bluuebunny/crossref_metadata_2025 huggingface dataset:
Hybrid cancer stem cells utilise vascular tracks for collective streaming invasion in a metastasis-on-a-chip device
Authors: Scemama Alice , Lunetto Sophia , Tailor Artysha , Di Cio Stefania , Ambler Leah , Coetzee Abigail , Cottom Hannah , Khurram Syed Ali , Gautrot Julien , Biddle Adrian
Published: January 2024

Cancer stem cells (CSCs) drive cancer metastatic dissemination. They do not do so in a vacuum, and the important influence of the tumour microenvironment (TME) on metastatic dissemination is becoming increasingly recognised. Therapeutic targeting of CSC-TME interactions may be a promising route to suppression of tumour metastasis. However, we must first understand how interactions with the TME influence CSC metastatic dissemination. To achieve this understanding, there is a need for experimental models that enable the analysis of dynamic interactions at single cell resolution within a complex environment. To this end, we utilise a metastasis-on-a-chip device to produce a 3Din vitromodel of CSC interaction with a developing microvasculature, that is amenable to precise imaging and real time studies at single cell resolution. We show that the invasive phenotype of oral squamous cell carcinoma (OSCC) cells is markedly altered when in proximity to a microvasculature, with a switch to a hybrid CSC phenotype that undergoes collective streaming invasion. Mechanistically, ECM compression by the developing vasculature creates an environment that is refractory to cancer invasion, whilst leaving abandoned vascular tracks that can be utilised by hybrid CSCs for collective streaming invasion. Human tissue studies identify streaming invasion in association with vascularised regions in OSCC specimens. These findings elucidate the influence of the vasculature on CSC metastatic dissemination in OSCC, and the role of hybrid CSC invasion plasticity in overcoming this TME constraint.
Mechanisms of Cholesterol Binding to LAT1
Authors: Hutchinson Keino , Schlessinger Avner
Published: January 2024

The human L-type amino acid transporter 1 (LAT1; SLC7A5), is an amino acid exchanger protein, primarily found in the blood-brain-barrier, placenta, and testis, where it plays a key role in amino acid homeostasis. Cholesterol is an essential lipid that has been highlighted to play a role in regulating the activity of membrane transporters such as LAT1, yet little is known about the molecular mechanisms driving this phenomenon. Here we perform a comprehensive computational analysis to investigate cholesterol’s role in LAT1 structure and function, focusing on four cholesterol binding sites (CHOL1-4) identified in a recent LAT1-apo inward-open conformation cryo-EM structure. We performed four independent molecular dynamics (MD) simulations of LAT1 bound to each cholesterol molecule, as well as molecular docking, free energy calculation by MM/GBSA, and other analysis tools, to investigate LAT1-cholesterol interactions. Our results indicate that CHOL3 provides the most stable binding interactions with LAT1, and CHOL3 and CHOL1 sites have the largest stabilizing effect on LAT1’s primary functional motifs (hash and bundle) and substrate binding site. Our analysis also uncovers an alternative cholesterol binding site to the originally assigned CHOL1. Our study improves the understanding of cholesterol’s modulatory effect on LAT1 and proposes candidate sites for discovery of future allosteric ligands with rational design.
A “double-edged” role for type-5 metabotropic glutamate receptors in pain disclosed by light-sensitive drugs
Authors: Notartomaso Serena , Antenucci Nico , Mazzitelli Mariacristina , Rovira Xavier , Boccella Serena , Ricciardi Flavia , Liberatore Francesca , Gomez-Santacana Xavier , Imbriglio Tiziana , Cannella Milena , Zussy Charleine , Luongo Livio , Maione Sabatino , Goudet Cyril , Battaglia Giuseppe , Llebaria Amadeu , Nicoletti Ferdinando , Neugebauer Volker
Published: January 2024

Knowing the site of drug action is important to optimize effectiveness and address any side effects. We used light-sensitive drugs to identify the brain region-specific role of mGlu5 metabotropic glutamate receptors in the control of pain. Optical activation of systemic JF-NP-26, a caged, normally inactive, negative allosteric modulator (NAM) of mGlu5 receptors, in cingulate, prelimbic and infralimbic cortices and thalamus inhibited neuropathic pain hypersensitivity. Systemic treatment of alloswitch-1, an intrinsically active mGlu5 receptor NAM, caused analgesia, and the effect was reversed by light-induced drug inactivation in in the prelimbic and infralimbic cortices, and thalamus. This demonstrates that mGlu5 receptor blockade in the medial prefrontal cortex and thalamus is both sufficient and necessary for the analgesic activity of mGlu5 receptor antagonists. Surprisingly, when light was delivered in the basolateral amygdala, local activation of systemic JF-NP-26 reduced pain thresholds, whereas inactivation of alloswitch-1 enhanced analgesia. Electrophysiological analysis showed that alloswitch-1 increased excitatory synaptic responses in prelimbic pyramidal neurons evoked by stimulation of BLA input, and decreased feedforward inhibition of amygdala output neurons by BLA. Both effects were reversed by optical silencing and reinstated by optical reactivation of alloswitch-1. These findings demonstrate for the first time that the action of mGlu5 receptors in the pain neuraxis is not homogenous, and suggest that blockade of mGlu5 receptors in the BLA may limit the overall analgesic activity of mGlu5 receptor antagonists. This could explain the suboptimal effect of mGlu5 NAMs on pain in human studies and validate photopharmacology as an important tool to determine ideal target sites for systemic drugs.
The NRF2/ID2 Axis in Vascular Smooth Muscle Cells: Novel Insights into the Interplay between Vascular Calcification and Aging
Authors: Xu Mulin , Wei Xiuxian , Wang Jinli , Li Yi , Huang Yi , Cheng Anying , He Fan , Zhang Le , Zhang Cuntai , Liu Yu
Published: January 2024

OBJECTIVE

Vascular calcification (VC) significantly contributes to cardiovascular morbidity and mortality and escalates with age. However, effective pharmaceutical interventions are lacking, and the molecular mechanisms linking aging to VC remain elusive. This study explores the role of nuclear factor erythroid 2-related factor 2 (NRF2) in VC, specifically focusing on the interplay between vascular senescence and oxidative stress (OS).

APPROACH AND RESULTS

Using a chronological aging mouse model, we noted a significant decline in the expression and activity of Nrf2 in the aortas of aged mice, coinciding with increased medial VC. Administering NRF2 activators effectively reduced this calcification. In the vascular smooth muscle cell (VSMC)-specific Nrf2 knockout (Nrf2SMCKO) models, created using adenine and Vitamin D, there was an increase in calcium deposition within the aortic medial layer, alongside heightened VSMC senescence and OS. Furthermore, NRF2 knockout exacerbated VC in aortic rings and primary VSMCs in high-phosphate conditions, while Nrf2 overexpression in VSMCs inhibited calcium deposition by alleviating cell senescence and OS. RNAseq analysis of the aortas fromNrf2SMCKOand control mice highlighted a significant downstream regulator of Inhibitor of DNA Binding 2 (ID2). Our results show that reduced NRF2 levels lead to increased VSMC senescence, characterized by heightened p16 expression and diminished ID2 expression. Inhibiting ID2 negated NRF2’s protective effects against VSMC senescence and VC.

CONCLUSION

This study emphasizes the critical role of NRF2 dysfunction in the nexus of vascular senescence, OS, and VC. It proposes the NRF2-ID2 axis in VSMCs as a promising therapeutic target for reducing VC and mitigating age-related cardiovascular diseases.

Highlights

Decline in NRF2 activity is linked to increased vascular calcification (VC) and aging.

VSMC-specificNrf2knockout causes a remarkable exacerbation of arterial calcification.

NRF2 alleviates VC by inhibiting oxidative stress and VSMC senescence.

ID2 contributes to the protective role of NRF2 in VSMC senescence and VC.
Reconstructing cell histories in space with image-readable base editor recording
Authors: Chadly Duncan M , Frieda Kirsten L , Gui Chen , Klock Leslie , Tran Martin , Sui Margaret Y , Takei Yodai , Bouckaert Remco , Lois Carlos , Cai Long , Elowitz Michael B.
Published: January 2024

Knowing the ancestral states and lineage relationships of individual cells could unravel the dynamic programs underlying development. Engineering cells to actively record information within their own genomic DNA could reveal these histories, but existing recording systems have limited information capacity or disrupt spatial context. Here, we introducebaseMEMOIR, which combines base editing, sequential hybridization imaging, and Bayesian inference to allow reconstruction of high-resolution cell lineage trees and cell state dynamics while preserving spatial organization. BaseMEMOIR stochastically and irreversibly edits engineered dinucleotides to one of three alternative image-readable states. By genomically integrating arrays of editable dinucleotides, we constructed an embryonic stem cell line with 792 bits of recordable, image-readable memory, a 50-fold increase over the state of the art. Simulations showed that this memory size was sufficient for accurate reconstruction of deep lineage trees. Experimentally, baseMEMOIR allowed precise reconstruction of lineage trees 6 or more generations deep in embryonic stem cell colonies. Further, it also allowed inference of ancestral cell states and their quantitative cell state transition rates, all from endpoint images. baseMEMOIR thus provides a scalable framework for reconstructing single cell histories in spatially organized multicellular systems.
Life stage impact on the human skin ecosystem: lipids and the microbial community
Authors: Pagac Martin P. , Davient Bala , Lam Hilbert Yuen In , Ravikrishnan Aarthi , Chua Wee Ling Esther , Muralidharan Sneha , Sridharan Aishwarya , Irudayaswamy Antony S. , Srinivas Ramasamy , Wearne Stephen , Mohamed Naim Ahmad Nazri , Ho Xin Pei Eliza , Ng H. Q. Amanda , Kwah Junmei Samantha , Png Eileen , Bendt Anne K. , Wenk Markus R. , Torta Federico , Nagarajan Niranjan , Common John , Seng Chong Yap , Tham Elizabeth Huiwen , Shek Lynette Pei-Chi , Loo Evelyn Xiu Ling , Chambers John , Yew Yik Weng , Loh Marie , Dawson Thomas L.
Published: January 2024

While research into gut-microbe interactions is common and advanced, with multiple defined impacts on human health, studies exploring the significance of skin-microbe interactions remain underrepresented. Skin is the largest human organ, has a vast surface area, and is inhabited by a plethora of microorganisms which metabolise sebaceous lipids. Sebaceous free fatty acids are metabolized into bioactive lipid mediators with immune-modulatory properties by skin-resident microbes, includingMalassezia. Intriguingly, many of the same lipid mediators are also found on human skin, implying these compounds may have microbial or mixed microbial/human origin. To support this hypothesis, we isolated lipids and microbial DNA from the skin of prepubescent, adult, pre- and post-menopausal volunteers and performed correlational analyses using skin lipidomics and metagenomics to compare lipid mediator profiles and microbiome compositions on skin with either low or high sebaceous gland activity. We found that specific microbial taxonomies were positively and negatively correlated with skin lipid mediator species with high statistical significance. 2Din vitroco-cultures withMalasseziaand keratinocytes also directly linked the production of specific lipid mediators, detected on healthy human skin, to secretion of immuno-stimulatory cytokines. Together, these findings further support the hypothesis that microbial-derived skin lipid mediators influence healthy skin homeostasis and skin disease development and progression, thereby spotlighting the relevance of the skin microbiome’s footprint on human health.
Fast and lightweight cell atlas approximations across organs and organisms
Authors: Xu Ying , Ahn Joanna , Zanini Fabio
Published: January 2024

Omic technologies at single-cell resolution are reshaping our understanding of cellular diversity. The generation of cell atlases that capture the cellular composition of an entire individual is progressing rapidly. However, the science of organising and extracting information from these atlases is still in its infancy and for many biomedical researchers atlas exploration remains challenging. Here, we leveraged extensive experience in single-cell data analytics to pinpoint three major accessibility barriers to cell atlases, related to (i) programming skill or language, (ii) scalability, and (iii) dissemination standards. To help researchers overcome these barriers, we developed cell atlas approximations, a computational approach enabling the analysis of cell atlases across organs and organisms without programming skills, rapidly, and at scale. The web interface athttps://atlasapprox.orgfacilitates the exploration of cell atlases in 19 species across the tree of life through a chatbot driven by frontend natural language processing. In parallel, application programming interfaces streamline data access for computational researchers and include specialised packages for Python, R, JavaScript, and Bash. Supported queries include marker gene identification, cross-organ comparisons, cell embeddings, gene sequences, searches for similar features, and bidirectional zoom between cell types and cell states. Most queries are answered in less than 1.5 seconds thanks to lossy data compression algorithms based on cell annotations and similarity graphs. Compared to traditional cell atlas analysis, this approach can reduce data size by more than 100 times and accelerate workflows by up to 100,000 times. Atlas approximations aim to make the exploration of cell atlases accessible to anyone in the world.
Tumor relapse-free survival prognosis related consistency between cancer tissue and adjacent normal tissue in drug repurposing for solid tumor via connectivity map
Authors: Hao Mingyue , Li Dandan , Qiao Yuanyuan , Xiong Ming , Li Jun , Ma Wei
Published: January 2024

Traditional drug discovery encounters challenges, including high costs, time-intensive processes, and inherent risks. Drug repurposing emerges as a compelling alternative strategy to identify new indications for investigational or approved drugs, circumventing these obstacles. Among the various drug repurposing methods, the Disease-specific Signature-based Connectivity Map (Cmap) approach is widely utilized. However, the commonly employed method for constructing disease-specific signatures, known as Differentially Expressed Genes (DEG), faces issues related to inconsistencies between dysregulated genes and the prognosis of genes in tumor tissue, as well as discrepancies in prognosis genes between tumor and normal tissues.

In this study, we propose a novel approach, Prognosis Consistency Scoring (PCS), aimed at addressing these inconsistencies. PCS measures the consistency of gene prognosis between tumor and normal tissues by combining the Recurrence-Free Survival (RFS) prognosis power of genes in both contexts. Disease-specific signatures are then constructed based on PCS, and drug repurposing is performed using the Cmap and Lincs Unified Environment (CLUE). Validation of predicted drugs is conducted using data from DrugBank and ClinicalTrials databases.

Our findings reveal that the aforementioned inconsistencies are pervasive. Compared to signatures based on DEGs, PCS-based signatures exhibit superior performance, identifying more drugs with higher prediction accuracy, as confirmed by DrugBank annotations. Notably, a significant proportion of predicted drugs without corresponding indications were subsequently validated in the ClinicalTrials database. Additionally, PCS-based signatures demonstrate elevated disease specificity and association with Drug Related Gene (DRG).
Threshold-Free Network-Oriented Statistics in Neuroscience
Authors: Hao Zexuan , Wang Pei , Xia Xiaoyu , Pan Yu , Dou Weibei
Published: January 2024

Network neuroscience has emerged as an indispensable tool for studying brain structure and function. Currently, the network-based statistic (NBS) procedure is widely used for dealing with massive multiple testing/comparison problems in brain networks. However, the NBS requires choosing a hard cluster-forming threshold, lacking objective rules. A powerful and flexible statistical framework is urgently needed with growing interest in finer-grained network explorations across modalities and scales. Here, we introduce a permutation-based framework—”Threshold-Free Network-Oriented Statistics” (TFNOS). It integrates two “threshold-free” pathways: traversing all cluster-forming thresholds (TT) and using predefined clusters (PC). The TT procedure, building upon the threshold-free network-based statistics, requires setting additional parameters. The PC procedures comprise six variants given the degree of freedom in pooling data, null distribution construction, and controlled error rate. Using numerical simulations, we evaluated the performance of the TT procedure under 600 parameter combinations, then benchmarked TFNOS procedures and baselines across different topologies of effects, sample sizes, and effect sizes, and finally provided illustrative examples with real data. We offer recommended parameter values that allow the TT procedure to stably maintain leading power, while empirically controlling the false discovery rate (FDR) beyond only weakly controlling the familywise error rate (FWER). Notably, the relevant parameters commonly employed in the field appear overly liberal. Furthermore, for the PC procedures, FDR-controlling variants showed improved power compared to FWER-controlling variants, and some of them are simple but do not compromise power. The nonparametric PC procedures allow the selection of any test statistics considered appropriate. Overall, the TFNOS is a generalized framework for inference on edges/nodes of undirected/directed brain networks. We provide empirical and principled criteria for selecting appropriate procedures and may enhance the reproducibility and sensitivity of future brain research.
Live-cell imaging under centrifugation characterized the cellular force for nuclear centration in theCaenorhabditis elegansembryo
Authors: Goda Makoto , Shribak Michael , Ikeda Zenki , Okada Naobumi , Tani Tomomi , Goshima Gohta , Oldenbourg Rudolf , Kimura Akatsuki
Published: January 2024

Organelles in cells are appropriately positioned, despite crowding in the cytoplasm. However, our understanding of the force required to move large organelles, such as the nucleus, inside the cytoplasm is limited, in part owing to a lack of accurate methods for measurement. We devised a novel method to apply forces to the nucleus of living, wild-typeCaenorhabditis elegansembryos to measure the force generated inside the cell. We utilized a centrifuge polarizing microscope (CPM) to apply centrifugal force and orientation-independent differential interference contrast (OI-DIC) microscopy to characterize the mass density of the nucleus and cytoplasm. The cellular forces moving the nucleus toward the cell center increased linearly at ∼14 pN/μm depending on the distance from the center. The frictional coefficient was ∼1,100 pN s/μm. The measured values were smaller than previously reported estimates for sea urchin embryos. The forces were consistent with the centrosome-organelle mutual pulling model for nuclear centration. Frictional coefficient was reduced when microtubules were shorter or detached from nuclei in mutant embryos, demonstrating the contribution of astral microtubules. Finally, the frictional coefficient was higher than a theoretical estimate, indicating the contribution of uncharacterized properties of the cytoplasm.
Rapid Motor Adaptation via Population-level Modulation of Cerebellar Error Signals
Authors: Nguyen Vinh , Stell Brandon M.
Published: January 2024

A core principle of cerebellar learning theories is that climbing fibers from the inferior olive convey error signals about movement execution to Purkinje cells in the cerebellar cortex. These inputs trigger synaptic changes which are purported to drive progressive adjustment of future movements. Individually, binary complex spike signals lack information about the sign and magnitude of errors which presents a problem for cerebellar learning paradigms exhibiting fast adaptation. Using a newly developed behavioral paradigm in mice, we introduced sensorimotor perturbations into a simple joystick pulling behavior and found parasagittal bands of Purkinje cells with reciprocal modulation of complex spike activity. Whereas complex spiking showed little modulation in the unperturbed condition, alternating bands were activated or inhibited when the perturbation was introduced, and this modulation encoded the sign and magnitude of the resulting sensorimotor mismatch. These findings provide an important piece of information for the understanding of cerebellar learning that helps to explain how the cerebellum could use supervised learning to quickly adapt motor behavior in response to perturbations.

One-Sentence Summary

Populations of Purkinje cells in the cerebellum facilitate trial-by-trial movement refinement by converting binary signals from movement errors into graded signals that encode the error’s direction and magnitude.
Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability
Authors: Lu Bingxin , Winnall Samuel , Cross William , Barnes Chris P.
Published: January 2024

Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic structural variants (SVs) are intimately related to copy number alterations but the two types of variant are often studied independently. In addition, despite numerous studies on detecting various SV patterns, there are still no general quantitative models of SV generation. To address this issue, we develop a computational cell-cycle model for the generation of SVs from end-joining repair and replication after double strand break formation. Our model provides quantitative information on the relationship between breakage fusion bridge cycle, chromothripsis, seismic amplification, and extra-chromosomal circular DNA. Given single-cell whole-genome sequencing data, the model also allows us to infer important parameters in SV generation with Bayesian inference. Our quantitative framework unifies disparate genomic patterns resulted from CIN, provides a null mutational model for SV, and reveals new insights into the impact of genome rearrangement on tumour evolution.
VLP-Based Model for Study of Airborne Viral Pathogens
Authors: Caffrey Michael , Jayakumar Nitin , Caffrey Veronique , Anirudan Varada , Rong Lijun , Paprotny Igor
Published: January 2024

The recent COVID-19 pandemic has underscored the danger of airborne viral pathogens. The lack of model systems to study airborne pathogens limits the understanding of airborne pathogen distribution, as well as potential surveillance and mitigation strategies. In this work, we develop a novel model system to study airborne pathogens using virus like particles (VLP). Specifically, we demonstrate the ability to aerosolize VLP and detect and quantify aerosolized VLP RNA by Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) in real-time fluorescent and colorimetric assays. Importantly, the VLP model presents many advantages for the study of airborne viral pathogens: (i) similarity in size and surface components; (ii) ease of generation and noninfectious nature enabling study of BSL3 and BSL4 viruses; (iii) facile characterization of aerosolization parameters; (iv) ability to adapt the system to other viral envelope proteins including those of newly discovered pathogens and mutant variants; (v) the ability to introduce viral sequences to develop nucleic acid amplification assays.

Importance

Study and detection of airborne pathogens is hampered by the lack of appropriate model systems. In this work we demonstrate that noninfectious Virus Like Particles (VLP) represent attractive models to study airborne viral pathogens. Specifically, VLP are readily prepared, are similar in size and composition to infectious viruses, and are amenable to highly sensitive nucleic acid amplification techniques.
Genomic dissection and mutation-specific target discovery for breast cancerPIK3CAhotspot mutations
Authors: Miranda Adam X. , Kemp Justin , Davidson Brad , Bellomo Sara Erika , Agan Verda , Manoni Alexandra , Marchiò Caterina , Croessmann Sarah , Park Ben H. , Hodges Emily
Published: January 2024

Background

Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype.

Results

In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspotPIK3CAmutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with eachPIK3CAhotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated throughin vitroanalysis and publicly available patient databases.

Conclusions

Using our multi-modal genomics framework, we discover distinct differences in genomic regulation betweenPIK3CAhotspot mutations, suggesting thePIK3CAmutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.
Consistent accumulation of transposable elements in species of the HawaiianTetragnathaspiny-leg adaptive radiation across the archipelago chronosequence
Authors: Yang Heidi , Goubert Clément , Cotoras Darko D. , Graham Natalie R , Cerca José , Gillespie Rosemary G.
Published: January 2024

The ecological and phenotypic diversity observed in oceanic island radiations presents an evolutionary paradox: a high level of genetic variation is typically required for diversification, but species colonizing a new island typically suffer from founder effects. This reduction in population size leads to a reduction in genetic diversity, which ultimately results in a reduction in the efficiency of natural selection. Then, what is the source of genetic variation which acts as the raw material for ecological and phenotypic diversification in oceanic archipelagos? Transposable elements (TEs) are mobile genetic elements that have been linked to the generation of genetic diversity, and evidence suggests that TE activity and accumulation along the genome can result from reductions in population size. Here, we use the Hawaiian spiny-leg spider radiation (Tetragnatha) to test whether TE accumulation increases due to demographic processes associated with island colonization. We sequenced and quantified TEs in 23 individuals from the spiny-leg radiation and 4 individuals from its sister radiation, the Hawaiian web-buildingTetragnatha. Our results show that founder effects resulting from colonization of new islands have not resulted in TE accumulation over evolutionary time. Specifically, we found no evidence for increase in abundance of specific TE superfamilies, nor an accumulation of ‘young TEs’ in lineages which have recently colonized a new island or are present in islands with active volcanoes. We also found that the DNA/hAT transposon superfamily is by far the most abundant TE superfamily in theTetragnatharadiation. This work shows that TE abundance has remained constant for the spiny-leg radiation across the archipelago chronosequence, and TE accumulation is not affected by population oscillations associated with island colonization events. Therefore, despite their known role in the generation of genetic diversity, TE activity does not appear to be the mechanism to explain the evolutionary paradox of the insularTetragnathaspiny-leg radiation.
NeuroMechanics: Electrophysiological and Computational Methods to Accurately Estimate the Neural Drive to Muscles in HumansIn Vivo
Authors: Caillet Arnault H. , Phillips Andrew T.M. , Modenese Luca , Farina Dario
Published: January 2024

The ultimate neural signal for muscle control is the neural drive sent from the spinal cord to muscles. This neural signal comprises the ensemble of action potentials discharged by the active spinal motoneurons, which is transmitted to the innervated muscle fibres to generate forces. Accurately estimating the neural drive to muscles in humansin vivois challenging since it requires the identification of the activity of a sample of motor units (MUs) that is representative of the active MU population. Current electrophysiological recordings usually fail in this task by identifying small MU samples with over-representation of higher-threshold with respect to lower-threshold MUs. Here, we describe recent advances in electrophysiological methods that allow the identification of more representative samples of greater numbers of MUs than previously possible. This is obtained with large and very dense arrays of electromyographic electrodes. Moreover, recently developed computational methods of data augmentation further extend experimental MU samples to infer the activity of the full MU pool. In conclusion, the combination of new electrode technologies and computational modelling allows for an accurate estimate of the neural drive to muscles and opens new perspectives in the study of the neural control of movement and in neural interfacing.
The Regulatory-Associated Protein of the Target of Rapamycin Complex, RAPTOR1B, interconnects with the photoperiod pathway to promote flowering inArabidopsis
Authors: Urrea-Castellanos Reynel , Calderan-Rodrigues Maria J. , Musialak-Lange Magdalena , Macharanda-Ganesh Appanna , Wahl Vanessa , Caldana Camila
Published: January 2024

Transition from vegetative to reproductive growth (floral transition) is a strictly regulated energy-demanding process. InArabidopsis, light perception coupled with internal circadian rhythms allows sensing changes in the duration of the light period (photoperiod) to accelerate flowering under long days (LD) in spring. This photoperiod-mediated floral induction relies on the accumulation of CONSTANS (CO) at dusk, a transcription factor that upregulatesFLOWERING LOCUS T(FT) in leaves. Subsequently, FT protein moves into the shoot apical meristem to trigger the floral transition. Light and circadian clock-related signals are known to control CO at the genetic and protein levels; however, less is known about how energy sensing regulates components of the photoperiod pathway to modulate flowering. Here, we found that RAPTOR, a component of the Target Of Rapamycin complex (TORC), contributes to the induction of specific flowering genes that are under CO control. While transcription ofCOremains intact inraptormutants, its protein levels are reduced at dusk compared to wild-type (Col-0). This is due to increased protein degradation. Remarkably, GIGANTEA (GI) protein levels, which contributes to CO stabilization at dusk, are likewise hampered in the mutant. We show that RAPTOR interacts with and co-localizes at the nucleus with GI, altering GI levels through an unknown posttranscriptional mechanism. Phenotypic and molecular analysis of genetic crosses placed RAPTOR upstream of CO and GI. Since TORC is an energy sensor, our work suggests that RAPTOR could convey energy status information into the photoperiod sensing mechanism to fine-tune flowering behavior.

Significance statement

For annual plants, such asArabidopsis, the correct timing of flowering in spring/summer is critical for reproductive success. Molecular mechanisms through which plants perceive and integrate day length with internal rhythms to accelerate flowering under long days are well described. However, little is known about the pathways sensing and conveying energy availability to the flowering programs. We found that RAPTOR, the regulatory unit of Target of Rapamycin complex (TORC), regulates CONSTANS post-transcriptionally through GIGANTEA. Both proteins are components of the photoperiod pathway of the flowering network and their miss-regulation inraptormutants hampers the upregulation of genes promoting flowering. Our work suggests that the high energy available in long days is sensed and integrated into the photoperiod pathway by TORC.
Physiological responses to a changing winter climate in an early spring-breeding amphibian
Authors: Schmidt Robin , Zummach Cecile , Sinai Noa , Sabino-Pinto Joana , Kuenzel Sven , Dausmann Kathrin H. , Ruthsatz Katharina
Published: January 2024

Climate change is swiftly altering environmental winter conditions, leading to significant ecological impacts such as phenological shifts in many species. As a result, animals might face physiological mismatches due to longer or earlier activity periods and are at risk of being exposed to late spring freezes. Our study points for the first time to the complex physiological challenges that amphibians face as a result of changing thermal conditions due to winter climate change. We investigated the physiological responses to a period of warmer winter days and sudden spring freeze in the common toad (Bufo bufo) by acclimating them to 4°C or 8°C for 48 h or exposing them to 4°C or -2°C for 6 h, respectively. We assessed the daily energy demands, determined body condition and cold tolerance, explored the molecular responses to freezing through hepatic tissue transcriptome analysis, and measured blood glucose levels. Toads acclimated to higher temperatures showed a higher daily energy expenditure and a reduced cold tolerance suggesting faster depletion of energy stores and the loss of winter acclimation during warmer winters. Blood sugar levels were higher in frozen toads indicating the mobilization of cryoprotective glucose with freezing which was further supported by changed patterns in proteins related to glucose metabolism. Overall, our results emphasize that increased thermal variability incurs physiological costs that may reduce energy reserves and thus affect amphibian health and survival. This might pose a serious threat to breeding adults and may have subsequent effects at the population level.
PRMT5 orchestrates EGFR and AKT networks to activate NFκB and promote EMT
Authors: Huang Lei , Ravi Manasa , Zhang Xiao-Ou , Verdejo-Torres Odette , Shendy Noha A.M. , Nezhady Mohammad A.M. , Gopalan Sneha , Wang Gang , Durbin Adam D. , Fazzio Thomas G. , Wu Qiong
Published: January 2024

Neuroblastoma remains a formidable challenge in pediatric oncology, representing 15% of cancer-related mortalities in children. Despite advancements in combinatorial and targeted treatments improving survival rates, nearly 50% of patients with high-risk neuroblastoma will ultimately succumb to their disease. Dysregulation of the epithelial-mesenchymal transition (EMT) is a key mechanism of tumor cell dissemination, resulting in metastasis and poor outcomes in many cancers. Our prior work identified PRMT5 as a key regulator of EMT via methylation of AKT at arginine 15, enhancing the expression of EMT-driving transcription factors and facilitating metastasis. Here, we identify that PRMT5 directly regulates the transcription of the epidermal growth factor receptor (EGFR). PRMT5, through independent modulation of the EGFR and AKT pathways, orchestrates the activation of NFκB, resulting in the upregulation of the pro-EMT transcription factors ZEB1, SNAIL, and TWIST1. Notably, EGFR and AKT form a compensatory feedback loop, reinforcing the expression of these EMT transcription factors. Small molecule inhibition of PRMT5 methyltransferase activity disrupts EGFR/AKT signaling, suppresses EMT transcription factor expression and ablates tumor growthin vivo. Our findings underscore the pivotal role of PRMT5 in the control of the EMT program in high-risk neuroblastoma.
Mutations in the non-catalytic polyproline motif destabilize TREX1 and amplify cGAS-STING signaling
Authors: Shim Abraham , Luan Xiaohan , Zhou Wen , Crow Yanick , Maciejowski John
Published: January 2024

The cGAS-STING pathway detects cytosolic DNA and activates a signaling cascade that results in a type I interferon (IFN) response. The endoplasmic reticulum (ER)-associated exonuclease TREX1 suppresses cGAS-STING by eliminating DNA from the cytosol. Mutations that compromise TREX1 function are linked to autoinflammatory disorders, including systemic lupus erythematosus (SLE) and Aicardi-Goutières syndrome (AGS). Despite key roles in regulating cGAS-STING and suppressing excessive inflammation, the impact of many disease-associatedTREX1mutations - particularly those outside of the core catalytic domains - remains poorly understood. Here, we characterize a recessive AGS-linked TREX1 P61Q mutation occurring within the poorly characterized polyproline helix (PPII) motif. In keeping with its position outside of the catalytic core or ER targeting motifs, neither the P61Q mutation, nor aggregate proline-to-alanine PPII mutation, disrupt TREX1 exonuclease activity, subcellular localization, or cGAS-STING regulation in overexpression systems. Introducing targeted mutations into the endogenousTREX1locus revealed that PPII mutations destabilize the protein, resulting in impaired exonuclease activity and unrestrained cGAS-STING activation. Overall, these results demonstrate that TREX1 PPII mutations, including P61Q, impair proper immune regulation and lead to autoimmune disease through TREX1 destabilization.
ROSALINDprotects the mitochondrial translational machinery from oxidative damage
Authors: Katopodi Vicky , Verheyden Yvessa , Cinque Sonia , Jimenez Elena Lara , Demesmaeker Ewout , Marino Alessandro , Derua Rita , Groaz Elisabetta , Leucci Eleonora
Published: January 2024

Upregulation of mitochondrial respiration coupled with high ROS-scavenging capacity is a characteristic shared by drug-tolerant cells in several cancers. As translational fidelity is essential for cell fitness, protection of the mitochondrial and cytosolic ribosomes from oxidative damage is pivotal. While mechanisms for recognizing and repairing such damage exist in the cytoplasm, the corresponding process in the mitochondria remains unclear.

By performing Ascorbate PEroXidase (APEX)-proximity ligation assay directed to the mitochondrial matrix followed by isolation and sequencing of RNA associated to mitochondrial proteins, we identified the nuclear-encoded lncRNAROSALINDas an interacting partner of ribosomes.ROSALINDis upregulated in recurrent tumours and its expression can discriminate between responders and non-responders to immune checkpoint blockade in a melanoma cohort of patients. Featuring an unusually high G content,ROSALINDserves as a substrate for oxidation. Consequently, inhibitingROSALINDleads to an increase in ROS and protein oxidation, resulting in severe mitochondrial respiration defects. This, in turn, impairs melanoma cell viability and increases immunogenicity bothin vitroandex vivoin preclinical humanized cancer models. These findings underscore the role ofROSALINDas a novel ROS buffering system, safeguarding mitochondrial translation from oxidative stress, and shed light on potential therapeutic strategies for overcoming cancer therapy resistance.
3-epicaryoptin induces G2/M phase cell cycle arrest and apoptosis in human breast cancer cells by disrupting the microtubule network, anin vitroandin silicoinvestigation
Authors: Barman Manabendu , Roy Sujit , Singh Nanda , Sarkar Debanjan , Barman Niharendu , Pal Amit , Bhattacharyya Sankar , Ray Sanjib
Published: January 2024

Breast cancer (BC) is a prevalent form of cancer observed in women across the globe, constituting over a quarter of all female BC cases. The treatment of BC continues to require significant efficacy, aiming to achieve high success rates while minimizing adverse effects on the body as a whole. In the current study, 3-epicaryoptin was tested for the molecular mechanism of its anti-cancer activity in the human breast cancer cell line, MCF-7. We investigated cell viability by MTT assay, cell cycle kinetics and apoptosis, immunofluorescence straining, molecular modelling, and ADMET profiling. MTT assay results showed that 3-epicaryoptin was found cytotoxic against MCF-7 cells with an IC50value of 344.64 µg mL-1for 48 h. Flow cytometric analysis exhibited that 3-epicaryoptin halted the MCF-7 cells in the G2/M phase and subsequently induced apoptosis in a time-dependent manner. Our immunofluorescence studies indicated that 3-epicaryoptin inhibited microtubule polymerization in MCF-7 cells. Furthermore, molecular docking followed by molecular dynamics (MD) simulation studies demonstrated the ability of 3-epicaryoptin to interact with the tubulin protein at the colchicine binding pockets. Overall, our results suggest that 3-epicaryoptin can inhibit the proliferation of human breast cancer cells by depolymerizing of cellular microtubule networks, which causes cell cycle arrest and promotes apoptotic cell death. Therefore, it has been indicated that the natural product 3-epicaryoptin exhibited considerable promise as a potent therapeutic agent capable of inducing apoptosis in breast cancer cells.
Altered Socio-Affective Communication and Amygdala Development in mice with Protocadherin10-deficient Interneurons
Authors: Aerts Tania , Boonen Anneleen , Geenen Lieve , Stulens Anne , Masin Luca , Pancho Anna , Francis Annick , Roy Frans Van , Wöhr Markus , Seuntjens Eve
Published: January 2024

Autism Spectrum Disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviors. The cell adhesion molecule Protocadherin10 (Pcdh10) has been implicated in the etiology of ASD.Pcdh10is expressed in the nervous system during embryonic and early postnatal development and has been linked to neural circuit formation. Here, we show strong expression ofPcdh10in the ganglionic eminences and in the basolateral complex of the amygdala at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressedPcdh10in the basolateral complex at perinatal stages and genes linked to vocalization behavior were enriched inPcdh10-expressing neurons in adult mice. To further investigate the involvement ofPcdh10in neurodevelopment with relevance to ASD, and to assess the functional and behavioral consequences of loss of Pcdh10 in basolateral amygdala interneurons, we combined a ubiquitous and a conditional Pcdh10 knockout mouse model. Conditional knockout of Pcdh10 reduced the number of interneurons in the basolateral complex. Both models exhibited altered developmental trajectories of socio-affective communication through isolation-induced ultrasonic vocalizations in neonatal pups, characterized by increased emission rates in heterozygous pups. Furthermore, acoustic call features were affected and heterozygous conditional knockout pups emitted calls characterized by reduced peak frequencies but increased frequency modulation. Additionally, we identified distinct clusters of call subtypes with specific developmental trajectories, suggesting the vocalization repertoire is extensive and dynamic during early life. The nuanced alterations in socio-affective communication at the level of call emission rates, acoustic call features, and clustering of call subtypes were primarily seen in heterozygous pups of the conditional knockout and less prominent in the ubiquitous Pcdh10 knockout, suggesting that changes in anxiety levels associated withGsh2-lineage interneurons might drive the observed behavioral effects. Together, this demonstrates that loss ofPcdh10specifically in interneurons contributes to behavioral alterations in socio-affective communication with relevance to ASD.
Species-associated bacterial diversity increases along a gradient of habitat degradation
Authors: Hanhimäki Elina , Linna Susanna , Beraldo Camila , Englund Mikael , Rezola Uxue , Cardoso Pedro , Thorogood Rose , Saastamoinen Marjo , Duplouy Anne
Published: January 2024

Alterations of microbial communities have evident impacts on development, digestion, fecundity, metabolism, immunity, and diverse other biological functions of their hosts. Yet, the factors affecting microbial communities associated with wild species often remain uncharacterized. For example, the impact of the host’s habitat degradation due to anthropogenic activities has received little attention, which contrasts with the large literature showing how such habitat degradation is at least partly responsible for the on-going global patterns of macro-biodiversity erosion. Here, we use metacommunities of herbivorous insect species specialized in feeding onPlantago lanceolatain the fragmented landscape of the Åland Islands, Finland, as a model system to test whether and how bacterial communities associated with wild species change along a gradient of habitat degradation. We evaluated microbial species diversity and community composition in two sympatric insect species sampled from local meadow habitats with various levels of human disturbance within or around these habitats (e.g. forests, roads, agriculture fields, buildings). Counter to our expectations, we found that bacterial diversity can increase with habitat degradation, with individuals from more degraded habitats hosting more rare bacterial species. In contrast, as the dominant microbial species remain similar across habitats, the community composition and function of the microbiota persist under habitat degradation. In this system, the strength of human activities might induce changes in habitat heterogeneity rather than changes in overall habitat quality, thus allowing local insects to encounter and host more rare microbes rather than trigger local microbial extinction.