bluuebunny/crossref_metadata_2025 huggingface dataset:
The puzzling case of the 3p25 homozygous deletion: the target is notVHLbutVGLL4andATG7
Authors: Muller Florian , Behr Eliot
Published: November 2023

The 3p25 locus experiences recurrent homozygous deletions in diverse carcinomas. A validated tumor suppressor gene (TSG),VHLhas long been assumed to be the target of this deletion.

Here, we show that homozygous deletions at the 3p25 locus are common in renal clear cell carcinoma (RCC) and squamous cell carcinomas but that these do not center onVHLbut on two nearby overlapping genes,VGLL4andATG7. While hypomorphic mutations ofVHLcoupled with heterozygous deletions are undoubtedly a driver in RCC, DepMap CRISPR data indicate that the complete absence ofVHLis broadly detrimental to cancer cells. Re-examination of TCGA and PDX data calls into question whetherVHLis ever homozygous deleted, even in RCC.

Instead, multiple lines of evidence support the homozygous deletion ofVGLL4as a driver event in squamous cell carcinomas and the homozygous deletion ofATG7as a driver in RCC, with important implication for precision oncology. VGLL4 is the major negative regulator of the YAP/TEAD complex, with elimination of VGLL4 leading to hyperactive oncogenic YAP-dependent transcriptional activity which could be targeted by clinically emerging YAP/TEAD inhibitors. ATG7 is a critical regulator of autophagy, limiting proliferation in conditions of nutrient limitation and its deletion may open novel vulnerabilities for synthetic lethality.
Single cell transcriptional profiling of benign prostatic hyperplasia reveals a progenitor-like luminal epithelial cell state within an inflammatory microenvironment
Authors: Unno Rei , Akutagawa Jon , Song Hanbing , Hui Keliana , Chen Yih-An , Pham Julia , Yang Heiko , Huang Franklin W. , Chi Thomas
Published: November 2023

Benign prostatic hyperplasia (BPH) is characterized by excessive cell proliferation and inflammation and affects most aging men. The development of new therapies for BPH requires a deeper understanding of the underlying pathophysiology and cellular components of BPH. Here, we characterize at single cell resolution the cellular states of BPH and identify cell populations enriched in BPH that contribute to cell proliferation and inflammation. Single-cell RNA-sequencing was performed on prostate tissue from 15 patients undergoing holmium laser enucleation of the prostate for treatment of BPH. Clustering and differential expression analysis on aligned single cell RNA-seq data was performed to annotate all cell types. Pseudotime, gene set enrichment, gene ontology, and ligand-receptor analyses were performed. 16,234 cells were analyzed and specific stromal, epithelial, and immune subgroups were found to be strongly associated with inflammation. A rare luminal subgroup was identified and pseudotime analysis indicated this luminal subgroup was more closely related to club and basal cells. Using a gene set derived from epithelial stem cells, we found that this luminal subgroup had a significantly higher stem cell signature score than all other epithelial subgroups, suggesting this subgroup is a luminal precursor state. Ligand-receptor interactions between stromal, epithelial, and immune cells were explored with CellPhoneDB. Unique interactions highlighting MIF, a pro-inflammatory cytokine that promotes epithelial cell growth and inflammation in the prostate, were found between fibroblasts and the progenitor luminal subgroup. This luminal subgroup also interacted with neutrophils and macrophages through MIF. Our single-cell profiling of BPH provides a roadmap for inflammation-linked cell subgroups and highlights a novel luminal progenitor subgroup interacting with other cell groups via MIF that may contribute to the inflammation and cell proliferation phenotype associated with BPH.
Understanding Age-Related Changes in Proprioception through Active and Passive Tasks
Authors: Carranza Erick , Franovic Sreten , Boos Amy , Pirondini Elvira
Published: November 2023

Voluntary control of motor actions requires precise regulation of proprioceptive and somatosensory functions. While aging has demonstrated to decline sensory processing functions, the effect of age on proprioception remains less clear. Indeed, previous studies contradict on whether passive proprioception (i.e., during externally driven movements) is affected over age. Moreover, no studies explored age-related modifications in active proprioception (i.e., during voluntary movements). Understanding these changes is critical to identify and prevent possible causes of reduced movement performances and mobility, in particular in age-related neurological conditions such as stroke or Parkinson disease. Here, we first refined a robotic protocol to assess upper-limb active proprioception and demonstrated the robustness and reliability of outcome measures over sessions. We then compared performances between young and elderly subjects during active and passive proprioceptive tasks. We found that while the two populations of subjects performed similarly in passive proprioception, elderly subjects’ acuity declined during active proprioception. Importantly, we confirmed that the decline could not be explained by impairments in voluntary motor control. Our data and robotic protocols further elucidate the debate over proprioception in elderly subjects and provide evidence that robust proprioceptive assessments should be an essential measurement in clinical settings.

New & Noteworthy

Upper limb position sense has been previously evaluated using passive matching protocols with the contralateral arm. These studies have found contradicting results regarding a possible decline in passive proprioception over age. Here we replicated this passive protocol and compared it to its active counterpart. Our results suggest that aging has an effect only in the active condition, leading to the hypothesis of a potential role of the cortico-spinal and cerebellar pathways in proprioception decline.
Inhibition of mitochondrial protein import and proteostasis by a pro-apoptotic lipid
Authors: Fita-Torró Josep , Garrido-Huarte José Luis , López-Gil Lucía , Michel Agnès H. , Kornmann Benoît , Pascual-Ahuir Amparo , Proft Markus
Published: November 2023

Mitochondria-mediated cell death is critically regulated by bioactive lipids derived from sphingolipid metabolism. The lipid aldehyde trans-2-hexadecenal (t-2-hex) induces mitochondrial dysfunction from yeast to humans. Here we apply unbiased transcriptomic, functional genomics and chemoproteomic approaches in the yeast model to uncover the principal mechanisms and biological targets underlying this lipid-induced mitochondrial inhibition. We find that loss of Hfd1 fatty aldehyde dehydrogenase function efficiently sensitizes cells for t-2-hex inhibition and apoptotic cell death. Excess of t-2-hex causes a profound transcriptomic response with characteristic hallmarks of impaired mitochondrial protein import like activation of mitochondrial and cytosolic chaperones or proteasomal function and severe repression of translation. We confirm that t-2-hex stress induces rapid accumulation of mitochondrial pre-proteins and protein aggregates and subsequent activation of Hsf1- and Rpn4-dependent gene expression. By saturated transposon mutagenesis we find that t-2-hex tolerance requires an efficient heat shock response and specific mitochondrial and ER functions and that mutations in ribosome, protein and amino acid biogenesis are beneficial upon t-2-hex stress. We further show that genetic and pharmacological inhibition of protein translation causes t-2-hex resistance indicating that loss of proteostasis is the predominant consequence of the pro-apoptotic lipid. Several TOM subunits, including the central Tom40 channel, are lipidated by t-2-hexin vitroand mutation of accessory subunits Tom20 or Tom70 confers t-2-hex tolerance. Moreover, the Hfd1 gene dose determines the strength of t-2-hex mediated inhibition of mitochondrial protein import and Hfd1 co-purifies with Tom70. Our results indicate that transport of mitochondrial precursor proteins through the outer mitochondrial membrane is sensitively inhibited by the pro-apoptotic lipid and thus represents a hotspot for pro- and anti-apoptotic signaling.
Energy of functional brain states correlates with cognition in adolescent-onset schizophrenia and healthy persons
Authors: Theis Nicholas , Bahuguna Jyotika , Rubin Jonathan E. , Banerjee Shubha Sankar , Muldoon Brendan , Prasad Konasale M.
Published: November 2023

Adolescent-onset schizophrenia (AOS) is rare, under-studied, and associated with more severe cognitive impairments and poorer outcomes than adult-onset schizophrenia. Neuroimaging has shown altered regional activations (first-order effects) and functional connectivity (second-order effects) in AOS compared to controls. The pairwise maximum entropy model (MEM) integrates first- and second-order factors into a single quantity called energy, which is inversely related to probability of occurrence of brain activity patterns. We take a combinatorial approach to study multiple brain-wide MEMs of task-associated components; hundreds of independent MEMs for various sub-systems are fit to 7 Tesla functional MRI scans. Acquisitions were collected from 23 AOS individuals and 53 healthy controls while performing the Penn Conditional Exclusion Test (PCET) for executive function, which is known to be impaired in AOS. Accuracy of PCET performance was significantly reduced among AOS compared to controls. A majority of the models showed significant negative correlation between PCET scores and the total energy attained over the fMRI. Across all instantiations, the AOS group was associated with significantly more frequent occurrence of states of higher energy, assessed with a mixed effects model. An example MEM instance was investigated further using energy landscapes, which visualize high and low energy states on a low-dimensional plane, and trajectory analysis, which quantify the evolution of brain states throughout this landscape. Both supported patient-control differences in the energy profiles. Severity of psychopathology was correlated positively with energy. The MEM’s integrated representation of energy in task-associated systems can help characterize pathophysiology of AOS, cognitive impairments, and psychopathology.
Protein interaction kinetics delimit the performance of phosphorylation-driven protein switches
Authors: Winter Daniel L. , Wairara Adelgisa R. , Bennett Jack L. , Donald William A. , Glover Dominic J.
Published: November 2023

Post-translational modifications (PTMs) such as phosphorylation and dephosphorylation can rapidly alter protein surface chemistry and structural conformation which can, in turn, switch protein-protein interactions (PPIs) within signaling networks. Recently,de novodesigned phosphorylation-responsive protein switches have been created that harness kinase- and phosphatase-mediated phosphorylation that modulate PPIs. PTM-driven protein switches could be useful for investigating PTM dynamics in living cells, developing biocompatible nanodevices, and engineering signaling pathways to program cell behavior. However, little is known about the physical and kinetic constraints of PTM-driven protein switches, which limits their practical application. In this study, we present a theoretical framework to evaluate two-component PTM-driven protein switches based on four performance metrics: effective concentration, dynamic range, response time, and reversibility. Our computational models reveal an intricate relationship between the binding kinetics, phosphorylation kinetics, and switch concentration that governs the sensitivity and reversibility of PTM-driven protein switches. Building upon the insights of our theoretical investigation, we built and evaluated two novel phosphorylation-driven protein switches consisting of phosphorylation-sensitive coiled coils as sensor domains fused to fluorescent proteins as actuator domains. By modulating the phosphorylation state of the switches with a specific protein kinase and phosphatase, we demonstrate fast, reversible transitions between easily differentiated “on” and “off” states. The response of the switches linearly correlated to the concentration of the kinase, demonstrating its potential as a biosensor for kinase measurements in real time. As intended, both switches responded to specific kinase activity with an increase in fluorescence signal and our model could be used to distinguish between two mechanisms of switch activation: dimerization or a structural rearrangement. In summary, the protein switch kinetics model presented here should be useful to guide the design of PTM-driven switches and tune their performance towards concrete applications.
EEG covariance patterns detects global cortical activity distribution following weak tactile inputs
Authors: Mellbin Astrid , Rongala Udaya , Jörntell Henrik , Bengtsson Fredrik
Published: November 2023

Many studies have suggested that the neocortex operates as a global network of functionally interconnected neurons, indicating that any sensory input could shift activity distributions across the whole brain. A tool assessing the activity distribution across cortical regions with high temporal resolution could then potentially detect subtle changes that may pass unnoticed in regionalized analyses. We used eight-channel, distributed electrocorticogram (ECoG) recordings to analyze changes in global activity distribution caused by single pulse electrical stimulations of the paw. We analyzed the temporally evolving covariance patterns of the activity distributions using principal component analysis (PCA). We found that localized tactile stimulation caused clearly measurable changes in global ECoG activity distribution. These changes in signal covariance patterns were detectable across a small number of ECoG channels, even when not including the somatosensory cortex, suggesting that the method has high sensitivity, potentially making it applicable to human EEG for detection of pathological changes.
Induction of immortal-like and functional CAR-T cells by defined factors
Authors: Wang Lixia , Jin Gang , Zhou Qiuping , Liu Yanyan , Zhao Xiaocui , Li Zhuoyang , Yin Na , Peng Min
Published: November 2023

Long-term antitumor efficacy of chimeric antigen receptor (CAR)-T cells depends on their functional persistence in vivo. T cells with stem-like property show better persistence, but factors conferring T cells bona fide stemness remain to be determined. Here, we demonstrate the induction of CAR-T cells into an immortal-like and functional state, termed TIF. The induction of CAR-TIF cells depends on repression of two factors: BCOR and ZC3H12A, and requires antigen or CAR tonic signaling. The reprogrammed CAR-TIF cells possess almost infinite stemness resembling induced pluripotent stem cells but retain functionality of mature T cells, which exhibit superior antitumor effect. CAR-TIF cells enter a metabolically dormant state after elimination of target cells, which persist in vivo with a saturable niche and mediate memory protection. CAR-TIF cells represent a novel state of T cells with unprecedented stemness conferring long-term functional persistence of CAR-T cells in vivo, which have broad potentials in T cell therapies.
Foraging task specialization in honey bees (Apis mellifera): the contribution of floral rewards on the learning performance of pollen and nectar foragers
Authors: Moreno Emilia , Arenas Andrés
Published: November 2023

Social insects live in communities where cooperative actions heavily rely on the individual cognitive abilities of their members. In the honey bee (Apis mellifera), the specialization in nectar or pollen collection is associated with variations in gustatory sensitivity, affecting both associative and non-associative learning. Gustatory sensitivity fluctuates as a function of changes in motivation for the specific floral resource throughout the foraging cycle, yet differences in learning abilities between nectar and pollen foragers at the onset of recollection remains unexplored. Here, we examined nectar and pollen foragers captured upon arrival at food sources. We subjected them to an olfactory PER conditioning using a 10% sucrose solution paired (S10%+P) or unpaired (S10%) with pollen as a co-reinforcement. For non-associative learning, we habituated foragers with a 10% sucrose solution paired (S10%+P) or unpaired (S10%) with pollen, followed by dishabituation tests with either S50% or S10%+P. Our results indicate that pollen foragers show lower performance than nectar foragers when conditioned with S10%. Interestingly, performance improves to levels similar to those of nectar foragers when pollen is included as rewarding stimulus (S10%+P). In non-associative learning, pollen foragers tested with S10%+P displayed a lower degree of habituation than nectar foragers and a higher degree of dishabituation when pollen was used as the dishabituating stimulus (S10%+P). Altogether, our results support the idea that pollen and nectar honey bee foragers differ in their perception of rewards, leading to inter-individual differences in learning that contribute to foraging specialization.
Gene Expression Meta-Analysis Reveals Aging and Cellular Senescence Signatures in Scleroderma-associated Interstitial Lung Disease
Authors: Yang Monica M. , Lee Seoyeon , Neely Jessica , Hinchcliff Monique , Wolters Paul J. , Sirota Marina
Published: November 2023

Aging and cellular senescence are increasingly recognized as key contributors to pulmonary fibrosis. However, our understanding in the context of scleroderma associated interstitial lung disease (SSc-ILD) is limited. To investigate, we leveraged previously established lung aging and cell-specific senescence signatures to determine their presence and potential relevance to SSc-ILD. We performed a gene expression meta-analysis of lung tissue from 38 SSc-ILD and 18 healthy controls and found markers (GDF15, COMP, CDKN2A) and pathways (p53) of senescence were significantly increased in SSc-ILD. When probing the established aging and cellular senescence signatures, we found epithelial and fibroblast senescence signatures had a 3.6-fold and 3.7-fold enrichment respectively in the lung tissue of SSc-ILD and that lung aging genes (CDKN2A, FRZB, PDE1A, NAPI12)were increased in SSc-ILD. These signatures were also enriched in SSc skin and associated with degree of skin involvement (limited vs. diffuse cutaneous). To further support these findings, we examined telomere length (TL), a surrogate for aging, in lung tissue and found independent of age, SSc-ILD had significantly shorter telomeres than controls in type II alveolar cells in the lung. TL in SSc-ILD was comparable to idiopathic pulmonary fibrosis, a disease of known aberrant aging. Taken together, this study provides novel insight into the possible mechanistic effects of accelerated aging and aberrant cellular senescence in SSc-ILD pathogenesis.
Dissecting the neuronal mechanisms of invariant word recognition
Authors: Agrawal Aakash , Dehaene Stanislas
Published: November 2023

Learning to read places a strong challenge on the visual system. Years of expertise lead to a remarkable capacity to separate highly similar letters and encode their relative positions, thus distinguishing words such as FORM and FROM invariantly over a large range of sizes and absolute positions. How neural circuits achieve invariant word recognition remains unknown. Here we address this issue through computational modeling and brain imaging. We first trained deep neural network models to recognize written words, then analyzed the reading-specialized units that emerged in deep layers. With literacy, units became sensitive to specific letter identities and their distance from the blank space at the left or right of a word, thus acting as “space bigrams” encoding ordinal position using an approximate number code. Using 7T functional MRI and magnetoencephalography in adults, we localized the predicted ordinal code anatomically (visual word form area) and temporally (∼220ms). The proposed neuronal mechanism for invariant word recognition can explain reading errors and makes precise predictions about how position-invariant neural codes arise in brains and artificial systems.
Using Extracellular miRNA Signatures to Identify Patients with LRRK2-Related Parkinson’s Disease
Authors: Braunger Luca Jannik , Knab Felix , Gasser Thomas
Published: November 2023

Background

Mutations in the Leucine Rich Repeat Kinase 2 gene are highly relevant in both sporadic and familial cases of Parkinson’s disease. Specific therapies are entering clinical trials but patient stratification remains challenging. Dysregulated microRNA expression levels have been proposed as biomarker candidates in sporadic Parkinson’s disease.

Objective

In this proof-of concept study we evaluate the potential of extracellular miRNA signatures to identify LRRK2-driven molecular patterns in Parkinson’s disease.

Methods

We measured expression levels of 91 miRNAs via RT-qPCR in ten individuals with sporadic Parkinson’s disease, tenLRRK2mutation carriers and eleven healthy controls using both plasma and cerebrospinal fluid. We compared miRNA signatures using heatmaps and t-tests. Next, we applied group sorting algorithms and tested sensitivity and specificity of their group predictions.

Results

miR-29c-3p was differentially expressed betweenLRRK2mutation carriers and sporadic cases, with miR-425-5p trending towards significance. Individuals clustered in principal component analysis along mutation status. Group affiliation was predicted with high accuracy in the prediction models (sensitivity up to 89%, specificity up to 70%). miRs-128-3p, 29c-3p, 223-3p and 424-5p were identified as promising discriminators among all analyses.

Conclusions

LRRK2 mutation status impacts the extracellular miRNA signature measured in plasma and separates mutation carriers from sporadic Parkinson’s disease patients. Monitoring LRRK2 miRNA signatures could be an interesting approach to test drug efficacy of LRRK2-targeting therapies. In light of small sample size, the suggested approach needs to be validated in larger cohorts.
Cdc73 majorly regulates apoptosis-inducing factor (AIF1) inSaccharomyces cerevisiaevia the H3K36 methylation
Authors: Saha Nitu , Acharjee Santoshi , Tomar Raghuvir Singh
Published: November 2023

AIF1overexpression is intimately linked to the sensitivity of the yeast cells towards hydrogen peroxide or acetic acid. Therefore, studying the mechanism of its regulation in the cell would provide a significant understanding of the factors ultimately guiding yeast apoptosis. In this report, we establish the time-dependent induction ofAIF1in hydrogen peroxide stress. Additionally, theAIF1expression in hydrogen peroxide is mediated by two transcription factors, Yap5 (DNA binding) and Cdc73 (non-DNA binding). Furthermore, substituting the H3K36 residue with another significantly abrogates theAIF1expression. However, substituting H3K4 or H3K79 with A does not affect theAIF1expression level under hydrogen peroxide stress. Altogether, the significant reduction ofAIF1expression incdc73Δ cells plausibly reflects the reduced H3K36me3 modification and is independent of the H3K4me3 modification.
Progressively shifting patterns of co-modulation among premotor cortex neurons carry dynamically similar signals during action execution and observation
Authors: Zhao Zhonghao , Schieber Marc H.
Published: November 2023

Many neurons in the premotor cortex show firing rate modulation whether the subject performs an action or observes another individual performing a similar action. Although such “mirror neurons” have been thought to have highly congruent discharge during execution and observation, many if not most actually show non-congruent activity. Studies of neuronal populations active during both execution and observation have shown that the most prevalent patterns of co-modulation—captured as neural trajectories—pass through subspaces which are shared in part, but in part are visited exclusively during either execution or observation. These studies focused on reaching movements for which low-dimensional neural trajectories exhibit comparatively simple dynamical motifs. But the neural dynamics of hand movements are more complex. We developed a novel approach to examine prevalent patterns of co-modulation during execution and observation of a task that involved reaching, grasping, and manipulation. Rather than following neural trajectories in subspaces that contain their entire time course, we identified time series of instantaneous subspaces, calculated principal angles among them, sampled trajectory segments at the times of selected behavioral events, and projected those segments into the time series of instantaneous subspaces. We found that instantaneous neural subspaces most often remained distinct during execution versus observation. Nevertheless, latent dynamics during execution and observation could be partially aligned with canonical correlation, indicating some similarity of the relationships among neural representations of different movements relative to one another during execution and observation. We also found that during action execution, mirror neurons showed consistent patterns of co-modulation both within and between sessions, but other non-mirror neurons that were modulated only during action execution and not during observation showed considerable variability of co-modulation.
Developing forebrain synapses are uniquely vulnerable to sleep loss
Authors: Gay Sean M. , Chartampila Elissavet , Lord Julia S. , Grizzard Sawyer , Maisashvili Tekla , Ye Michael , Barker Natalie K. , Mordant Angie L. , Mills C. Allie , Herring Laura E. , Diering Graham H.
Published: November 2023

Sleep is an essential behavior that supports lifelong brain health and cognition. Neuronal synapses are a major target for restorative sleep function and a locus of dysfunction in response to sleep deprivation (SD). Synapse density is highly dynamic during development, becoming stabilized with maturation to adulthood, suggesting sleep exerts distinct synaptic functions between development and adulthood. Importantly, problems with sleep are common in neurodevelopmental disorders including autism spectrum disorder (ASD). Moreover, early life sleep disruption in animal models causes long lasting changes in adult behavior. Different plasticity engaged during sleep necessarily implies that developing and adult synapses will show differential vulnerability to SD. To investigate distinct sleep functions and mechanisms of vulnerability to SD across development, we systematically examined the behavioral and molecular responses to acute SD between juvenile (P21-28), adolescent (P42-49) and adult (P70-100) mice of both sexes. Compared to adults, juveniles lack robust adaptations to SD, precipitating cognitive deficits in the novel object recognition test. Subcellular fractionation, combined with proteome and phosphoproteome analysis revealed the developing synapse is profoundly vulnerable to SD, whereas adults exhibit comparative resilience. SD in juveniles, and not older mice, aberrantly drives induction of synapse potentiation, synaptogenesis, and expression of peri-neuronal nets. Our analysis further reveals the developing synapse as a convergent node between vulnerability to SD and ASD genetic risk. Together, our systematic analysis supports a distinct developmental function of sleep and reveals how sleep disruption impacts key aspects of brain development, providing mechanistic insights for ASD susceptibility.

Significance Statement

Sleep is a fundamental pillar of lifelong health. Sleep disruption is commonly associated with neurodevelopmental conditions including autism spectrum disorder (ASD) and schizophrenia. Therefore, understanding the vulnerabilities associated with developmental sleep loss is an essential research question. Here we systemically examine the molecular and behavioral consequence of sleep deprivation (SD) in developing and adult mice. Compared to adults, developing mice show absent or blunted adaptive responses to SD, and heightened sensitivity to SD-induced cognitive deficits. Our molecular analysis indicates sleep plays an important role in key aspects of brain development including synaptogenesis, and that the effects of SD converge on nodes of genetic risk for ASD. This study provides new insights into the role of sleep in healthy brain development.
An output-null signature of inertial load in motor cortex
Authors: Kirk Eric A. , Hope Keenan T. , Sober Samuel J. , Sauerbrei Britton A.
Published: November 2023

Coordinated movement requires the nervous system to continuously compensate for changes in mechanical load across different contexts. For voluntary movements like reaching, the motor cortex is a critical hub that generates commands to move the limbs and counteract loads. How does cortex contribute to load compensation when rhythmic movements are clocked by a spinal pattern generator? Here, we address this question by manipulating the mass of the forelimb in unrestrained mice during locomotion. While load produces changes in motor output that are robust to inactivation of motor cortex, it also induces a profound shift in cortical dynamics, which is minimally affected by cerebellar perturbation and significantly larger than the response in the spinal motoneuron population. This latent representation may enable motor cortex to generate appropriate commands when a voluntary movement must be integrated with an ongoing, spinally-generated rhythm.
Histone H1x in mouse ventral hippocampus correlates with, but does not cause behavioral adaptations to stress
Authors: Kim R. Kijoon , Truby Natalie L. , Silva Gabriella M. , Picone Joseph A. , Miller Cary S. , Neve Rachael L. , Cui Xiaohong , Hamilton Peter J.
Published: November 2023

Prior research has identified differential protein expression levels of linker histone H1x within the ventral hippocampus (vHipp) of stress-susceptible versus stress-resilient mice. These mice are behaviorally classified based on their divergent responses to chronic social stress. Here, we sought to determine whether elevated vHipp H1x protein levels directly contribute to these diverging behavioral adaptations to stress. First, we demonstrate that stress-susceptible mice uniquely express elevated vHipp H1x protein levels following chronic stress. Given that linker histones coordinate heterochromatin compaction, we hypothesize that elevated levels of H1x in the vHipp may impede pro-resilience transcriptional adaptations and prevent development of the resilient phenotype following social stress. To test this, 8–10-week-old male C57BL/6J mice were randomly assigned to stressed and unstressed groups undergoing 10 days of chronic social defeat stress (CSDS) or single housing respectively. Following CSDS, mice were classified as susceptible versus resilient based on their social interaction behaviors. We synthesized a viral overexpression (OE) vector for H1x and transduced experimental mice with either H1x or control GFP within vHipp. Following viral delivery, we conducted social, anxiety-like, and memory-reliant behavior tests on distinct cohorts of mice. We found no behavioral adaptations following H1x OE compared to GFP controls in susceptible, resilient, or unstressed mice. In sum, although we confirm vHipp protein levels of H1x correlate with susceptibility to social stress, we observe no significant behavioral consequence of H1x OE. Thus, we conclude elevated levels of H1x are correlated with, but are not singularly sufficient to drive development of behavioral adaptations to stress.
Structure-based design of small molecule inhibitors of the cagT4SS ATPase Cagα of Helicobacter pylori
Authors: Morin Claire , Verma Vijay Tailor , Arya Tarun , Casu Bastien , Jolicoeur Eric , Ruel Réjean , Marinier Anne , Sygusch Jurgen , Baron Christian
Published: November 2023

We here describe the structure-based design of small molecule inhibitors of the type IV secretion system ofHelicobacter pylori. The secretion system is encoded by the□cag□pathogenicity island, and we chose Cagα, a hexameric ATPase and member of the family of VirB11-like proteins, as target for inhibitor design. We first solved the crystal structure of Cagα in a complex with the previously identified small molecule inhibitor 1G2. The molecule binds at the interface between two Cagα subunits and mutagenesis of the binding site identified Cagα residues F39 and R73 as critical for 1G2 binding. Based on the inhibitor binding site we synthesized 98 small molecule derivates of 1G2 to improve binding of the inhibitor. We used the production of interleukin-8 of gastric cancer cells duringH. pyloriinfection to screen the potency of inhibitors and we identified five molecules (1G2_1313, 1G2_1338, 1G2_2886, 1G2_2889 and 1G2_2902) that have similar or higher potency than 1G2. Differential scanning fluorimetry suggested that these five molecules bind Cagα, and enzyme assays demonstrated that some are more potent ATPase inhibitors than 1G2. Finally, scanning electron microscopy revealed that 1G2 and its derivatives inhibit the assembly of T4SS-determined extracellular pili suggesting a mechanism for their anti-virulence effect.
Regulation of chromatin transcription dynamics by DNA supercoiling
Authors: Brahmachari Sumitabha , Tripathi Shubham , Onuchic José N , Levine Herbert
Published: November 2023

Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a possible regulator of eukaryotic transcription, however, the modes and mechanisms of this regulation are elusive. Here, we first take a statistical mechanics approach to model the torsional response of topology-constrained chromatin. Our model recapitulates the experimentally observed weaker torsional rigidity of chromatin compared to bare DNA, and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. Coupling chromatin mechanics with RNAP translocation in stochastic simulations, we reveal a complex interplay of DNA supercoiling and nucleosome dynamics in governing RNAP velocity. Nucleosomes play a dual role in controlling the transcription dynamics. The steric barrier aspect of nucleosomes in the gene body counteracts transcription via hindering RNAP motion, whereas the chiral transitions facilitate RNAP motion via driving a low restoring torque upon twisting the DNA. While nucleosomes with low dissociation rates are typically transcriptionally repressive, highly dynamic nucleosomes offer less of a steric barrier and enhance the transcription elongation dynamics of weakly transcribed genes via buffering DNA twist. We use the model to predict transcription-dependent levels of DNA supercoiling in segments of the budding yeast genome that are in accord with available experimental data. The model unveils a paradigm of DNA supercoiling-mediated interaction between genes and makes testable predictions that will guide experimental design.
A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments
Authors: Loewinger Gabriel , Cui Erjia , Lovinger David , Pereira Francisco
Published: November 2023

Fiber photometry has become a popular technique to measure neural activity in vivo, but common analysis strategies can reduce detection of effects because they condensewithin-trialsignals into summary measures, and discard trial-level information by averagingacross-trials. We propose a novel photometry statistical framework based on functional linear mixed modeling, which enables hypothesis testing of variable effects atevery trial time-point, and uses trial-level signals without averaging. This makes it possible to compare the timing and magnitude of signals across conditions while accounting for between-animal differences. Our framework produces a series of plots that illustrate covariate effect estimates and statistical significance at each trial time-point. By exploiting signal autocorrelation, our methodology yieldsjoint95% confidence intervals that account for inspecting effects across the entire trial and improve the detection of event-related signal changes over common multiple comparisons correction strategies. We reanalyze data from a recent study proposing a theory for the role of mesolimbic dopamine in reward learning, and show the capability of our framework to reveal significant effects obscured by standard analysis approaches. For example, our method identifies two dopamine components with distinct temporal dynamics in response to reward delivery. In simulation experiments, our methodology yields improved statistical power over common analysis approaches. Finally, we provide an open-source package and analysis guide for applying our framework.
Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex
Authors: Kim Sonia Nan , Viswanadham Vinayak V. , Doan Ryan N. , Dou Yanmei , Bizzotto Sara , Khoshkhoo Sattar , Huang August Yue , Yeh Rebecca , Chhouk Brian , Truong Alex , Chappell Kathleen M. , Beaudin Marc , Barton Alison , Akula Shyam K. , Rento Lariza , Lodato Michael , Ganz Javier , Szeto Ryan A. , Li Pengpeng , Tsai Jessica W. , Hill Robert Sean , Park Peter J. , Walsh Christopher A.
Published: November 2023

The mammalian cerebral cortex shows functional specialization into regions with distinct neuronal compositions, most strikingly in the human brain, but little is known in about how cellular lineages shape cortical regional variation and neuronal cell types during development. Here, we use somatic single nucleotide variants (sSNVs) to map lineages of neuronal sub-types and cortical regions. Early-occurring sSNVs rarely respect Brodmann area (BA) borders, while late-occurring sSNVs mark neuron-generating clones with modest regional restriction, though descendants often dispersed into neighboring BAs. Nevertheless, in visual cortex, BA17 contains 30-70% more sSNVs compared to the neighboring BA18, with clones across the BA17/18 border distributed asymmetrically and thus displaying different cortex-wide dispersion patterns. Moreover, we find that excitatory neuron-generating clones with modest regional restriction consistently share low-mosaic sSNVs with some inhibitory neurons, suggesting significant co-generation of excitatory and some inhibitory neurons in the dorsal cortex. Our analysis reveals human-specific cortical cell lineage patterns, with both regional inhomogeneities in progenitor proliferation and late divergence of excitatory/inhibitory lineages.
Tweek-dependent formation of ER-PM contact sites enables astrocyte phagocytic function and remodeling of neurons
Authors: Kang Yunsik , Jefferson Amanda , Sheehan Amy , La Torre Rachel De , Jay Taylor , Chiao Lucia , Hulegaard Alex , Corty Megan , Baconguis Isabelle , Zhou Zheng , Freeman Marc R.
Published: November 2023

Neuronal remodeling generates an enormous amount of cellular debris, which is cleared from the nervous system by glia. At the larva-to-adult transition,Drosophilaastrocytes transform into phagocytes and engulf degenerating larval synapses, axonal and dendritic debris. Here we show Tweek, a member of the bridge-like lipid transfer protein family, is upregulated in astrocytes as they ramp up their phagocytic function early in metamorphosis, and is essential for internalization and degradation of neuronal debris. Tweek forms a bridge between the endoplasmic reticulum (ER) and plasma membrane (PM), and loss of Tweek disrupts ER-PM contact formation and membrane lipid distribution. Patient-identified mutations in the human homolog associated with Alkuraya-Kucinskas syndrome resulted in similar defects in neuronal remodeling, indicating these are loss of function mutations. We propose Tweek helps establish and maintain ER-PM contacts during astrocyte phagocytic function and drives bulk lipid transfer to the plasma membrane for continued efficient internalization and degradation of neuronal debris.
Development of a multi-scanner facility for data acquisition for digital pathology artificial intelligence
Authors: Humphries Matthew P. , Kaye Danny , Stankeviciute Gaby , Halliwell Jacob , Wright Alexander I , Bansal Daljeet , Brettle David , Treanor Darren
Published: November 2023

Whole slide imaging (WSI) of pathology glass slides with high-resolution scanners has enabled the large-scale application of artificial intelligence (AI) in pathology, to support the detection and diagnosis of disease, potentially increasing efficiency and accuracy in tissue diagnosis.

Despite the promise of AI, it has limitations. “Brittleness” or sensitivity to variation in inputs necessitates that large amounts of data are used for training. AI is often trained on data from different scanners but not usually by replicating the same slide across scanners. The utilisation of multiple WSI instruments to produce digital replicas of the same glass slides will make more comprehensive datasets and may improve the robustness and generalisability of AI algorithms as well as reduce the overall data requirements of AI training.

To this end, the National Pathology Imagine Cooperative (NPIC) has built the AI FORGE (FacilitatingOpportunities forRobustGeneralisable dataEmulation), a unique multi-scanner facility embedded in a clinical site in the NHS to (a) compare scanner performance and (b) replicate digital pathology image datasets across WSI systems.

The NPIC AI FORGE currently comprises 15 scanners from 9 manufacturers. It can generate approximately 4000 WSI images per day (approximately 7Tb of image data). This paper describes the process followed to plan and build such a facility.
The non-codingGBA1rs3115534 variant is associated with REM sleep behavior disorder in Nigerians
Authors: Ojo Oluwadamilola O. , Bandres-Ciga Sara , Makarious Mary B. , Crea Peter Wild , Hernandez Dena G. , Houlden Henry , Rizig Mie , Singleton Andrew B. , Noyce Alastair J. , Nalls Mike A. , Blauwendraat Cornelis , Okubadejo Njideka U.
Published: November 2023

Background

Damaging coding variants inGBA1are a genetic risk factor for rapid eye movement sleep behavior disorder (RBD), which is a known early feature of synucleinopathies. Recently, a population-specific non-coding variant (rs3115534) was found to be associated with PD risk and earlier disease onset in individuals of African ancestry.

Objectives

To investigate whether theGBA1rs3115534 PD risk variant is associated with RBD.

Methods

We studied 709 persons with PD and 776 neurologically healthy controls from Nigeria. TheGBA1rs3115534 risk variant status was imputed from previous genotyping for all. Symptoms of RBD were assessed with the RBD screening questionnaire (RBDSQ).

Results

The non-codingGBA1rs3115534 risk variant is associated with possible RBD in individuals of Nigerian origin (Beta = 0.3640, SE = 0.103, P =4.093e-04), as well as after adjusting for PD status (Beta = 0.2542, SE = 0.108, P = 0.019) suggesting that this variant may have the same downstream consequences asGBA1coding variants.

Conclusions

We show that the non-codingGBA1rs3115534 risk variant is associated with increased RBD symptomatology in Nigerians with PD. Further research is required to assess association with polysomnography-defined RBD.
Three and Four Dimensional Characteristics of Color Doppler M-Mode Echocardiography
Authors: Moosavi Toomatari Seyed Babak , Khademvatani Kamal , Karimi Sarabi Seyedeh Zahra
Published: November 2023

M-mode echocardiography is one of the basic modes of ultrasound imaging that is generally used in echocardiography. In this article we introduce a new approach to display three and four dimensional color M-mode echocardiography.
Repression of pattern-triggered immune responses by hypoxia in Arabidopsis
Authors: Mooney Brian C. , Doorly Catherine M. , Mantz Melissa , García Pablo , Huesgen Pitter F. , Graciet Emmanuelle
Published: November 2023

Biotic and abiotic stresses frequently co-occur in nature, yet, relatively little is known about how plants co-ordinate the response to combined stresses. Previous research has shown that protein degradation by the ubiquitin/proteasome system is central to the regulation of multiple independent stress response pathways in plants. The Arg/N-degron pathway is a subset of the ubiquitin/proteasome system that targets proteins based on their N-termini and has been specifically implicated in the responses to biotic and abiotic stresses, including hypoxiaviaaccumulation of ERF-VII transcription factors, which orchestrate the onset of the hypoxia response program. Here, we investigated the role of the Arg/N-degron pathway in mediating the crosstalk between coinciding abiotic and biotic stresses using hypoxia treatments and the flg22 elicitor of pattern-triggered immunity (PTI), respectively. We uncovered a link between the transcriptional responses of plants to hypoxia and flg22. Combined hypoxia/flg22 treatments showed that hypoxia represses the flg22 transcriptional program, as well as the expression of pattern recognition receptors, MAPK signalling and callose deposition during PTI, through mechanisms that are mostly independent from the ERF-VIIs. These findings aid understanding of the trade-offs between plant responses to combined abiotic/biotic stresses in the context of our efforts to increase crop resilience to global climate change. Our results also show that the well-known repressive effect of hypoxia on innate immunity in animals also applies to plants.

Significance statement

Understanding how plants regulate the crosstalk between stress response pathways is key to our efforts to increase crop resilience and mitigate yield losses caused by global climate change. Despite the urgency to do so, relatively little is known about how plants respond to combined stresses, which frequently occur in nature. Here, we show that the hypoxia response program and the basal layer of plant immunity (pattern-triggered immunity or PTI) share components. Our data also show that hypoxia represses several key aspects of PTI, a situation akin to that discovered in animals decades ago. These findings have implications for our ability to develop resilient crops by limiting the negative trade-offs that exist between hypoxia response and immunity.
Form factor of helical structures and twisted fibres
Authors: van der Maarel Johan R. C.
Published: November 2023

A general formalism is presented for the isotropically averaged single-chain scattering function (form factor) of single, double, triple and higher-order helices, as well as twisted fibres consisting of concentric layers of strands. Form factors for double and triple helices with differently sized grooves have also been derived. The formulas include the longitudinal and transverse interference over the pitch and radius of the helices, respectively. The results may be useful for the analysis of small-angle scattering data of (bio)macromolecules or molecular assemblies exhibiting a helical arrangement.
UnwarpCalculator: a utility to estimate intensity distribution in reciprocal space for an arbitrary 3D set of atoms
Authors: Zakharov Boris A.
Published: November 2023

UnwarpCalculator is a command-line utility developed to calculate intensity distribution in reciprocal space. The program uses CIF syntax input files and can work either with periodic crystals or with arbitrary atomic distribution, including incommensurately modulated and defect structures. With this program the intensity can be calculated for any reciprocal space point using the three main options available, including intensity calculation at a point with (h, k, l) coordinates, intensity distribution calculation along a line in reciprocal space and building an unwarped layer pixel by pixel. The program has an interactive interface and uses a fairly simple diffraction calculation model. The tool can be used for teaching crystallography since it offers much easier options and input file creation compared with existing software for defect and diffraction pattern simulations. These features along with input files with CIF syntax allow easy use of the program even for beginners. The utility can also be applied for the interpretation of experimental diffraction patterns and comparison of calculated versus experimental diffraction images to validate crystal structure models.