utility in early stages of disease development has not been extensively investigated. Additionally, given their role in intercellular communication, decoding the landscape of underlying cell–to–cell signaling in a clinical or subclinical condition based on EV-specific analyses has so far remained challenging. Here, we demonstrate the utility of urinary EVs for cross-week biomonitoring and for capturing the perturbation of underlying organismal signaling in a small well–characterized group of workers with inhalational exposure to methylene diphenyl diisocyanate (MDI) in fabric coating factory. Workers wore organic vapor cartridge respirators during the week to eliminate respiratory exposures. Spot urine was collected before and after the respirator intervention — pre–RESP and post–RESP, respectively. Following extensive characterization of EVs isolated from the urine samples, the relative enrichment of EV–specific RNAs and proteins and their associated biological processes were determined between pre–RESP and post–RESP samples. Distinct EV–specific RNA and protein signatures between the two groups strongly correlated with established biological and immune–related processes involved in asthma and lung inflammation. Using single cell transcriptomics data from the human cell atlas, EV–mRNAs highly enriched in pre–RESP, but not post–RESP, samples revealed global immune dysregulation and enrichment of associated cell types, such as monocytes, macrophages, and neutrophils. The findings indicate that urinary EVs and their contents can be utilized for biomonitoring of lung health and can reveal the effects of exposure on the underlying organismal signaling.
An Fc-SPINK1 fusion protein inhibits pancreatic inflammation in a mouse model
Authors: Way J. C. , Heid D. , Theiss M. , Nørrelykke S. , Barck L. , Burger L. , Bredl J. A. , Dobbertin T. , Höflich P. , Stadelmann T. , Niopek D. , Chan K. Redfield , Sivaraman R. , Graveline A. R. , Vernet A. , Sanchez-Ventura M. , Silver P. A.
Published: February 2025

Pancreatitis results from premature activation and impaired inactivation of pancreatic proteases, primarily trypsin, leading to self-digestion, tissue necrosis, fibrosis, and inflammation. SPINK1 is a pancreas-specific inhibitor of trypsin that prevents premature trypsin activation, and could be a candidate therapeutic. However, because of its small size, SPINK1 would be subject to rapid renal clearance, making it ineffective. To construct a long half-life therapeutic inhibitor of trypsin for pancreatitis treatment we fused this protein to the C-terminus of an IgG1 antibody Fc element, increasing the size to ∼78 kDa, thereby exceeding the renal clearance threshold and providing for FcRn-mediated recycling out of cells. A non-glycosylated form of Fc-SPINK1 was expressed in the yeastPichia pastoris. Fc-SPINK1 inhibits trypsin enzyme activityin vitro. The blood pharmacokinetics in mice are consistent with a three-compartment distribution model and a terminal half-life of ∼3 days. In a caerulein-induced mouse model of pancreatitis, Fc-SPINK1 significantly ameliorated cell death and immune cell infiltration. We developed an automated image analysis technique to quantify pancreatitis-associated loss of tissue cohesion, and found that Fc-SPINK1 also reduced this effect. This study demonstrates the potential of Fc-SPINK1 as a rationally designed therapy for pancreatitis.
Dissection of Gαs and Hedgehog signaling crosstalk reveals therapeutic opportunities to target adenosine receptor 2b in Hedgehog-dependent tumors
Authors: Krantz Sarah , Bell Braden , Lund Katherine , Salinas Parra Natalia , Ng Yeap , De Oliveira Rosa Natalia , Mukhopadhyay Saikat , St Croix Brad , Sarin Kavita Y , Weigert Roberto , Raimondi Francesco , Iglesias-Bartolome Ramiro
Published: February 2025

Basal cell carcinoma (BCC), the most common human cancer, is driven by hyperactivation of Hedgehog Smoothened (SMO) and GLI transcription. Gαs and protein kinase A (PKA) negatively regulate Hedgehog signaling, offering an alternative BCC development and treatment pathway. Here, using histology alongside bulk and single-cell RNA sequencing, we find that mouse BCC-like tumors that originate from Gαs pathway inactivation are strikingly similar to those driven by canonical Hedgehog SMO. Interestingly, mutations that reduce Gαs and PKA activity are present in human BCC. Tumors from Gαs pathway inactivation are independent of the canonical Hedgehog regulators SMO and GPR161, establishing them as an SMO-independent oncogenic Hedgehog signaling model. Finally, we demonstrate that activation of the Gαs-coupled adenosine 2B receptor counteracts oncogenic SMO, reducing Hedgehog signaling and tumor formation and offering a potential therapeutic strategy for BCC.
CyclicCAE: A Conformational Autoencoder for Efficient Heterochiral Macrocyclic Backbone Sampling
Authors: Powers Andrew C , Renfrew P Douglas , Hosseinzadeh Parisa , Mulligan Vikram Khipple
Published: February 2025

Macrocycles are a promising therapeutic class. The incorporation of heterochiral and non-natural chemical building-blocks presents challenges for rational design, however. With no existing machine learning methods tailored for heterochiral macrocycle design, we developed a novel convolutional autoencoder model to rapidly generate energetically favorable macrocycle backbones for heterochiral design and structure prediction. Our approach surpasses the current state-of-the-art method, Generalized Kinematic loop closure (GenKIC) in the Rosetta software suite. Given the absence of large, available macrocycle datasets, we created a custom dataset in-house and in silico. Our model, CyclicCAE, produces energetically stable backbones and designable structures more rapidly than GenKIC. It enables users to perform energy minimization, generate structurally similar or diverse inputs via MCMC, and conduct inpainting with fixed anchors or motifs. We propose that this novel method will accelerate the development of stable macrocycles, speeding up macrocycle drug design pipelines.
Dynamics of spinal fluid immune cell alterations following cladribine tablet treatment in multiple sclerosis
Authors: Smirnov Roman A , Cantoni Claudia , Lee Kenneth , Agnihotri Rea A , Axtell Robert C , Salter Amber , Lancia Samantha , Paley Michael A , Hayward Brooke , Korich Julie , Evans Emily , Pardo Gabriel , Stuve Olaf , Bar-Or Amit , Artyomov Maxim N , Cross Anne H , Edelson Brian T , Wu Gregory F
Published: February 2025

Background and Objectives: Oral cladribine tablet (CladT) therapy is efficacious for relapsing multiple sclerosis (MS). However, the mechanisms by which cladribine exerts benefit in MS remain unclear, particularly regarding its effects on compartmentalized inflammation within the cerebrospinal fluid (CSF). Methods: Transcriptional profiles along with T and B lymphocyte receptor repertoires from CSF and blood were obtained by single cell sequencing methods from a single site participating in a phase IV clinical trial investigating the impact of cladribine treatment for MS. All subjects provided blood and CSF samples immediately before starting CladT therapy and were randomized to also provide samples at either five weeks, ten weeks, one year, or two years post-CladT therapy. Thirty-four samples from 13 individuals with relapsing MS before and after treatment were available to test the hypothesis that CladT alters the composition and phenotype of lymphocytes in the CSF. Results: We found that treatment with CladT profoundly altered cellular composition, but not the transcriptional phenotype, of immune cells in the CSF. In particular, we identified a reduction of switched memory B cells but recovery of naive B cells in the CSF, similar to our findings in blood. Additionally, populations of CD4 Treg cells emerged early after CladT therapy and remained elevated one year later in the CSF, but not in the blood. Antigen receptor sequencing revealed a moderate decrease in numbers of large clonally expanded CD8 T cell clones (>10 cells/clone) primarily in the CSF, but also in the blood post-CladT treatment. Discussion: Our results identified unique cellular dynamics and changes in T and B cell clonality in both tissues which can potentially explain long-term beneficial effects of CladT therapy in MS, including preservation of immune function and relatively low number of side effects. Altogether, this study demonstrates that CladT treatment had a substantial impact not only on blood, but also on the CSF compartment highlighting the importance of cross-tissue analysis for better understanding of effect and the mechanism of action of DMTs.
Granular hydrogels as brittle yield stress fluids
Authors: Thompson Gunnar B , Lee Jiye , Kamani Krutarth M , Flores-Velasco Noah , Rogers Simon A , Harley Brendan
Published: February 2025

While granular hydrogels are increasingly used in biomedical applications, methods to capture their rheological behavior generally consider shear-thinning and self-healing properties or produce ensemble metrics such as the dynamic moduli. Analytical approaches paired with common oscillatory shear tests can describe not only solid-like and fluid-like behavior of granular hydrogels but also transient characteristics inherent in yielding and unyielding processes. Combining oscillatory shear testing with consideration of Brittility (Bt) via the Kamani-Donley-Rogers (KDR) model, we show granular hydrogels behave as brittle yield stress fluids with complex transient rheology. We quantify steady and transient rheology as a function of microgel (composition; diameter) and granular (packing; droplet heterogeneity) assembly properties for mixtures of polyethylene glycol and gelatin microgels. The KDR model with Bt captures granular hydrogel behavior for a wide range of design parameters, reducing the complex transient rheology to a determination of model parameters. We describe the impact of composition on rheological behavior and model parameters in monolithic and mixed granular hydrogels. The model robustly captures self-healing behavior and reveals granular relaxation time depends on strain amplitude. This quantitative framework is an important step toward rational design of granular hydrogels for applications ranging from injection and in situ stabilization to 3D bioprinting.
Mixotrophy for carbon-conserving waste upcycling
Authors: Weldon Michael , Euler Christian
Published: February 2025

Modern chemical production, on which human quality of life depends, is unsustainable. Alternative, sustainable manufacturing routes must therefore be developed. Electrochemical and biological processes offer promise for upgrading waste streams, including recalcitrant CO2and plastic-derived wastes. However, these processes are challenged by the inherent heterogeneity and high energy input requirements for upcycling of the chemical endpoints of the "take-make-waste" economy.Cupriavidus necatoris emerging as a potentially useful catalyst to valorize such complex feedstocks because of its extreme metabolic flexibility, which allows it to utilize a wide array of substrates, and its ability to use CO2directly via the Calvin-Benson-Bassham cycle.C. necatornatively oxidizes hydrogen to power carbon utilization, but its inherent flexibility offers an as-yet unexplored opportunity to couple waste stream oxidation with CO2utilization instead, potentially enabling carbon conservative waste upcycling. Here, we uncover the constraints on carbon conservative chemical transformation usingC. necatoras a model. We systematically examine the carbon yield and thermodynamic feasibility of mixotrophic scenarios that combine waste-derived carbon sources with hydrogen oxidation to power carbon reassimilation. Then, we evaluate carbon-carbon mixotrophic scenarios, with one carbon source providing electrons in place of hydrogen oxidation. We show that acetate, ethylene glycol, and glycerol all have high potential as inputs to carbon-neutral or carbon-negative mixotrophic fermentative upgrading, with acetate being critical to all scenarios explored here. In contrast, we find that carbon conservation is likely infeasible for most other waste-derived carbon sources. This work provides a roadmap to establishing novelC. necatorstrains capable of carbon efficient waste upcycling.
Cell Contractile Force-Mediated Morphodynamical Tissue Engineering via 4D Printed Degradable Hydrogel Scaffolds
Authors: Ding Aixiang , Gasvoda Kaelyn L. , Cleveland David S. , Alsberg Eben
Published: February 2025

Tissue morphogenesis is a critical aspect tissue development. Recent advances in four-dimensional (4D) cell scaffolds have shown promise for modeling morphogenic processes. While current 4D systems often rely on external stimuli, they tend to overlook the role of intrinsic cell-generated forces, such as cell contractile forces (CCFs), in driving tissue morphogenesis. The paradox between the inherent weakness of CCFs and the robustness of tissue scaffolds presents a significant challenge in achieving effective shape transformations. In this study, we introduce an easily printable, freestanding, cell-laden hydrogel platform designed to harness CCFs for 4D shape morphing. These hydrogels initially provide mechanical support to maintain structural integrity, followed by rapid degradation that amplifies CCFs through enhanced cell-cell interactions and increased local cell density, thereby inducing tissue morphogenesis. This platform enables the formation of scaffold-free constructs with programmed shape transformations. By modulating the initial printed geometries, complex and large tissue constructs can be generated via controlled global shape transformations. Furthermore, the platform supports 4D tissue engineering by facilitating tissue differentiation coupled with dynamic shape evolution. This CCF-4D system represents a significant advancement in biomimetic tissue engineering, offering new avenues for creating dynamic tissue models that closely replicate native morphogenesis.
Housekeeping genes are enriched in rheumatoid arthritis-related genes
Authors: Lv Wenhua , Tang Hao , Feng Guanglong , Zhang Shuhao , Shang Zhenwei , Zhang Mingming , Chen Rui , Cheng Xiangshu , Meng Xin , Lv Hongchao , Zhang Ruijie
Published: February 2025

Background: The molecular mechanisms of rheumatoid arthritis (RA) have not been fully elucidated. Housekeeping genes are often considered to be genes stably expressed in any tissue, cell, or disease state, and the relationship between housekeeping genes and RA has never been systematically analyzed. Results: Therefore, by collecting and analyzing 140 gene expression profiling data, this study aimed to explore whether housekeeping genes are abnormal expressed in RA. Fifteen datasets were included in this study based on the set inclusion exclusion criteria. By cumulative hypergeometric test, for 73.3% (11/15) of the datasets, housekeeping genes were significantly (p < 0.05) enriched in the set of differentially expressed genes (DEGs) between RA patients and healthy controls. Using the relative enrichment factor (Re) as an effect size, a Meta-analysis strategy was performed to integrate the individual results. The logarithmic Re for multiple studies was 0.48 with the 95% confidence interval ranging from 0.17 to 0.80. The combined effect size was significantly higher than that of the randomized case (p = 0.0012) suggesting a consistent result with the hypergeometric test. Sensitivity analysis showed that the results obtained in this study were stable. Furthermore, by analyzing the standard deviation of the housekeeping gene expression values, we found that the fluctuation of housekeeping gene expression was indeed significantly higher in patients than in healthy controls. Conclusion: This study identified for the first time a significant enrichment of housekeeping genes in DEGs of RA, which might provide new perspectives for understanding the role of housekeeping genes in RA.
Fibrillarin-mediated ribosomal RNA maturation is a novel therapeutic vulnerability in triple-negative breast cancer
Authors: Jouines Camille , Lo Monaco Piero , Gaucherot Angéline , Radermecker Julie , Isaac Caroline , Bourdelais Fleur , Monet Marie-Ambre , Meyer Marion , Chalabi-Dchar Mounira , Nguyen Van Long Flora , Baillon Laury , Froment Carine , Marcoux Julien , Vanbelle Christophe , Fenouil Tanguy , Durand Sébastien , Giraud Stéphane , Diaz Jean-Jacques , Marcel Virginie , Catez Frédéric
Published: February 2025

Triple-negative breast cancer (TNBC) remains one of the most challenging breast cancer subtypes to treat due to the lack of effective therapeutic options. Ribosome biogenesis has recently emerged as a promising therapeutic target across various cancers. Despite the current targeting of ribosome biogenesis through RNA polymerase I (RNA Pol I) inhibition, we speculated that other factors essential for ribosome assembly, such as rRNA maturation factors, may also represent therapeutic targets in TNBC. Here, we demonstrate that ribosome biogenesis-related genes are notably overexpressed in TNBC compared to other breast cancer subtypes, highlighting its critical role in TNBC progression. Accordingly, we show that RNA Pol I inhibition exerts potent anti-proliferative effects in pre-clinical models of TNBC, bothin vitroandin vivo. However, the DNA-damaging activity of RNA Pol I inhibitors raises safety concerns, highlighting the need for alternative strategies to inhibit ribosome biogenesis. To this end, we show that targeting a downstream rRNA maturation step, specifically pre-rRNA cleavage, by inhibiting the maturation factor Fibrillarin, also inhibits tumor growth in TNBC models. Notably, ribosome biogenesis inhibition, through either RNA Pol I or Fibrillarin targeting, induces cell cycle arrest without triggering significant cell death. These findings establish ribosome biogenesis as a therapeutic vulnerability in TNBC and identify rRNA maturation, and Fibrillarin in particular, as novel targets for potential therapeutic intervention.

Significance

Targeting ribosome biogenesis, through inhibition of either rRNA synthesis or maturation, induces anti-tumoral effects in TNBC, representing a novel therapeutic vulnerability with potential to improve patient outcomes.
pholidosis: an R package to compare biological surface patterns
Authors: Krone Isaac W
Published: February 2025

Atop the heads of many lizards and snakes sit complex patterns of flattened scales, differing in their sizes, shapes, colors, textures, and inter-relationships. These patterns of head scalation-called "pholidosis"-are often diagnostic to species or genera and therefore of great importance to reptile taxonomy, yet they have never been investigated in a detailed comparative context. Similar patterns can be seen in the scutes of turtle shells and the "cells" of insect wings; these each consist of a surface pattern made up of discrete units that can be considered homologous between individuals, populations, and species. Here, I describe an R package, pholidosis, designed to analyze these patterns as networks, providing tools for their construction, analysis, and visualization, and comparative analysis via an edit distance metric.
Enrichment of helminth mitochondrial genomes from faecal samples using hybridisation capture
Authors: Papaiakovou Marina , Waeschenbach Andrea , Anderson Roy M , Cools Piet , Mekonnen Zeleke , Littlewood D. Timothy J , Cantacessi Cinzia , Doyle Stephen R
Published: February 2025

New approaches are urgently needed to enrich rare or low-abundant DNA in complex samples. Soil-transmitted helminths (STHs) inhabit heterogeneous environments, including the gastrointestinal tract of their host as adults and are excreted as eggs and larvae in faeces, complicating our understanding of their biology and the use of genetic tools for species monitoring and population tracking. We have developed a hybridisation capture approach to enrich mitochondrial genome sequences of two STH species, the roundworm Ascaris lumbricoides and whipworm Trichuris trichiura, from extracted DNA from faecal material and worm specimens. Employing ~1000 targeted probes, we achieved >6,000 and >12,000 fold enrichment for A. lumbricoides and T. trichiura, respectively, relative to direct whole genome shotgun (WGS) sequencing. Sequencing coverage was highly concordant with probe targets and correlated with the number of eggs per gram (EPG) of parasites present, from which DNA from as few as 336 EPG for Ascaris and 48 EPG for Trichuris were efficiently captured and sufficient to provide effective mitochondrial genome data. Finally, allele frequencies were highly concordant between WGS and hybridisation capture, suggesting little genetic information is lost with additional sample processing required for enrichment. Our hybridisation capture design and approach enables sensitive and scalable STH mitochondrial genome sampling from faecal DNA extracts and paves the way for broader hybridisation capture-based genome-wide applications and molecular epidemiology studies of STHs.
Impact of cell culture model systems on SARS-CoV-2 and MERS-CoV infection dynamics and antiviral responses
Authors: Chiok Kim , Fenton Mark , Falzarano Darryl , Dhar Neeraj , Banerjee Arinjay
Published: February 2025

Cell cultures are widely used to study infectious respiratory diseases and to test therapeutics; however, they do not faithfully recapitulate the architecture and complexity of the human respiratory tract. Lung organoids have emerged as an alternative model that partially overcomes this key disadvantage. Lung organoids can be cultured in various formats that offer potential for studying highly pathogenic viruses. However, the effects of these different formats on virus infection remain unexplored, leaving their relative value unclear. In this study, we generated primary lung organoids from human donor cells and used them to derive monolayers and air-liquid interface (ALI) cultures with the goal of comparing the replication kinetics of two circulating highly pathogenic coronaviruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV). Infection studies revealed that organoid-derived monolayers displayed limited infection and the innate immune response was impaired against bacterial lipopolysaccharide (LPS) but not against virus-like double-stranded dsRNA or poly(I:C). Meanwhile, organoids and organoid-derived ALI cultures retained viral permissivity, with ALI cultures displaying diverse antiviral immune responses against both coronaviruses. SARS-CoV-2 and MERS-CoV demonstrated differential replication kinetics in organoid and organoid-derived ALI cultures. Therefore, primary organoid-derived cells in two-dimensional monolayer or three-dimensional ALI formats influence virus infection and host antiviral responses. Our study informs the selection of culture conditions for organoid-based respiratory disease research and therapeutic testing.
Structure of the human TWIK-2 potassium channel and its inhibition by pimozide
Authors: Khanra Nandish , Wang Chongyuan , Delgado Bryce D , Long Stephen Barstow
Published: February 2025

The potassium channel TWIK-2 is crucial for ATP-induced activation of the NLRP3 inflammasome in macrophages. The channel is a member of the two-pore domain potassium (K2P) channel superfamily and an emerging therapeutic target to mitigate severe inflammatory injury involving NLRP3 activation. We report the cryo-EM structure of human TWIK-2. In comparison to other K2P channels, the structure reveals a unique up conformation of Tyr111 in the selectivity filter and a SF1-P1 pocket behind the filter that could serve as a binding site for channel modulators. Density for acyl chains is present in fenestrations within the transmembrane region that connect the central cavity of the pore to the lipid membrane. Limited pharmacological tools are available for TWIK-2 despite its importance as a drug target. We show that the small molecule pimozide inhibits TWIK-2 and determine a structure of the channel with pimozide. Pimozide displaces the acyl chains and binds below the selectivity filter to block ion conduction. The drug may access its binding site via the membrane, suggesting that other hydrophobic small molecules could have utility for inhibiting TWIK-2. The work defines the structure of TWIK-2 and provides a structural foundation for development of specific inhibitors with potential utility as anti-inflammatory drugs.
Exploration of the influence of environmental changes on the conformational and amyloidogenic landscapes of the zinc finger protein DPF3a by combining biophysical and molecular dynamics approaches
Authors: Mignon Julien , Leyder Tanguy , Monari Antonio , Mottet Denis , Michaux Catherine
Published: February 2025

In the past few years, the double PHD fingers 3 (DPF3) protein isoforms (DPF3b and DPF3a) have been identified as new amyloidogenic intrinsically disordered proteins (IDPs). Although such discovery is coherent and promising in the light of their involvement in proteinopathies, their amyloidogenic pathway remains largely unexplored. As environmental variations in pH and ionic strength are relevant to DPF3 pathophysiological landscape, we therefore enquired the effect of these physicochemical parameters on the protein structural and prone-to-aggregation properties, by focusing on the more disordered DPF3a isoform. In the present study, we exploited in vitro and in silico strategies by combining spectroscopy, microscopy, and all-atom molecular dynamics methods. Very good consistency and complementary information were found between the experiments and the simulations. Acidification unequivocally abrogated DPF3a fibrillation upon maintaining the protein in highly hydrated and expanded conformers due to extensive repulsion between positively charged regions. In contrast, alkaline pH delayed the aggregation process due to loss in intramolecular contacts and chain decompaction, the extent of which was partly reduced thanks to the compensation of negative charge by arginine side chains. Through screening attractive electrostatic interactions, high ionic strength conditions (300 and 500 mM NaCl) shifted the conformational ensemble towards more swollen, heterogeneous, and less H-bonded structures, which were responsible for slowing down the conversion into β-sheeted species and restricting the fibril elongation. For defining the self-assembly pathway of DPF3a, we unveiled that the protein amyloidogenicity intimately communicates with its conformational landscape, which is particularly sensitive to modification of its physicochemical environment. As such, understanding how to modulate DPF3a conformational ensemble will help designing novel protein-specific strategies for targeting neurodegeneration.
Ketamine-Assisted Psychotherapy for Generalized Anxiety Disorder: A Comprehensive Case Report with Integrated Neurophysiological Imaging Using Magnetoencephalography
Authors: Cohen Jacob , Reichelt Amy Claire , Zamyadi Rouzbeh , Roberts Gillian , Hardy Samuel , Fernandes Brian , Rhind Shawn G , Lewis Evan C , Bhat Venkat , Palner Mikael , Jetly Rakesh , Dunkley Benjamin Thomas
Published: February 2025

This detailed case report explores the application of ketamine-assisted psychotherapy (KAP) in the treatment of a 39-year-old male patient with Generalized Anxiety Disorder (GAD) and depressive symptoms. The N-methyl-D-aspartate (NMDA) receptor antagonist ketamine represents a significant breakthrough in the treatment of mood and anxiety disorders due to its rapid and robust antidepressant effects. Preclinical studies demonstrate that ketamine promotes biological alterations in the brain, including enhancing neuroplasticity. However, no studies to date have examined the longitudinal effects of KAP using magnetoencephalography (MEG), a powerful functional neuroimaging modality. Resting state MEG (rsMEG) scanning allowed the exploration of the neural correlates of KAP-related changes in mood and anxiety symptoms, including the functional connectivity between brain networks involved in cognition and emotion regulation. In this case study, an adult male participant with moderate-severe GAD underwent two rsMEG scans and cognitive testing at baseline and after 4 of 6 sessions of a standard ketamine administration and 2 integration sessions, part of a protocol consisting of a total of six KAP sessions and four sessions of integration. We measured functional connectivity in 5 functional networks - default mode, attention, central executive, motor, and visual, as well as neural oscillatory activity. We saw functional connectivity increases in 4 of the 5 networks. This coincided with significant increases in cortical beta activity, a marker of inhibition, decrease in theta oscillations, reductions in GAD7 and PHQ9 scores, and improved attention. In summary, these findings emphasize the ability of rsMEG to detect KAP-induced brain network changes, offering a promising tool for identifying clinically relevant neural correlates that can both predict and monitor therapeutic outcomes via electrophysiological changes.
Bridging the scales: leveraging personalized disease models and deep phenotyping to dissect cognitive impairment in schizophrenia
Authors: Raabe Florian J. , Popovic David , Vetter Clara , Hasanaj Genc , Karsli Berkhan , Fischer Laura E. , Boudriot Emanuel , Almeida Valeria , Atella Alessia , Schaefer Tim J. , Gagliardi Miriam , Trastulla Lucia , Yakimov Vladislav , Roell Lukas , Moussiopoulou Joanna , Krcmar Lenka , Galinski Sabrina , Papazova Irina ,   CDP Working Group, Pogarell Oliver , Hasan Alkomiet , Schulte Eva C. , Schmitt Andrea , Wagner Elias , Levina Anna , Rossner Moritz J. , Koutsouleris Nikolaos , Papiol Sergi , Falkai Peter , Keeser Daniel , Ziller Michael J.
Published: February 2025

Schizophrenia (SCZ) is a highly heritable brain disorder marked by a wide range of changes throughout the central nervous system. These changes include alterations at the molecular and cellular levels, suggesting significant disruptions in synapse function, as well as modifications in brain structure and activity. However, it remains unclear, how changes in molecular synapse biology translate into neurophysiological and ultimately behavioral consequences across scales. Here, we narrow this translational gap in contemporary biological psychiatry by establishing a generalizable framework to bridge the scales and pinpoint biological mechanisms underlying individual psychiatric symptoms. We show that genetically driven changes in neuronal gene expression and a resulting reduction in excitatory synaptic density in vitro are linked to alterations of brain structure, electrophysiology and ultimately cognitive function in vivo. These results provide a direct connection between the molecular origins of synapse reduction in SCZ and its neurobiological and phenotypic consequences on the individual patient level, paving the way to develop new mechanism informed treatment options.
Chlamydia trachomatis and Neisseria gonorrhoeae bacterial loads in co-infected men who have sex with men on pre-exposure prophylaxis: a cross-sectional study
Authors: Rayo Enrique , Malingamba Giulia , Marti Hanna , Onorini Delia , Leonard Cory Ann , Low Nicola , Hampel Benjamin , Borel Nicole
Published: February 2025

Objective: Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most commonly reported sexually transmitted infections globally. Anorectal CT/NG detection among men who have sex with men (MSM) and co-infections are common. Epidemiological studies suggest that CT/NG co-infections might result in greater bacterial load and transmissibility than single infection. The purpose of this study was to compare bacterial load and symptoms between CT/NG single and co-infections in MSM. Methods: MSM positive for CT or NG on a triple swab (throat, urethra, and rectal locations combined) were enrolled. Before treatment, they self-collected anorectal swabs. Bacterial loads for CT/NG were calculated using real-time PCR, and compared between single or co-infected individuals, and with or without rectal symptoms. Results: We enrolled 382 MSM from December 2021 to December 2024. Among all samples: total CT (n=114), CT/NG co-infection 29/114 (25.4%); total NG (n=125), CT/NG co-infection 29/125 (23.2%). The bacterial loads in single and co-infected samples were comparable. The mean difference between CT alone and CT/NG was 0.40 copies/mL (95% CI: [-0.09, 0.11], P value = 0.107). The mean difference for NG alone and CT/NG was 0.24 copies/mL (95% CI: [-0.49, 0.99], P value = 0.498). Among 382 MSM, 15.4% (n=59/382) experienced anorectal symptoms. There was no statistical difference in bacterial burdens between symptomatic and asymptomatic (CT difference of the means 0.52 copies/mL, 95% CI: [-0.51, 1.55]; P value = 0.313) (NG difference of the means 0.63, CI: [0.01, 1.28]; P value = 0.05). Conclusions: In contrast to prior research, we found similar bacterial burdens in anorectal MSM samples with single CT/NG vs coinfection. Further research is needed to understand the clinical implications of CT/NG co-infections. Future should investigate factors influencing anorectal CT/NG bacterial burden, transmissibility, and susceptibility, including the function of PrEP and the rectal microbiota.
Determinants of practice location choices among physicians and medical students in Mali: insights into addressing medical deserts through evidence-based strategies.
Authors: Kalossi Issa , COULIBALY Dielika , N'Diaye Kassoum Alou , Dramé Modibo Salia , Sissoko Djibril , Almont Thiery , Kayentao Kassoum
Published: February 2025

The shortage of medical professionals in rural and remote areas is a global issue that significantly challenges equitable healthcare delivery. Worldwide, various studies have examined the motivations of medical professionals in choosing their practice location. However, for Mali, this topic remains underexplored, motivating us to conduct this study to identify factors influencing doctors' workplace decisions in Mali. We conducted a cross-sectional and prospective study targeting doctors and final-year medical students. Using simple random sampling, we selected 358 respondents, 69% of whom were doctors. Approximately 38% of the respondents preferred rural areas for their practice, primarily citing career development and opportunities for continuing education (38%). The likelihood of choosing rural practice was higher (OR = 5.09; CI = [2.52-10.8]) among participants with family residing in rural areas. Conversely, financial incentives, access to technical platforms, and infrastructure favored urban practice. This study elucidates doctors' motivations and identifies key factors associated with their choice of practice location.
Diagnostic Yield from Screening and Health Status Burden of Outpatients at Risk for Heart Failure
Authors: Cantu Martinez Omar , Girard Andrew A. , Jin Weiwei , Rinderknecht Derek , Cheek Thomas , Spertus John A.
Published: February 2025

Background: Heart failure (HF) is frequently underrecognized in primary care due to nonspecific symptoms and limited screening, resulting in many patients presenting with severely compromised health status (symptoms, functional ability, and quality of life) at the time of diagnosis. Objectives: To evaluate the diagnostic yield of screening outpatients at risk for HF using a noninvasive assessment of left ventricular end-diastolic pressure (LVEDP) and to describe the health status of patients newly identified with elevated LVEDP. Methods: A convenience sample of adults with diabetes mellitus (DM), chronic kidney disease (CKD), or suspected HF were screened at three primary care clinics using the Vivio System to identify patients with LVEDP >18 mmHg (positive screening). Among patients with a positive screening result, their health status was evaluated using the Kansas City Cardiomyopathy Questionnaire Overall Summary (KCCQ-OS) score. Results: Among 2040 screened patients (mean age 74±8 years; 49.8% women; 64.6% with DM; and 34.9% with CKD) 38.5% had an elevated LVEDP. Older patients, women, and those with CKD were more likely to have an elevated LVEDP (p<0.01 for all). Of 653 KCCQ-OS scores collected (mean 85±20), 31.4% had a KCCQ-OS of 100 (asymptomatic), and 26.5% had a KCCQ-OS <80, consistent with NYHA class II-IV. Conclusion: Nearly 40% of patients had a positive screening, and over two-thirds reported significant health status impairments. Combining the KCCQ with noninvasive LVEDP assessment can identify patients who may require further HF evaluation. Future studies can assess the impact of these strategies on patients′ subsequent health status and clinical events.
A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs
Authors: Pai Hsuan , Sakai Toshiyuki , Posbeyikian Andres , Frijters Raoul , Sugihara Yu , Contreras Mauricio P. , Kourelis Jiorgos , Adachi Hiroaki , Kamoun Sophien , Toghani AmirAli
Published: February 2025

Nucleotide-binding domain and leucine-rich repeat immune receptors (NLRs) are known for their rapid evolution, even at the intraspecific level, yet the rates of evolution differ significantly across various NLR classes. Within the NRC (NLR Required for Cell Death) network, NLRs operate in complex sensor-helper configurations to confer immunity against a diverse array of pathogens, particularly in Asterids. While helper NLRs are typically conserved and evolve slowly, sensor NLRs tend to evolve more rapidly. However, the functional connections between slow and fast-evolving NLRs remain poorly understood, notably in important crop species. We conducted a comparative analysis of NLRs across 40 Solanales and 29 Asterales genomes to explore NRC network expansion and diversification within the less-studied Asterales order. Our findings reveal that the NRC network has expanded less in Asterales compared to Solanales. We functionally validated a minimal Asterales NRC network with 2 helpers and 9 sensors in common lettuce (Lactuca sativa). Through selection and diversification analysis and structural modeling of NRC helper and sensor subclades in theLactucagenus, we found varying evolutionary diversification rates between NRC helpers and sensors. We found a correlation between sensor diversification rates and helper dependency, with sensors reliant on a phylogenetically conserved helpers experiencing limited diversification pressure. Our results highlight the lineage- and function-specific evolution of the NRC network, offering insights into the evolutionary pressures shaping plant immune receptor networks.
Food supplementation with molybdenum complexes improves honey bee health
Authors: Floquet Sebastien , Fuior Arcadie , Colin-Duchevet Loic , Cebotari Valentina , Noel Amelie , Ribaud Isabelle , Gerard Isabelle , Garbuz Olga , Fregnaux Mathieu , Lopez Javier , Larcher Virginie , Shestopalov Michael A. , Solovieva Anastasiya O. , Pozmogova Tatiana N. , Gliga Olesea , Railean Nadejda , Cochard Precillia , Poirot Benjamin , Charistos Leonidas , Hatjina Fani , Somogyi Andrea , Medjoubi Kadda , Gaumer Sebastien , Gulea Aurelian , Toderas Ion , Sandoz Jean-Christophe
Published: February 2025

In this study, we evaluated the impact of supplementing honey bee feed with molybdenum-based compounds. Among a dozen of dinuclear Mo(V) complexes, we first selected the most stable and non-toxic complexes, which were tested as food supplements in an extensive eight-year campaign involving more than 700 beehives across various environmental conditions in Moldova, France, Greece and USA. This unprecedented field campaign revealed that a few milligrams of compounds Na-Mo2O4-EDTA or Li-Mo2O4-EDTA provided in spring or autumn, increased queen fecundity, hygienic behavior, and honey production, while infestation rates of worker bees and brood by the mite Varroa destructor, and mortality rates in winter were dramatically reduced. Hive monitoring showed that the Mo-containing syrup can be consumed over 1.5 months and is well assimilated by larvae and workers within the hive. In particular, Mo levels increased significantly in the head of the bees. X-ray fluorescence measurements demonstrated that Na-Mo2O4-EDTA increases Mo levels in brain, neurolemma and hypopharyngeal glands. The metabolism of Mo complexes was addressed using X-Ray photoelectron spectroscopy (XPS) on bee faeces, which revealed that the complexes are oxidized into Mo(VI) species and thus suggesting that Mo complexes may function as antioxidant agents in bees. These findings offer promising solutions for the beekeeping industry, which is struggling with weakening honey bee colonies.
Class I histone deacetylases catalyze lysine lactylation
Authors: Tsusaka Takeshi , Najar Mohd. Altaf , Sharma Isha , Marcinkiewicz Mariola M. , Crispim Claudia Veronica Da Silva , Snyder Nathaniel W , Burslem George , Goldberg Emily L
Published: February 2025

Metabolism and post-translational modifications (PTMs) are intrinsically linked and the number of identified metabolites that can covalently modify proteins continues to increase. This metabolism/PTM crosstalk is especially true for lactate, the product of anaerobic metabolism following glycolysis. Lactate forms an amide bond with the ε-amino group of lysine, a modification known as lysine lactylation, or Kla. Multiple independent mechanisms have been proposed in the formation of Kla, including p300/CBP-dependent transfer from lactyl-CoA, via a high-energy intermediate lactoylglutathione species that non-enzymatically lactylates proteins, and several enzymes are reported to have lactyl transferase capability. We recently discovered that class I histone deacetylases (HDACs) 1, 2, and 3 can all reverse their canonical chemical reaction to catalyze lysine β-hydroxybutyrylation. Here we tested the hypothesis that HDACs can also catalyze Kla formation. Using biochemical, pharmacological, and genetic approaches, we found that HDAC-catalyzed lysine lactylation accounts for the majority of Kla formation in cells. Dialysis experiments confirm this is a reversible reaction that depends on lactate concentration. We also directly quantified intracellular lactyl-CoA and found that Kla abundance can be uncoupled from lactyl-CoA levels. Therefore, we propose a model in which the majority of Kla is formed through enzymatic addition of lactate by HDACs 1, 2, and 3.