bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of antigen-dextramers for detection and evaluation of CAR T cells
Authors: Friis Rasmus U. W. , Ormhøj Maria , Krüger-Jensen Cecilie S. , Barden Markus , Ramanathan Keerthana , Hansen Mikkel R. , Abken Hinrich , Hadrup Sine R. 
Published: November 2024

AbstractBackgroundChimeric antigen receptor (CAR) T cell therapy has transformed the treatment landscape of hematologic cancers by engineering T cells to specifically target and destroy cancer cells. Monitoring CAR T cell activity and function is essential for optimizing therapeutic outcomes, but existing tools for CAR detection are often limited in specificity and functional assessment capability.MethodsWe developed antigen-dextramers by conjugating multiple CAR-specific antigens to a dextran backbone. The dextramers were compared to previously reported antigen-tetramers for their ability to stain and detect CAR T cells. Because these multimers incorporate the CAR target antigen, they uniquely enable assessment of CAR T cell functionality by facilitating binding and activation analyses. We tested the staining and functional properties of the multimers across a range of CAR constructs with different affinities, using flow cytometry, microscopy, and NFAT-luciferase reporter assays.ResultsThe antigen-dextramers demonstrated high specificity and sensitivity in staining CAR T cells, with adjustable antigen density to optimize binding. Antigen-dextramers also enabled effective clustering and subsequent activation of CARs, showing their utility as both a staining and functional assessment tool. The dextramers revealed that CARs with different affinities and clustering tendencies displayed varied binding and activation in response to different antigen densities.ConclusionAntigen-dextramers offer a dual advantage as versatile reagents for both staining and functional analysis of CAR T cells. Their capacity to engage CARs with the specific antigen provides a valuable platform for evaluating CAR functionality, informing CAR design improvements, and enhancing therapeutic precision.
Raver1 linksRipk1RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance
Authors: Zhang Boyao , Orning Pontus , Lehman Jesse W. , Dinis Alexandre , Torres-Ulloa Leslie , Elling Roland , Kelliher Michelle A. , Bertin John , Proulx Megan K. , Ryan Liv , Kandasamy Richard , Espevik Terje , Pai Athma A. , Fitzgerald Katherine A. , Lien Egil 
Published: November 2024

AbstractMultiple cell death and inflammatory signaling pathways converge on two critical factors: receptor interacting serine/threonine kinase 1 (RIPK1) and caspase-8. Careful regulation of these molecules is critical to control apoptosis, pyroptosis and inflammation. Here we discovered a pivotal role of Raver1 as an essential regulator ofRipk1pre-mRNA splicing, expression, and functionality, and the subsequent caspase-8-dependent inflammatory cell death. Macrophages fromRaver1-deficient mice exhibit altered splicing ofRipk1, accompanied by diminished cell death and reduced activation of caspase-8, Gasdermin D and E, caspase-1, as well as decreased interleukin-18 (IL-18) and IL-1ß production. These effects were triggered byYersiniabacteria, or by restraining TAK1 or IKKβ in the presence of LPS, TNF family members, or IFNγ. Consequently, animals lackingRaver1showed heightened susceptibility toYersiniainfection. Raver1 and RIPK1 also controlled the expression and function of the C-type lectin receptor Mincle. Our study underscores the critical regulatory role of Raver1 in modulating innate immune responses and highlights its significance in directingin vivoandin vitroinflammatory processes.SignificanceCaspase-8 and the kinase RIPK1 are at focal points of several inflammation and cell death pathways. Thus, a careful regulation of their actions is needed. Our work identifies the RNA splicing factor Raver1 as a critical factor directing the splicing ofRipk1in order to modulate RIPK1/caspase-8-driven pyroptosis, apoptosis and inflammation. Raver1 is central for macrophage responses toYersiniabacteria, initiated after blockade of kinases TAK1 and IKK, measured as activation of RIPK1, caspase-8, Gasdermin D, caspase-3, IL-1ß and IL-18. Importantly, Raver1 is necessary for host resistance toYersiniainfectionin vivo. We propose that Raver1 is key for correct tuning of RIPK1-caspase-8 dependent processes.
Reliable amplification of highly repetitive or low complexity sequence DNA enabled by superhelicase-mediated isothermal amplification
Authors: Kang Jimin , Rashid Fahad , Murray Peter J. , Merino-Urteaga Raquel , Gavrilov Momčilo , Shang Tiantian , Jo Wonyoung , Ahmed Arman , Aksel Tural , Barrick Doug , Berger James M. , Ha Taekjip 
Published: November 2024

AbstractPolymerase Chain Reaction (PCR) requires thermal cycling to melt DNA and proceed through the subsequent cycles of DNA synthesis needed for exponential amplification. Previously, we engineered a superhelicase, with enhanced processivity and speed, to replace this traditional PCR melting step with enzymatic DNA unwinding while retaining desired PCR characteristics, such as multi-kb amplicon size and applicability to cloning and gene editing outcome assessment. This isothermal amplification method is named SHARP (SSB-Helicase Assisted Rapid PCR) because single-stranded DNA binding protein (SSB) and superhelicases are added to standard PCR reagents. Here, we show that SHARP can be effective for DNA sequences that PCR is unable to amplify or that produce side products of. SHARP is demonstrated to be capable of amplifying up to six identical repeats of the Widom 601 nucleosome positioning sequence and up to 35 identical repeats of ankyrin sequence. We also show that a sequence with 91% AT-content can be amplified using SHARP and that the amplification product can be validated using single-molecule optical tweezers experiments.
Design of high specificity binders for peptide-MHC-I complexes
Authors: Liu Bingxu , Greenwood Nathan F. , Bonzanini Julia E. , Motmaen Amir , Sharp Jazmin , Wang Chunyu , Visani Gian Marco , Vafeados Dionne K. , Roullier Nicole , Nourmohammad Armita , Garcia K. Christopher , Baker David 
Published: November 2024

AbstractClass I MHC molecules present peptides derived from intracellular antigens on the cell surface for immune surveillance, and specific targeting of these peptide-MHC (pMHC) complexes could have considerable utility for treating diseases. Such targeting is challenging as it requires readout of the few outward facing peptide antigen residues and the avoidance of extensive contacts with the MHC carrier which is present on almost all cells. Here we describe the use of deep learning-based protein design tools tode novodesign small proteins that arc above the peptide binding groove of pMHC complexes and make extensive contacts with the peptide. We identify specific binders for ten target pMHCs which when displayed on yeast bind the on-target pMHC tetramer but not closely related peptides. For five targets, incorporation of designs into chimeric antigen receptors leads to T-cell activation by the cognate pMHC complexes well above the background from complexes with peptides derived from proteome. Our approach can generate high specificity binders starting from either experimental or predicted structures of the target pMHC complexes, and should be widely useful for both protein and cell based pMHC targeting.
Enhanced Brain-Heart Connectivity as a Precursor of Reduced State Anxiety After Therapeutic Virtual Reality Immersion
Authors: Sezer Idil , Moreau Paul , El Sayed Hussein Jomaa Mohamad , Godefroy Valérie , Batrancourt Bénédicte , Lévy Richard , Filipchuk Anton 
Published: November 2024

AbstractState anxiety involves transient feelings of tension and nervousness in response to threats, which can escalate into anxiety disorders if persistent. Despite treatments, 30%-50% of individuals show limited improvement, and neurophysiological mechanisms of treatment responsiveness remain unclear, requiring the development of objective biomarkers.In this study, we monitored multimodal electrophysiological parameters: heart rate variability (high-frequency, low-frequency, LF/HF ratio), EEG beta and alpha relative power, and brain-to-heart connectivity in participants with real-life state anxiety. Participants underwent a therapeutic intervention combining virtual-reality immersion, hypnotic script, and a breath control exercise. Real-life state anxiety was captured using the STAI-Y1 scale before and after the intervention.We observed reduced anxiety immediately after the intervention in 16 out of 27 participants. While all participants, independently of their STAI-Y1 score, showed increased HRV low frequency power, only treatment-responders displayed increased overall autonomic tone (high and low frequency HRV), increased midline beta power and brain-to-heart connectivity. Notably, the LF/HF ratio showed a significant linear relationship with anxiety reduction, with higher ratios linked to greater therapeutic response.These findings suggest that increased cognitive regulation of brain-to-heart connectivity could serve as a biomarker for therapeutic efficacy, with elevated midline beta power facilitating improved cardiac tone in responders.Significance StatementElevated state anxiety can escalate into debilitating disorders, such as generalized anxiety disorder, yet treatment efficacy remains inconsistent, and reliable biomarkers predicting therapeutic outcomes are lacking. This study identifies key neural and physiological markers linked to effective anxiety reduction following a virtual reality-based non-pharmacological intervention in healthy participants with increased state anxiety. Anxiety reduction is associated with increased midline beta power, heightened heart rate variability (LF/HF ratio), and enhanced brain-to-heart connectivity. These findings highlight the role of brain-to-heart modulation and autonomic nervous system functioning in therapeutic response. By highlighting these biomarkers, this research aims at advancing our understanding of anxiety treatment mechanisms and offering insights into the development of biomarker-driven, scalable interventions.
A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
Authors: Mighell Taylor L. , Lehner Ben 
Published: November 2024

AbstractReduced protein stability is the most frequent mechanism by which rare missense variants cause disease. A promising therapeutic avenue for treating destabilizing variants is pharmacological chaperones (PCs, also known as correctors or stabilizers), small molecules that bind to and stabilize target proteins. PCs have been approved as clinical treatments for specific variants, but protein energetics suggest their effects might be much more general. Here, we test this hypothesis for the first time by comprehensively quantifying PC efficacy for all missense variants in a human disease gene, the vasopressin 2 receptor (V2R), a G-protein coupled receptor in which loss-of-function variants cause nephrogenic diabetes insipidus (NDI). Strikingly, treatment with a PC rescues the expression of nearly all destabilized variants, with non-rescued variants identifying the drug’s binding site. Our results provide proof-of-principle that a single small molecule can rescue destabilizing variants throughout a protein’s structure. The application of this principle to other proteins should allow the development of effective therapies for many genetic diseases.
Cardiac Reprogramming with Drug Resistance Alleviates Doxorubicin-induced Cardiotoxicity in Mice and Pigs
Authors: Zhang Yixin , Li Weirun , Xiao Yingxian , Luo Li , Ai Jiacong , Mo Shushan , Li Lanya , Deng Junyao , Wang Xueyi , Li Qishan , Zeng Yan , Liu Huifang , Wang Fei , Li Zhenhua 
Published: November 2024

AbstractDoxorubicin (Dox)-induced cardiotoxicity represents a significant clinical adverse effect associated with cancer chemotherapy treatment. The systematic toxicity associated with the currently available drug dexrazoxane has limited its clinical utility. Inspired by cancer drug resistance mechanisms, we propose a novel strategy termedTransientoverexpression ofp-glycoprotein (P-gp) forCardiacreprogramming (TopCare) to induce cardiac drug resistance as a treatment for cardiotoxicity. This approach involves reprogramming cardiomyocytes by delivering lipid nanoparticles (LNPs)-based mRNA therapeutics to induce temporary P-gp overexpression, which in turn reduces intracellular Dox levels and suppresses cytotoxic effects. Our results demonstrated that LNPs with P-gp mRNAs (P-gp LNPs) enhance P-gp expression in H9c2 cells, significantly lowering the cytotoxicity of both Dox and paclitaxel (PTX). In a mouse model with Dox-induced cardiotoxicity, it was observed that P-gp LNPs effectively promoted P-gp overexpression in cardiomyocytes, with a time-dependent decline in P-gp protein levels. This TopCare strategy resulted in improved survival rates, restored cardiac function, and reduced myocardial fibrosis and structural cardiac alterations. Furthermore, studies in large animals have shown that intrapericardial (iPC) injection of P-gp LNPs effectively mitigates adverse effects and restores cardiac function in pig models of Dox-induced cardiotoxicity. The significant cardioprotective effects achieved through cardiac drug resistance highlight the safety, efficacy, and clinical potential of the TopCare strategy for alleviating doxorubicin-induced cardiotoxicity.
Ecological Scaling of Temporal Fluctuations with Bacterial Abundance in Gut Microbiota Depends on Functional Properties of Individual Microbial Species and Bacterial Communities
Authors: Su Peng , Tchourine Konstantine , Vitkup Dennis 
Published: November 2024

AbstractMacroecological relationships that describe various statistical associations between species’ abundances, their spatial, and temporal variability are among the most general laws in ecology and biology. One of the most commonly observed relationships is a power-law scaling between means and variances of temporal species abundances, known in ecology as Taylor’s law. Taylor’s law has been observed across many ecosystems, from diverse plant and animal ecosystems to complex microbial communities. While many mathematical models have been proposed to explain the potential origins of Taylor’s law, what determines its scaling exponents across species and ecosystems is not understood. Here, we use temporal trajectories of human and baboon gut microbiota to analyze the relationship between functional properties of individual bacterial species and microbial communities with the scaling of species-specific and community-level Taylor’s law. The species Taylor law characterizes – for each individual species – the relationship between the species’ temporal abundance means and temporal abundance variances across host organisms. On the other hand, community-level Taylor’s law characterizes – in each host organism – the scaling across multiple species between their temporal abundance means and temporal abundance variances. For community Taylor’s law, we find that the power law scaling is strongly associated with the microbiota abundance of certain nutrient-degrading enzymes in the gut. Notably, our results demonstrate that the availability of enzymes metabolizing starch glycogen significantly increases Taylor’s law scaling. We also find that species Taylor’s law depends on the individual species’ functional properties. Specifically, we observe lower Taylor’s law scaling for species with larger metabolic networks, for species that are able to grow on a larger number of carbon sources, and for species with particular metabolic functions, such as glutamine and folate metabolism. Overall, our study reveals that Taylor’s law scaling is strongly associated with the functional capabilities of bacterial communities and individual microbial species’ biosynthetic properties, which are likely related to their ecological roles in the gut microbiota.
Dynamic regulation of RNA Polymerase III transcription in mouse embryonic stem cells during heat shock stress
Authors: Nguyen Thomas F. , Kwan James Z.J. , Mitchell Jennifer E. , Cui Jieying H. , Teves Sheila S. 
Published: November 2024

AbstractCells respond to many different types of stresses by overhauling gene expression patterns, both at the transcriptional and translational level. Under heat stress, global transcription and translation are inhibited, while the expression of chaperone proteins are preferentially favored. As the direct link between mRNA transcription and protein translation, tRNA expression is intricately regulated during the stress response. Despite extensive research into the heat shock response (HSR), the regulation of tRNA expression by RNA Polymerase III (Pol III) transcription has yet to be fully elucidated in mammalian cells. Here, we examine the regulation of Pol III transcription during different stages of heat shock stress in mouse embryonic stem cells (mESCs). We observe that Pol III transcription is downregulated after 30 minutes of heat shock, followed by an overall increase in transcription after 60 minutes of heat shock. This effect is more evident in tRNAs, though other Pol III gene targets are also similarly affected. Notably, we show that the downregulation at 30 minutes of heat shock is independent of HSF1, the master transcription factor of the HSR, but that the subsequent increase in expression at 60 minutes requires HSF1. Taken together, these results demonstrate an adaptive RNA Pol III response to heat stress, and an intricate relationship between the canonical HSR and tRNA expression.Article SummaryThis study explores the regulation of RNA Polymerase III (Pol III) transcription during heat shock in mouse embryonic stem cells (mESCs). Results show that tRNA transcription is downregulated after 30 minutes of heat shock, but increases after 60 minutes, while other Pol III targets remain unaffected. Importantly, the initial downregulation is independent of heat shock factor 1 (HSF1), the key regulator of the heat shock response, but the subsequent increase in tRNA expression depends on HSF1. These findings reveal an adaptive mechanism of Pol III activity under heat stress, highlighting a complex interplay between heat shock response and tRNA expression.
Bridging immunotypes and enterotypes using a systems immunology approach
Authors: Affaticati Fabio , Ha My K. , Gehrmann Thies , Boeck Ilke De , Kuznetsova Maria , Vandoren Romi , Deuren Vincent Van , Jansens Hilde , Reu Hans De , Schippers Jolien , Peeters Karin , Bartholomeus Esther , Ierssel Sabrina Van , Coenen Samuel , Naesens Reinout , Ariën Kevin K. , Vercauteren Koen , Vlieghe Erika , Beutels Philippe , Damme Pierre Van , Goossens Herman , Lion Eva , Suls Arvid , Lebeer Sarah , Laukens Kris , Meysman Pieter , Ogunjimi Benson 
Published: November 2024

AbstractUnveiling the systemic effects of disease and health requires an holistic approach that has mainly revolved around well established, directly determinable molecular relationships such as the protein synthesis cascade and epigenetic mechanisms. In this study, involving 394 individuals, we found direct linkage of branches spanning human biological functions often not studied in conjunction, using clinical data, gut microbial abundances, blood immune cell repertoires, blood transcriptomic and blood T cell receptor data. Contrary to current paradigms, we demonstrate that immunotypes and enterotypes are orthogonal, likely fulfilling distinct roles in maintaining homeostasis, only bridged via the blood transcriptome. We also identified two distinct inflammatory profiles: the first driven by interferon signalling and the other characterised by non-viral, NF-kB and IL-6 markers. Lastly, we present compelling data showing strong associations of the Ruminococcaceae and Christensenellaceae bacteria with a healthy immunotype and transcriptomic pattern, highlighting their potential role in immune health.Graphical Abstract
Intestinal Dysbiosis Alters Acute Seizure Burden and Antiseizure Medicine Activity in the Theiler’s Virus Model of Encephalitis
Authors: Erickson Inga , Davidson Stephanie , Choi Hanna , Rho Seongheon , Guignet Michelle , Peagler Kristen , Thummel Kenneth , Ericsson Aaron , Barker-Haliski Melissa 
Published: November 2024

AbstractObjectiveBrain infection with Theiler’s virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify acute seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.MethodsMale C57BL/6J mice (4-5 weeks) received oral (p.o.) ABX or saline (SAL) once daily beginning on arrival through Day 7 post-TMEV infection (p.i.). Mice were infected with TMEV or PBS on Day 0. Mice received intraperitoneal (i.p.; 20 mg/kg) CBZ or vehicle (VEH) twice daily Days 3-7 p.i. and were assessed for handling-induced seizures 30 min after treatment. Plasma was collected on Day 7 p.i. at 15 and 60 min post-CBZ administration for bioanalysis.ResultsTMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX- CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment x ASM interaction (p=0.0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p=0.004). CBZ significantly increased latency to seizure presentation; an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.SignificanceABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV- induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an under- recognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.Key Points:Theiler’s virus infection in mice models encephalitis that exhibits differential disease trajectory with gut microbiome modulation.Experimentally evoked gut dysbiosis, i.e. a disrupted gut microbiome, dramatically shifts the anticonvulsant activity of carbamazepine.There is no concomitant shift in circulating carbamazepine concentrations in TMEV- infected mice with and without a dysbiotic microbiome.The gut microbiome is an under-recognized driver of seizure risk and antiseizure medicine activity in the Theiler’s virus mouse model.