bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying immune cell telomere content at single-cell resolution in context of PD-1 checkpoint immunotherapy
Authors: Engel Niklas L. , Herzel Lea , Surmely Julie , Frieß Hanna , Simon Malte , Brors Benedikt , Imbusch Charles , Feuerbach Lars
Published: August 2024

Introduction

Biological processes such as aging, carcinogenesis, and immune response rely on the ability to maintain or rapidly expand cell populations. The fitness of the involved cells is constrained by their replicative potential, which is reflected in the cellular telomere content.

Method

We apply TelomereHunter to scATAC-seq data to determine telomere content on single-cell level, in a hematopoietic dataset consisting of 35,139 cells from samples of basal cell carcinoma patients receiving programmed cell death protein 1 (PD1) blockade treatment. Integrating information from open-chromatin-based signatures to assess cell identity, we characterize the heterogeneity of telomere length for individual cell populations pre- and post-immunotherapy.

Results

The extracted telomeric reads reflect the expected telomereome-to-genome fraction. Telomere content distributions differ significantly between cell populations, and the median telomere content in intermediate and terminal exhausted CD8+ T-cells pre-treatment is significantly correlated to response to PD-1 checkpoint blockade. Likewise, telomere content correlates with post-treatment cell proliferation in terminally exhausted and T follicular helper cells from responding patients.

Conclusion

Telomere content measurement from scATAC-seq data has a sufficiently high signal-to-noise ratio to detect significant differences between cell types. Furthermore, the telomere content of CD8+ exhausted T-cells pre-treatment is a putative biomarker for successful PD-1-based immunotherapy.
ThevprAB-ompV-virKoperon ofVibrio choleraesenses antimicrobial peptides and activates the expression of multiple resistance systems
Authors: Mathieu-Denoncourt Annabelle , Whitfield Gregory B. , Vincent Antony T. , Pauzé-Foixet Julien , Mahieddine Feriel , Brun Yves V. , Duperthuy Marylise
Published: August 2024

Antimicrobial peptides are small cationic molecules produced by eukaryotic cells to combat infection, as well as by bacteria for niche competition. Polymyxin B (PmB), a cationic cyclic antimicrobial peptide, is used prophylactically in livestock for infection prevention and as a last-resort treatment for multidrug-resistant bacterial infections in humans. In this study, a transcriptomic analysis inVibrio choleraeshowed that expression of the uncharacterized geneompVis stimulated in response to PmB. We found thatompVis organized in a conserved four-gene operon with the two-component systemvprAB(carRS) andvirKinV. cholerae, and that these genes are also upregulated in response to PmB treatment. AvirKdeletion mutant was more sensitive to the human cathelicidin LL-37 than the wild-type strain, while anompVmutant was more sensitive to PmB and LL-37, suggesting that both OmpV and VirK contribute to antimicrobial resistance inV. cholerae. This increased sensitivity to antimicrobial peptides was not due to membrane destabilization or reduced sequestration by membrane vesicles as a result ofompVdeletion. Instead, our transcriptomic analysis showed that the efflux pumpvexAB, a known effector of PmB resistance, was also upregulated in the presence of PmB in anompV-dependent manner. Examination of the predicted structure of OmpV revealed a lateral opening in the β-barrel wall with access to an electronegative pocket in the barrel lumen that can accommodate PmB. Such an interaction could facilitate intracellular signaling through a conformational change in OmpV. This is the first evidence of a specialized operon governing multiple systems for antimicrobial resistance inV. cholerae.

Author Summary

In this study, we identified the first specialized operon controlling multiple systems of antimicrobial resistance inV. cholerae. The operon encodes the two-component systemvprAB, which activates the main mechanism of polymyxin B resistance inV. cholerae, and the uncharacterized genesompVandvirK. We provide evidence that OmpV and VirK are implicated in antimicrobial resistance and show that OmpV has a membrane-accessible lateral opening into a pocket that could accommodate the antimicrobial peptide polymyxin B. We propose that OmpV acts as an outer membrane sensor that signals the presence of antimicrobial peptides to activate the expression of the operon, leading to the activation of multiple mechanisms of resistance, including modifications of the outer membrane and the multi-drug efflux systemvexAB.
Fast Low-Input Efficient Hi-C
Authors: Guetta Mor , Avidan Nili , Kariti Hagai , Davis Liron , Shemer Revital , Elliot Evan , Kaplan Noam
Published: August 2024

We developed FLIE (Fast Low-Input Efficient) Hi-C, a highly optimized and simplified version of Hi-C. Our method shortens the duration of Hi-C from five days to two days and decreases key reagent amounts 5-20 fold, while maintaining experimental controls and data quality. Importantly, the method also reduces the required input material by 100-1000 fold, as we demonstrate by generating detailed high complexity interaction maps from low-input sorted mouse frozen neuron nuclei and from 5,000-10,000 human Hap1 cells.
Single-nucleosome imaging reveals principles of transient multiscale chromatin unfolding triggered by histone ADP-ribosylation at DNA lesions
Authors: García Fernández Fabiola , Chapuis Catherine , Park Junwoo , Pinto Eva , Imburchia Victor , Longarini Edoardo José , Taddei Angela , Sokolovska Nataliya , Matić Ivan , Huet Sébastien , Miné-Hattab Judith
Published: August 2024

Timely access to DNA lesions is crucial for genome integrity. This process requires profound remodeling of densely packed chromatin to establish a repair-competent architecture. However, limited resolution has made it impossible to fully understand these remodeling events. Here, combining microirradiation with live-cell multiscale imaging, we report that DNA damage-induced changes in genome packing rely on the conformational behaviour of the chromatin fiber. Immediately after damage, a transient increase in nucleosome mobility switches chromatin from a densely-packed state to a looser conformation, making it accessible to repair. While histone poly-ADP-ribosylation is required to trigger this switch, mono-ADP-ribosylation is sufficient to maintain the open-chromatin state. The removal of these histone marks by the ARH3 hydrolase then leads to chromatin recondensation. Together, our multiscale study of chromatin dynamics establishes a global model: distinct waves of histone ADP-ribosylation control nucleosome mobility, triggering a transient breathing of chromatin, crucial for initiating the DNA damage response.
Charting the Silent Signals of Social Gaze: Automating Eye Contact Assessment in Face-to-Face Conversations
Authors: Schmälzle Ralf , Jahn Nolan T. , Bente Gary
Published: August 2024

Social gaze is a crucial yet often overlooked aspect of nonverbal communication. During conversations, it typically operates subconsciously, following automatic co-regulation patterns. However, deviations from typical patterns, such as avoiding eye contact or excessive gazing, can significantly affect social interactions and perceived relationship quality. The principles and effects of social gaze have intrigued researchers across various fields, including communication science, social psychology, animal biology, and psychiatry. Despite its significance, research in social gaze has been limited by methodological challenges in assessing eye movements and gaze direction during natural social interactions. To address these obstacles, we have developed a new approach combining mobile eye tracking technology with automated analysis tools. In this paper, we introduce, validate, and apply a pipeline for recording and analyzing gaze behavior in dyadic conversations. We present a sample study where dyads engaged in two types of interactions: a get-to-know conversation and a conflictual conversation. Our new analysis pipeline corroborated previous findings, such as people directing more eye gaze while listening than talking, and gaze typically lasting about three seconds before averting. These results demonstrate the potential of our methodology to advance the study of social gaze in natural interactions.
AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1
Authors: El Ahdab Dina S. , Lagardère Louis , Hobaika Zeina , Inizan Théo Jaffrelot , Célerse Frédéric , Gresh Nohad , Maroun Richard G. , Piquemal Jean-Philip
Published: August 2024

Long oligomer sequences, rich in guanine and cytosine, such asc-kit1and the HIV-1 LTR-III sequence, are prevalent in oncogenes and retroviruses and play crucial roles in cancer. Understanding the conformational dynamics of such guanine quadruplexes and identifying druggable regions are therefore essential for developing new inhibition strategies. In this study, we used extensive AMOEBA polarizable force field molecular dynamics simulations combined with data-driven adaptive sampling and clustering algorithms, reaching a cumulative simulation time of 7.5µs forc-kit1. Our results reveal novel structural stabilizations and flexible loop dynamics, as well as the critical role of polarizable water in stabilizing the G-quadruplex, leading to the identification of two new druggable pockets inc-kit1. Additionally, 400 ns simulation of the HIV-1 LTR-III sequence confirmed its quadruplex stability and uncovered a potentially druggable cryptic pocket.

Abstract Figure
Inflammatory pain in mice induces light cycle-dependent effects on sleep architecture
Authors: Burek Dominika J. , Ibrahim Khairunisa Mohamad , Hall Andrew G. , Sharma Ashish , Musiek Erik S. , Morón Jose A. , Carlezon William A.
Published: August 2024

As a syndrome, chronic pain comprises physical, emotional, and cognitive symptoms such as disability, negative affect, feelings of stress, and fatigue. A rodent model of long-term inflammatory pain, induced by complete Freund’s adjuvant (CFA) injection, has previously been shown to cause anhedonia and dysregulated naturalistic behaviors, in a manner similar to animal models of stress. We examined whether this extended to alterations in circadian rhythms and sleep, such as those induced by chronic social defeat stress, using actigraphy and wireless EEG. CFA-induced inflammatory pain profoundly altered sleep architecture in male and female mice. Injection of the hind paw, whether with CFA or saline, reduced some measures of circadian rhythmicity such as variance, period, and amplitude. CFA increased sleep duration primarily in the dark phase, while sleep bout length was decreased in the light and increased in the dark phase. Additionally, CFA reduced wake bout length, especially during the dark phase. Increases in REM and SWS duration and bouts were most significant in the dark phase, regardless of whether CFA had been injected at its onset or 12 hours prior. Taken together, these results indicate that inflammatory pain acutely promotes but also fragments sleep.
Prefrontal working memory signal controls phase-coded information within extrastriate cortex
Authors: Parto-Dezfouli Mohsen , Vanegas M Isabel , Zarei Mohammad , Nesse William H. , Clark Kelsey L. , Noudoost Behrad
Published: August 2024

In order to understand how prefrontal cortex provides the benefits of working memory (WM) for visual processing we examined the influence of WM on the representation of visual signals in V4 neurons in two macaque monkeys. We found that WM induces strong β oscillations in V4 and that the timing of action potentials relative to this oscillation reflects sensory information- i.e., a phase coding of visual information. Pharmacologically inactivating the Frontal Eye Field part of prefrontal cortex, we confirmed the necessity of prefrontal signals for the WM-driven boost in phase coding of visual information. Indeed, changes in the average firing rate of V4 neurons were correlated with WM-induced oscillatory changes. We present a network model to describe how WM signals can recruit sensory areas by inducing oscillations within these areas and discuss the implications of these findings for a sensory recruitment theory of WM through coherence.
Glutamate uptake is transiently compromised in the perilesional cortex following controlled cortical impact
Authors: Garcia Jacqueline P , Armbruster Moritz , Sommer Mary , Nunez-Beringer Aliana , Dulla Chris G
Published: August 2024

Glutamate, the primary excitatory neurotransmitter in the CNS, is regulated by the excitatory amino acid transporters (EAATs) GLT-1 and GLAST. Following traumatic brain injury (TBI), extracellular glutamate levels increase, contributing to excitotoxicity, circuit dysfunction, and morbidity. Increased neuronal glutamate release and compromised astrocyte-mediated uptake contribute to elevated glutamate, but the mechanistic and spatiotemporal underpinnings of these changes are not well established. Using the controlled cortical impact (CCI) model of TBI and iGluSnFR glutamate imaging, we quantified extracellular glutamate dynamics after injury. Three days post-injury, glutamate release was increased, and glutamate uptake and GLT-1 expression were reduced. 7- and 14-days post-injury, glutamate dynamics were comparable between sham and CCI animals. Changes in peak glutamate response were unique to specific cortical layers and proximity to injury. This was likely driven by increases in glutamate release, which was spatially heterogenous, rather than reduced uptake, which was spatially uniform. The astrocyte K+channel, Kir4.1, regulates activity-dependent slowing of glutamate uptake. Surprisingly, Kir4.1 was unchanged after CCI and accordingly, activity-dependent slowing of glutamate uptake was unaltered. This dynamic glutamate dysregulation after TBI underscores a brief period in which disrupted glutamate uptake may contribute to dysfunction and highlights a potential therapeutic window to restore glutamate homeostasis.
Altered functional connectivity and spatiotemporal dynamics in individuals with sleep disorders
Authors: Daley Lauren , Saini Prabhjyot , Watters Harrison , Bassil Yasmine , Schumacher Eric , Trotti Lynn Marie , Keilholz Shella
Published: August 2024

Idiopathic hypersomnia (IH) is a sleep disorder characterized by highly disruptive symptoms. Like narcolepsy type 1, a well-characterized sleep disorder, individuals with IH suffer from excessive daytime sleepiness, though there is little overlap in metabolic or neural biomarkers across these two disorders. This lack of common pathophysiology, combined with the clear overlap in symptoms presents an ideal paradigm for better understanding the impact of IH on an individual's functional activity and organization, and potentially, the underlying pathophysiology. This study examines the observed functional connectivity in patients with IH, and patients with narcolepsy type 1 (NT1) against healthy control individuals. Static functional connectivity is compared, as are quasi-periodic patterns, acquired from the BOLD timecourse, for all groups. In addition to baseline data comparison, the study also included a post-nap condition, where the individuals included in this analysis napped for at least 10 minutes prior to the scanning session, to explore why individuals with IH do not feel refreshed after a nap like individuals with NT1 do. Assessing the groups' spatiotemporal patterns revealed key differences across both disorders and conditions: static connectivity revealed at baseline higher subcortical connectivity in the NT1 group. There was also observably less connectivity in the IH group both at baseline and post-nap, though none of these static analyses survived multiple comparisons correction to reach significance. The QPP results however found significant differences in the IH group in key networks, particularly the DAN/FPCN correlation is significantly different at baseline vs. post-nap, a trend not observed in either the control or NT1 groups. The DAN and FPCN are drastically altered both at baseline and post-nap when compared to the other groups, and may likely be a disorder-specific result. This study demonstrates that key networks for arousal are more heavily disrupted in IH patients, who are less affected by a nap, confirmed through both subject reporting and functional evidence through spatiotemporal patterns.
Temperature and host plant ecotype drive nitrogen fixation, but not nodule community composition, in hairy vetch
Authors: Fudge Rebecca , Gardner Paula , Denison R Ford , Burghardt Liana , Grossman Julie
Published: August 2024

Hairy vetch (Vicia villosaRoth) is a commonly grown cover crop throughout the U.S., which can contribute nitrogen for subsequent cash crops through biological nitrogen fixation (BNF) in association withRhizobium leguminosarumbiovarviciae(Rlv) bacteria. Hairy vetch is one of the few cover crops sufficiently cold-tolerant to over-winter in the Upper Midwestern U.S. However, nitrogen contributions by hairy vetch vary across locations, potentially due to cold impacts on the legume/rhizobia symbiosis. The traditional route to improve BNF in legumes involves selecting superior rhizobia strains to create more effective inoculants to apply at planting, but inoculants often fail to compete and survive in agricultural soils. Instead, this study tested the effects of temperature and host plant ecotype on hairy vetch BNF and Rlv community composition in nodules, with the goal of potentially identifying vetch ecotypes able to select beneficial Rlv strains from the soil community. Four hairy vetch ecotypes trapped Rlv from three Minnesota soils, at warm or cold temperatures. Vetch ecotype was a key driver of BNF and nodule formation under warm and cold conditions. However, temperature and plant ecotype did not drive Rlv community composition in nodules, and Rlv community composition did not affect plant productivity. Taken together, these results suggest that the best strategy to improve BNF at low temperatures in hairy vetch likely depends on breeding for improved biomass accumulation and nitrogen fixation in host plants, rather than focusing on host plant selection of beneficial rhizobia.
Isotope analysis of birds’ eye lens provides early-life information
Authors: Hasegawa Emi Arai , Matsubayashi Jun , Tayasu Ichiro , Goto Tatsuhiko , Inoue Haruka , Rossberg Axel G. , Yoshimizu Chikage , Hasegawa Masaru , Akasaka Takumi
Published: August 2024

Early-life environment has a long-lasting effect on later life, though its estimation is often prevented in the wild because of a lack of available methods. Recently, isotope analysis of eye lenses has attracted considerable interest as a means to reconstruct the environmental conditions experienced by animals during the developmental period. This analysis has mostly been confined to fish for practical reasons and remains to be resolved for application to other animals. In this study, we broadened its applicability by developing a novel approach and verifying its usability for the reconstruction of early-life environments. We performed a feeding experiment using Japanese quail (Coturnix japonica), in which we administered two diets: one composed mainly of C3 plants (lowδ13C and highδ15N) and the other of C4 plants (highδ13C and lowδ15N). Quails in the control group were continuously fed a C3-based diet from hatching until 200 days old, whereas those in the treatment groups (T10, T15, T20, and T40) were switched from the C3 to the C4-based diet at 10, 15, 20, and 40 days after hatching, respectively. We found that theδ13C in the eye lenses of the treatment groups decreased from the center layer to the middle layer of the lens and then increased toward the outer layer, thus reflecting the diet change. In contrast, those of the control group exhibited a decreasing trend and equilibrated at the middle layer of the eye lens, with no increase thereafter. This novel approach revealed the postnatal feeding histories of the diet-shift experiment. The highδ13C values observed in the center of the eye lenses would reflect the prenatal feeding environment, i.e., the C4-based diet consumed by their mothers, which is further reinforced by higherδ15N values at this position due to the consumption of egg yolk-derived nutrition. These results indicate that the avian eye lens can be used as an “isotopic chronicle,” which is a useful tool for reconstructing chronological isotopic information about their early-life history.
Unsupervised learning of progress coordinates during weighted ensemble simulations: Application to millisecond protein folding
Authors: Leung Jeremy , Frazee Nicolas , Brace Alex , Ramanathan Arvind , Chong Lillian
Published: August 2024

Our method identifies outliers in a latent space model of the system′s sampled conformations that is periodically trained using a convolutional variational autoencoder. As a proof of principle, we applied our DL-enhanced WE method to simulate a millisecond protein folding process. To enable rapid tests, our simulations propagated discrete-state synthetic molecular dynamics trajectories using a generative, fine-grained Markov state model. Results revealed that our ″on-the-fly″ DL of outliers enhanced the efficiency of WE by >3-fold in estimating the folding rate constant. Our efforts are a significant step forward in the unsupervised learning of slow coordinates during rare event sampling.
Brain Charts for the Rhesus Macaque Lifespan
Authors: Alldritt S. , Ramirez J.S.B. , Vos de Wael R. , Bethlehem R. , Seidlitz J. , Wang Z. , Nenning K. , Esper N.B. , Smallwood J. , Franco A.R. , Byeon K. , Alexander-Bloch A. , Amaral D.G. , Amiez C. , Balezeau F. , Baxter M.G. , Becker G. , Bennett J. , Berkner O. , Blezer E.L.A. , Brambrink A.M. , Brochier T. , Butler B. , Campos L.J. , Canet-Soulas E. , Chalet L. , Chen A. , Cléry J. , Constantinidis C. , Cook D.J. , Dehaene S. , Dorfschmidt L. , Drzewiecki C.M. , Erdman J.W. , Everling S. , Falchier A. , Fleysher L. , Fox A. , Freiwald W. , Froesel M. , Froudist-Walsh S. , Fudge J. , Funck T. , Gacoin M. , Gale D.J. , Gallivan J. , Garin C.M. , Griffiths T.D. , Guedj C. , Hadj-Bouziane F. , Hamed S.B. , Harel N. , Hartig R. , Hiba B. , Howell B.R. , Jarraya B. , Jung B. , Kalin N. , Karpf J. , Kastner S. , Klink C. , Kovacs-Balint Z.A. , Kroenke C. , Kuchan M.J. , Kwok S.C. , Lala K.N. , Leopold D.A. , Li G. , Lindenfors P. , Linn G. , Mars R.B. , Masiello K. , Menon R.S. , Messinger A. , Meunier M. , Mok K. , Morrison J.H. , Nacef J. , Nagy J. , Neudecker V. , Neuringer M. , Noonan M.P. , Ortiz-Rios M. , Perez-Zoghbi J.F. , Petkov C.I. , Pinsk M. , Poirier C. , Procyk E. , Rajimehr R. , Reader S.M. , Rudko D.A. , Rushworth M.F.S. , Russ B.E. , Sallet J. , Sanchez M.M. , Schmid M.C. , Schwiedrzik C.M. , Scott J.A. , Sein J. , Sharma K.K. , Shmuel A. , Styner M. , Sullivan E.L. , Thiele A. , Todorov O.S. , Tsao D. , Tusche A. , Vlasova R. , Wang Z. , Wang L. , Wang J. , Weiss A.R. , Wilson C.R.E. , Yacoub E. , Zarco W. , Zhou Y. , Zhu J. , Margulies D. , Fair D. , Schroeder C. , Milham M. , Xu T.
Published: August 2024

Recent efforts to chart human brain growth across the lifespan using large-scale MRI data have provided reference standards for human brain development. However, similar models for nonhuman primate (NHP) growth are lacking. The rhesus macaque, a widely used NHP in translational neuroscience due to its similarities in brain anatomy, phylogenetics, cognitive, and social behaviors to humans, serves as an ideal NHP model. This study aimed to create normative growth charts for brain structure across the macaque lifespan, enhancing our understanding of neurodevelopment and aging, and facilitating cross-species translational research. Leveraging data from the PRIMatE Data Exchange (PRIME-DE) and other sources, we aggregated 1,522 MRI scans from 1,024 rhesus macaques. We mapped non-linear developmental trajectories for global and regional brain structural changes in volume, cortical thickness, and surface area over the lifespan. Our findings provided normative charts with centile scores for macaque brain structures and revealed key developmental milestones from prenatal stages to aging, highlighting both species-specific and comparable brain maturation patterns between macaques and humans. The charts offer a valuable resource for future NHP studies, particularly those with small sample sizes. Furthermore, the interactive open resource (https://interspeciesmap.childmind.org) supports cross-species comparisons to advance translational neuroscience research.
Systematic evaluation ofde novomutation calling tools using whole genome sequencing data
Authors: Shah Anushi , Monger Steven , Troup Michael , Ip Eddie KK , Giannoulatou Eleni
Published: August 2024

De novomutations (DNMs) are genetic alterations that occur for the first time in an offspring. DNMs have been found to be a significant cause of severe developmental disorders. With the widespread use of next-generation sequencing (NGS) technologies, accurate detection of DNMs is crucial. Several bioinformatics tools have been developed to call DNMs from NGS data, but no study to date has systematically compared these tools. We used both real whole genome sequencing (WGS) data from a trio from the 1000 Genomes Project (1000G) and simulated trio data to evaluate four DNM calling tools: DeNovoGear, TrioDeNovo, PhaseByTransmission, and VarScan 2. For DNMs called in the real dataset, we observed 8.7% concordance between all tools, while up to 36.2% of DNMs were unique to each caller. For simulated trio WGS datasets spiked with 100 DNMs, the concordance rate was also low at 4.1%. DeNovoGear achieved the highest F1-score on both the real and simulated datasets. Our study provides valuable recommendations for the selection and application of DNM callers on WGS trio data.
Uncovering the genetic underpinnings for different psychiatric disorder combinations
Authors: Yin Liangying , Liu Menghui , Shi Yujia , Zhang Ruoyu , Lui Simon Sai-Yu , So Hon-Cheong
Published: August 2024

Psychiatric disorders are highly heterogeneous. Clinically, it is meaningful to distinguish psychiatric disorders by the presence or absence of a specific comorbid condition. In this study, we employed a recently developed algorithm (CombGWAS) to decipher the genetic basis of psychiatric disorder combinations using GWAS summary statistics. We focused on comorbidities and combinations of diseases, such as schizophrenia(SCZ) with and without depression, which can be considered as two 'subtypes' of SCZ. We also studied psychiatric disorders comorbid with obesity as disease subtypes. Our study identified genetic signatures that distinguish different 'subtypes' and revealed the genetic architecture underlying 16 psychiatric disorder combinations. We discovered both shared and unique susceptibility genes/variants across different psychiatric disorder 'subtypes'. Notably, despite high genetic correlations between subtypes, most subtype pairs exhibited distinct genetic correlations with the same cardiovascular disease (CVD). Some pairs even displayed opposite genetic correlations, especially those involving obesity. For instance, the genetic correlation (rg) between SCZ with obesity and type 2 diabetes(T2DM) was 0.248(p=4.42E-28), while the rg between SCZ without obesity and T2DM was -0.154(p=6.79E-12). Many psychiatric disease combinations studied were causally associated with increased CVD risks. Moreover, comorbid psychiatric disorders often showed different causal relationships with CVD compared to single psychiatric disorders. This study represents a significant step toward understanding the genetic heterogeneity underlying psychiatric disorder comorbidities, providing new insights into their pathophysiology.
Efficient molecular mendelian randomization screens with LaScaMolMR.jl
Authors: Mathieu Samuel , Minvielle Moncla Louis-Hippolyte , Briend Mewen , Duclos Valentine , Rufiange Anne , Bossé Yohan , Mathieu Patrick
Published: August 2024

The ever-growing genetic cohorts lead to an increase in scale of molecular Quantitative Trait Loci (QTL) studies, creating opportunities for more extensive two samples Mendelian randomization (MR) investigations aiming to identify causal relationships between molecular traits and diseases. This increase led to the identification of multiple causal candidates and potential drug targets over time. However, the increase in scale of such studies and higher dimension multi-omic data come with computational challenges. We present “LArge SCAle MOLecular Mendelian Randomization with Julia” (LaScaMolMR.jl), an open-sourced integrated Julia package optimized for Omic-wide Mendelian Randomization (OWMR) Studies. This versatile package eliminates the two-language problem and implements fast algorithms for instrumental variable selection approaches with both cis and trans instruments and performs the most popular regression estimators for MR studies with molecular exposures. It reduces the compute time via meta-programming allowing easy deployment of multi-threaded approach and the internalization of linkage disequilibrium investigation of potential instrumental variables. Via its integrated approach and high-computational performance, LaScaMolMR.jl allows users who have minimal programming experience to perform large scale OWMR studies.

Implementation and availability

LaScaMolMR is freely available atgithub.com/SamuelMathieu-code/LaScaMolMR.jl.
Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA fully clarify DNA binding by NtcA and recruitment of RNA polymerase by PipX
Authors: Forcada-Nadal Alicia , Bibak Sirine , Salinas Paloma , Contreras Asunción , Rubio Vicente , Llácer José L.
Published: August 2024

The CRP-FNR superfamily of transcriptional regulators includes the cyanobacterial master regulator NtcA, which orchestrates large responses of cyanobacteria to nitrogen scarcity. NtcA uses as allosteric activator 2-oxoglutarate (2OG), a signal of nitrogen poorness and carbon richness, and binds a coactivating protein (PipX) that shuttles between the signaling protein PII and NtcA depending on nitrogen richness, thus connecting PII signaling and gene expression regulation. Here, combining structural (X-ray crystallography of six types of crystals including NtcA complexes with DNA, 2OG and PipX), modelling and functional (EMSA and bacterial two-hybrid) studies, we clarify the reasons for the exquisite specificity for the binding of NtcA to its target DNA, its mechanisms of activation by 2OG, and its coactivation by PipX. Our crystal structures of PipX-NtcA-DNA complexes prove that PipX does not interact with DNA, although it increases NtcA-DNA contacts, and that it stabilizes the active, DNA-binding-competent conformation of NtcA. Superimposition of this complex on a very recently reported cryoEM structure of NtcA in a Transcription Activity Complex with RNA polymerase (RNAP), shows that PipX binding helps recruit RNAP by PipX interaction with RNAP, particularly with its gamma and sigma (region 4) subunits, a structural prediction supported here by bacterial two-hybrid experiments.
Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species
Authors: Magesh Shruthi , Schrope Jonathan H. , Mercado Soto Nayanna , Li Chao , Hurley Amanda I. , Huttenlocher Anna , Beebe David J. , Handelsman Jo
Published: August 2024

Biofilms are three-dimensional structures containing one or more bacterial species embedded in extracellular polymeric substances. Although most biofilms are stationary,Flavobacterium johnsoniaeforms a motile spherical biofilm called a zorb, which is propelled by its base cells and contains a polysaccharide core. Here, we report formation of spatially organized, motile, multispecies biofilms, designated “co-zorbs,” that are distinguished by a core-shell structure.F. johnsoniaeforms zorbs whose cells collect other bacterial species and transport them to the zorb core, forming a co-zorb. Live imaging revealed that co-zorbs also form in zebrafish, thereby demonstrating a new type of bacterial movement in vivo. This discovery opens new avenues for understanding community behaviors, the role of biofilms in bulk bacterial transport, and collective strategies for microbial success in various environments.

Significance Statement

This paper reports the discovery of co-zorbs, which are spherical aggregates of bacteria that move and transport other bacteria. Zorbs move toward other bacteria and collect them in a manner reminiscent of phagocytes. Once inside the zorb, the new species form a striking, organized core. The discovery of co-zorbs introduces an entirely new type of bacterial movement and transport involving cooperation among bacterial species. Co-zorbs have potential for engineering microbial systems for biotechnology applications and for managing spread of bacterial pathogens in their hosts.
The C2 domain augments Ras GTPase Activating Protein catalytic activity
Authors: Paul Maxum E. , Chen Di , Vish Kimberly J. , Lartey Nathaniel L. , Hughes Elizabeth , Freeman Zachary T. , Saunders Thomas L. , Stiegler Amy L. , King Philip D. , Boggon Titus J.
Published: August 2024

Regulation of Ras GTPases by GTPase activating proteins (GAP) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP;RASA1) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity towards Ras. Analysis of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domainin vitro. In mice,R707Cmutation phenocopies the vascular and signaling defects resulting from constitutive disruption of theRASA1gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of Ras GTPase activating proteins.
Invariant Natural Killer T cells control positively and negatively the development of hepatocellular carcinoma
Authors: Papanastasatou Maria , Gioulbasani Marianthi , Nakou Evangelia , Galaras Alexandros , Rubio-Tomás Teresa , Talianidis Iannis , Eliopoulos Aristides , Hatzis Pantelis , Verykokakis Mihalis
Published: August 2024

The liver routinely encounters antigens from the gut, triggering pro- inflammatory responses. Unresolved inflammation can lead to liver damage, steatosis, fibrosis, cirrhosis, and eventually hepatocellular carcinoma (HCC). HCC is influenced by various immune cells, including invariant natural killer T (iNKT) cells, which exhibit both innate and adaptive immunity traits. Here, we examined iNKT cell dynamics in a diethyl-nitrosamine (DEN)-induced HCC mouse model. We observed a significant reduction in iNKT cell numbers in HCC livers due to apoptosis and impaired cytokine production.CD1d-deficient mice, which lack iNKT cells, displayed delayed tumor initiation and lower tumor and foci number. However, these tumors were larger in size and characterized by enhanced proliferation and immunosuppression. Interestingly, adoptive transfer of healthy iNKT cells post-tumor establishment reduced tumor burden, highlighting their potential therapeutic role. Our findings suggest that iNKT cells contribute to early HCC development, while in later stages they help to control tumor growth, thus underscoring their complex role in liver carcinogenesis. Further understanding of iNKT cell functions may inform novel immunotherapeutic strategies for HCC management.
5’UTR translational inhibition of neuroblastoma dependency factors using the CR-1-31-B rocaglate
Authors: Nunes C , Bekaert SL , Parsa S , Nelen I , Martens F , De Stanchina E , Sanders E , Hilgert E , T’sas S , Zhao P , De Vloed F , Eggermont A , Goossens S , Sablina A , Depestel L , Wendel HG , Durinck K
Published: August 2024

Current therapies for neuroblastoma are often ineffective and survivors suffer from severe long-term therapy related side-effects, underscoring the need for identification of novel drugging strategies. We performed an in-depth evaluation of phenotypic and molecular responses following exposure of neuroblastoma cells to the rocaglate CR-1-31-B, scrutinizing its mode-of-action through integrative ribosome footprinting and shotgun proteome profiling. We could show that CR-1-31-B significantly reduces tumor growthin vivowithout apparent toxicity. By means of combined ribosome footprinting and transcriptome analysis we uncovered that CR-1-31-B treatment downregulates translation efficiencies of several major neuroblastoma dependencies includingMYCN,CCND1andALKas well as factors involved in the G2/M checkpoint. Upregulated targets are enriched for oxidative phosphorylation pathway components and DNA repair. At the proteome level, CR-1-31-B imposed downregulation of a FOXM1 driven signature, including the FOXM1 target geneTPX2. We show that neuroblastoma cells are dependent on TPX2 for growth and DNA repair and further demonstrate enhanced CHK1 sensitivity upon TPX2 knockdown. Next, we also observed synergistic effects of CHK1 inhibition with CR-1-31-B. In conclusion, our data support CR-1-31-B as a potent novel therapeutic agent in neuroblastoma, in particular in combination with DNA damage or replication stress inducing agents.
Liprin-α/RIM complex regulates the dynamic assembly of presynaptic active zones via liquid-liquid phase separation
Authors: Jin Gaowei , Campos Joaquín , Liu Yang , de la Cruz Berta Marcó , Zhang Shujing , Liang Mingfu , Li Kaiyue , Xie Xingqiao , Yu Cong , Sterky Fredrik H. , Acuna Claudio , Wei Zhiyi
Published: August 2024

Presynaptic scaffold proteins, including liprin-α, RIM, and ELKS, are pivotal to the assembly of the active zone and regulating the coupling of calcium signals and neurotransmitter release, yet the underlying mechanism remains poorly understood. Here, we determined the crystal structure of the liprin-α2/RIM1 complex, revealing a multifaceted intermolecular interaction that drives the liprin-α/RIM assembly. Neurodevelopmental disease-associated mutations block the formation of the complex. Disrupting this interaction in neurons impairs synaptic transmission and reduces the readily releasable pool of synaptic vesicles. Super-resolution imaging analysis supports a role for liprin-α in recruiting RIM1 to the active zone, presumably by promoting the liquid-liquid phase separation (LLPS) of RIM1. Strikingly, the liprin-α/RIM interaction modulates the competitive distribution of ELKS1 and voltage-gated calcium channels (VGCCs) in RIM1 condensates. Disrupting the liprin-α/RIM interaction significantly decreased VGCC accumulation in the condensed phase and rendered release more sensitive to the slow calcium buffer EGTA, suggesting an increased physical distance between VGCC and vesicular calcium sensors. Together, our findings provide a plausible mechanism of the liprin-α/RIM complex in regulating the coupling of calcium channels and primed synaptic vesicles via LLPS for efficient synaptic transmission and uncover the pathological implication of liprin-α mutations in neurodevelopmental disorders.
Genetic risk for neurodegenerative conditions is linked to disease-specific microglial pathways
Authors: Askarova Aydan , Yaa Reuben M. , Marzi Sarah J. , Nott Alexi
Published: August 2024

Genome-wide association studies have identified thousands of common variants associated with an increased risk of neurodegenerative disorders. However, the noncoding localization of these variants has made the assignment of target genes for brain cell types challenging. Genomic approaches that infer chromosomal 3D architecture can link noncoding risk variants and distal gene regulatory elements such as enhancers to gene promoters. By using enhancer-to-promoter interactome maps for microglia, neurons, and oligodendrocytes, we identified cell-type-specific enrichment of genetic heritability for brain disorders through stratified linkage disequilibrium score regression. Our analysis suggests that genetic heritability for multiple neurodegenerative disorders is enriched at microglial chromatin contact sites. Through Hi-C coupled multimarker analysis of genomic annotation (H-MAGMA) we identified disease risk genes for Alzheimer’s disease, Parkinson’s disease, multiple sclerosis and amyotrophic lateral sclerosis. We found that disease-risk genes were overrepresented in microglia compared to other brain cell types across neurodegenerative conditions. Notably, the microglial risk genes and pathways identified were largely specific to each disease. Our findings reinforce microglia as an important, genetically informed cell type for therapeutic interventions in neurodegenerative conditions and highlight potentially targetable disease-relevant pathways.
NRH, a potent NAD+ booster, improves glucose homeostasis and lipid metabolism in diet-induced obese mice though an active adenosine kinase pathway
Authors: Zeng Xinliu , Wang Yongjie , Farias Karina , Rappa Andrew , Darko Chirstine , Sauve Anthony , Yang Yue
Published: August 2024

NAD+deficiency underlies obesity-induced metabolic disturbances. Here we evaluated the treatment effect of a new and potent NAD+enhancer, dihydronicotinamide riboside (NRH), in diet-induced obese mice with hyperglycemia and hyperlipidemia. Administering NRH for 7 weeks improved glucose homeostasis by enhancing pancreatic beta-cell functional mass, increasing muscle insulin sensitivity, and reducing hepatic gluconeogenesis. NRH treatment also mobilized fat deposition, reduced circulating lipid, and improved white adipose function. Significant elevation in multi-tissue NAD+levels and sirtuin (SIRT) activities, especially SIRT3, mediated these metabolic improvements. Inhibiting adenosine kinase (ADK), a newly recognized enzyme in the NRH-induced NAD+synthesis pathway, blocked NRH’s effect in improving glucose and lipid metabolism. ADK inhibition also reduced tissue NAD+elevation and the subsequent activation of SIRT3, suggesting an active ADK pathway is necessary for NRH-induced metabolic benefits. These observations, for the first time, establish NRH as a promising intervention for correcting obesity-induced metabolic syndrome.
Transcription factors SlMYB41, SlMYB92 and SlWRKY71 regulate gene expression in the tomato exodermis
Authors: Jo Leonardo , Buti Sara , Artur Mariana A. S. , Kluck Rianne M.C. , Cantó-Pastor Alex , Brady Siobhán M. , Kajala Kaisa
Published: August 2024

Root barrier cell types, like the endodermis and exodermis, are crucial for plant acclimation to environmental stresses. Deposition of suberin, a hydrophobic polymer, in these cell layers restricts the movement of molecules and plays a vital role in stress responses. This study investigates the role of SlMYB41, SlMYB92 and SlWRKY71 transcription factors (TFs) in regulating suberin biosynthesis in the tomato (Solanum lycopersicum) root exodermis by genetic perturbation. Genetic perturbation of these TFs altered exodermal suberin deposition patterns, indicating the SlMYBs as positive and SlWRKY71 negative regulators of suberization. RNA sequencing revealed a significant overlap between differentially expressed genes regulated by these TFs, suggesting a shared regulatory network. Gene set enrichment analyses highlighted their role in lipid and suberin biosynthesis as well as overrepresentation of exodermis-enriched transcripts. Furthermore, transactivation assays demonstrated that these two MYBs promote the expression of suberin-related genes, while SlWRKY71 represses them. These results indicate a complex antagonistic relationship, advancing our understanding of the regulatory mechanisms controlling exodermis suberization in tomato roots.

Highlight

MYB and WRKY transcription factors collaboratively regulate suberin biosynthesis in the tomato root exodermis. Antagonistic interactions may fine-tune suberization or act as a break to stop overaccumulation.
Movement-related activity in the internal globus pallidus of the parkinsonian macaque
Authors: Kase Daisuke , Zimnik Andrew J. , Han Yan , Harsch Devin R. , Bacha Sarah , Cox Karin M. , Bostan Andreea C. , Richardson R. Mark , Turner Robert S.
Published: August 2024

Although the basal ganglia (BG) plays a central role in the motor symptoms of Parkinson’s disease, few studies have investigated the influence of parkinsonism on movement-related activity in the BG. Here, we studied the perimovement activity of neurons in globus pallidus internus (GPi) of non-human primates before and after the induction of parkinsonism by administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Neuronal responses were equally common in the parkinsonian brain as seen prior to MPTP and the distribution of different response types was largely unchanged. The slowing of behavioral reaction times and movement durations following the induction of parkinsonism was accompanied by a prolongation of the time interval between neuronal response onset and movement initiation. Neuronal responses were also reduced in magnitude and prolonged in duration after the induction of parkinsonism. Importantly, those two effects were more pronounced among decrease-type responses, and they persisted after controlling for MPTP-induced changes in the trial-by-trial timing of neuronal responses. Following MPTP The timing of neuronal responses also became uncoupled from the time of movement onset and more variable from trial-to-trial. Overall, the effects of MPTP on temporal features of neural responses correlated most consistently with the severity of parkinsonian motor impairments whereas the changes in response magnitude and duration were either anticorrelated with symptom severity or inconsistent. These findings point to a potential previously underappreciated role for abnormalities in the timing of GPi task-related activity in the generation of parkinsonian motor signs.

New & Noteworthy

Perimovement responses were present in the parkinsonian GPi at roughly the same overall abundance as seen in the neurologically normal state. Nonetheless, parkinsonism was associated with three abnormalities in perimovement activity: 1) Timings of GPi response became uncoupled from movement onset both with respect to both mean latency and trial-to-trial timing variability. 2) Response magnitudes were attenuated. 3) Response durations were prolonged. The effects on both response magnitude and duration were accentuated in decrease-type responses.