bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microglia signals to fibroblasts and neural progenitor cells to control regenerative neurogenesis after spinal cord injury in zebrafish
Authors: Docampo-Seara Alberto , Cosacak M. Ilyas , Heilemann Kim , Kessel Friederike , Oprişoreanu Ana-Maria , Westphal Markus , Çark Özge , Zöller Daniela , Arnold Josi , Bretschneider Anja , Hnatiuk Alisa , Ninov Nikolay , Becker Catherina G. , Becker Thomas 
Published: October 2024

ABSTRACTZebrafish, in contrast to mammals, regenerate neurons after spinal cord injury, but little is known about the control mechanisms of this process. Here we show that microglia are the main cell type to express the evolutionarily conserved signalling moleculesema4abin the injury site. Deletion ofsema4abdoubles the number of newly generated progenitor cells and neurons after spinal injury. Using scRNAseq of all lesion site cell types after gene disruption, we find thatsema4absupports the microglial activation state and promotes interactions with fibroblasts and neural progenitor cells. Mechanistically,sema4absignals throughplxn1a/breceptors on spinal progenitors and attenuates expression of the neurogenesis-promoting cytokinetgfb3in fibroblasts. Hence, microglia regulate neurogenesis viasema4abin successful spinal cord regeneration in zebrafish, which may be one of the mechanisms preventing regenerative neurogenesis in the mammalian spinal cord.HIGHLIGHTS- Microglia control signalling from fibroblasts in a spinal injury site- Fibroblasts promote regenerative neurogenesis via Tgfb3 signalling- scRNAseq reveals full complement ofsema4ab-dependent cell type interactions in a spinal injury site-sema4abstabilises activation state of microglia after injury
AI-Driven Spatial Transcriptomics Unlocks Large-Scale Breast Cancer Biomarker Discovery from Histopathology
Authors: Shulman Eldad D. , Campagnolo Emma M. , Lodha Roshan , Stemmer Amos , Cantore Thomas , Ru Beibei , Chang Tian-Gen , Biswas Sumona , Dhruba Saugato Rahman , Wang Andrew , Paul Rohit , Kalisetty Sarath , Hu Tom , Nasrallah Maclean , Rajagopal Sheila , Sammut Stephen-John , Lipkowitz Stanley , Jiang Peng , Caldas Carlos , Knott Simon , Hoang Danh-Tai , Aldape Kenneth , Ruppin Eytan 
Published: October 2024

AbstractSpatial transcriptomics (ST) is transforming our understanding of tumor heterogeneity by enabling high-resolution, location-specific mapping of gene expression across tumors and their microenvironment. However, the associated high cost of the assay has limited cohort size and hence large-scale biomarker discovery. Here we presentPath2Space, a deep learning approach that predicts spatial gene expression directly from histopathology slides. Trained on substantial breast cancer ST data, it robustly predicts the spatial expression of over 4,300 genes in independent validations, markedly outperforming existing ST predictors.Path2Spaceadditionally accurately infers cell-type abundances in the tumor microenvironment (TME) based on the inferred ST data. Applied to more than a thousand breast tumor histopathology slides from the TCGA,Path2Spacecharacterizes their TME on an unprecedented scale and identifies three new spatially-grounded breast cancer subgroups with distinct survival rates.Path2Space-inferred TME landscapes enable more accurate predictions of patients’ response to chemotherapy and trastuzumab directly from H&E slides than those obtained by existing established sequencing-based biomarkers.Path2Spacethus offers a transformative, fast and cost-effective approach to robustly delineate the TME directly from their histopathology slides, facilitating the development of spatially-grounded biomarkers to advance precision oncology.
Switch in parasitic and autotrophic-dominated protist assemblages coupled to seasonal oligotrophic-mesotrophic gradients in the sunlit layer of a subtropical marine ecosystem
Authors: Avrahami Yoav , Siano Raffaele , Rubin-Blum Max , Koplovitz Gil , Henry Nicolas , de Vargas Colomban , Frada Miguel J. 
Published: October 2024

AbstractProtists are major functional players in the oceans. Time-resolved epipelagic protist successions remain poorly described in subtropical ecosystems, limiting current understanding of food web dynamics and responses to environmental changes in these major world-ocean regions. Here, we used amplicon sequencing data and their trait-based annotation to examine the seasonality of planktonic protists in the subtropical Gulf of Aqaba (northern Red Sea). Temperature and nutrients were identified as major drivers of succession. Marked seasonal shifts in protists were detected. The warm, stratified oligotrophic period spanning through spring and summer were dominated by heterotrophs, including parasitic Syndiniales. By contrast, nutrient influx during deep convective-mixing in winter triggered a progressive shift to photoautotrophic communities dominated by few chlorophyte genera. Ephemeral phytoplankton blooms were detected during the mixing-to-stratification transition. Deeper winter mixing resulted in larger blooms dominated by diatoms and coccolithophores relative to chlorophytes prevalent during shallower mixing. This illustrates the impact of mixing-depth in the development and compostion of blooms. Comparisons with oceanwide rDNA datasets indicate that the oligotrophic protist assemblages from the Gulf of Aqaba resemble those from warm, open-oceans. This work provides a detailed assessment of the seasonality in protist communities and dominant functional strategies in a coastal subtropical planktonic ecosystem.
The role of IAA and its transport in the complex streptophyte algaeChara braunii
Authors: Kurtović Katarina , Vosolsobě Stanislav , Nedvěd Daniel , Müller Karel , Dobrev Petre , Schmidt Vojtěch , Piszczek Piotr , Kuhn Andre , Smoljan Adrijana , Fisher Tom J. , Weijers Dolf , Friml Jiří , Bowman John L. , Petrášek Jan 
Published: October 2024

AbstractThe role of auxin indole-3-acetic acid (IAA), a phytohormone with numerous morphogenic functions, is now well-established in land plants. Although the role of IAA and its transport in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within Streptophytes. Among streptophyte algae,Chararepresents a genus with a considerable degree of complexity in body arrangement. This study investigates the auxin response and characterizes homologs of land plant PIN auxin efflux carriers inChara braunii. Through regeneration experiments, we observed that IAA significantly promotes elongation of thallus and side branch development upon thallus tip decapitation, indicating an effect on morphogenesis. We show that IAA is actively uptaken and metabolized by thallus cells and that this process is influenced by N-1-naphthylphthalamic acid (NPA). To elucidate the underlying mechanisms, we cloned and sequenced the most expressedChara brauniiPINs, CbPINa and CbPINc. Using epitope-specific antibodies, we showed their presence in the plasma membrane (PM) of vegetative internodal cells and generative antheridial cells. Functional tests in tobacco BY-2 cells, supported byin silicodocking of IAA and NPA to CbPINa and CbPINc, showed that PM-localized CbPINa interferes with auxin transport in contrast to ER-localized CbPINc. Finally, our phosphoproteome analysis indicated that IAA rapidly induces specific phosphorylation events, including RAF-like kinase phosphorylation, highlighting a potential role for IAA in fast signaling processes inChara braunii.Altogether, we provide new insights into IAA role inChara brauniimorphogenesis and suggest that while the canonical auxin transport mechanism may not be conserved, auxin still may likely play a role in rapid signaling pathways in this close relative of land plants.
Weaker neuroligin 2 – neurexin 1β interaction tethers membranes and signal synaptogenesis through clustering
Authors: Boyd Robbie , Jaqaman Khuloud , Wang Weiwei 
Published: October 2024

AbstractSingle-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules (SAMs) that are essential for the formation of functional synapses. Binding affinities vary by ∼ 1000 folds between arrays of NL and NRX subtypes, which contribute to chemical and spatial specificities. Current structures are obtained with truncated extracellular domains of NL and NRX and are limited to the higher-affinity NL1/4-NRX complexes. How NL-NRX interaction leads to functional synapses remains unknown. Here we report structures of full-length NL2 alone, and in complex with NRX1β in several conformations, which has the lowest affinity among major NL-NRX subtypes. We show how conformational flexibilities may help in adapting local membrane geometry, and reveal mechanisms underlying variations in NL-NRX affinities modulation. We further show that, despite lower affinity, NL2-NRX1β interaction alone is capable of tethering different lipid membranes in total reconstitution, and that NL2 and NRX1β cluster at inter-cellular junctions without the need of other synaptic components. In addition, NL2 combines with the master post-synaptic scaffolding protein gephyrin and clusters neurotransmitter receptors at cellular membrane. These findings suggest dual roles of NL2 - NRX1β interaction – both as mechanical tether, and as signaling receptors, to ensure correct spatial and chemical coordination between two cells to generate function synapses.
Deciphering stiffness-driven changes in colorectal cancer by proteomics
Authors: Cresens Charlotte , Montero-Calle Ana , Solís-Fernández Guillermo , Shaghaghi Behrad , Gerrits Lotte , Aytekin Samet , Kouwer Paul H. J. , Barderas Rodrigo , Rocha Susana 
Published: October 2024

AbstractTumor stiffening plays a pivotal role in cancer progression. Increased tumor stiffness, resulting from interactions between cancer cells and their surrounding microenvironment, alters the tumor’s mechanical properties and significantly impacts cancer growth and metastasis, the primary cause of cancer-related deaths. Despite the importance of tumor stiffness, systematic studies exploring its effect on proteomic profiles are limited. In this study, focused on colorectal cancer, we show that matrix stiffness significantly alters the expression of secreted proteins, while intracellular protein levels remain largely unaffected. Functional assays reveal that the changes in the secretome, driven by matrix stiffness, enhance cell migration, angiogenesis, and matrix remodeling, which collectively contribute to a more aggressive cancer phenotype. Our findings emphasize the critical role of matrix stiffness in driving colorectal cancer progression through changes in the secretome, offering valuable insights for the development of biomechanical cancer therapies.Abstract Figure
Why do bats fly into cave doors? Inattentional blindness in echolocating animals
Authors: Finger Nikita M , Eveland Keegan E , Yin Xiaoyan , Moss Cynthia F 
Published: October 2024

AbstractEcholocating bats can navigate complex 3D environments by integrating prior knowledge of spatial layouts and real-time sensory cues. This study demonstrates that inattentional blindness to sensory information undermines successful navigation in Egyptian fruit bats,Rousettus aegyptiacus, a species that has access to vision and echolocation to traverse natural environments. Bats flew over repeated trials to a perch at a fixed location in the light, allowing them to navigate using both vision and echolocation. The experiment was then repeated in the dark to exclude the bat’s use of vision. The perch was subsequently displaced by either 15 or 30 cm in one of six different directions (up, down, left, right, front, back). Echolocation behavior was recorded using a 25-channel microphone array, while flight paths were tracked using 13 motion capture cameras. The directional aim of echolocation clicks served as a metric for the bat’s spatial attention to locations in their environment. In the light, bats modified their flight paths to successfully land on a perch that was moved 15 cm but surprisingly, often failed to land on it when displaced by 30 cm. In the dark, bats often failed to land on the perch after it was moved by only 15 cm. Landing failures suggest that learned spatial priors invoked inattentional blindness to changes in the environment, which interfered with successful navigation. In both the light and dark, when bats failed to land on the perch at its new location, they directed their attention toward the original perch position. Performance differences in the light and dark suggest that the bat’s attentional spotlight may be narrower when it relies on echolocation than vision. To our knowledge, these findings provide the first evidence of inattentional blindness in a flying echolocating animal, demonstrating that spatial priors can dominate sensory processing during navigation.
Human TRPV4 engineering yields an ultrasound-sensitive actuator for sonogenetics
Authors: Zhao Lu , Xu Kevin , Talyzina Irina , Shi Jingyi , Li Shisheng , Yang Yaoheng , Zhang Shuming , Zheng Jie , Sobolevsky Alexander I. , Chen Hong , Cui Jianmin 
Published: October 2024

AbstractSonogenetics offers non-invasive and cell-type specific modulation of cells genetically engineered to express ultrasound-sensitive actuators. Finding an ion channel to serve as sonogenetic actuator it critical for advancing this promising technique. Here, we show that ultrasound can activate human TRP channel hTRPV4. By screening different hTRPV4 variants, we identify a mutation F617L that increases mechano-sensitivity of this channel to ultrasound, while reduces its sensitivity to hypo-osmolarity, elevated temperature, and agonist. This altered sensitivity profile correlates with structural differences in hTRPV4-F617L compared to wild-type channels revealed by our cryo-electron microscopy analysis. We also show that hTRPV4-F617L can serve as a sonogenetic actuator for neuromodulation in freely moving mice. Our findings demonstrate the use of structure-guided mutagenesis to engineer ion channels with tailored properties of ideal sonogenetic actuators.
In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth
Authors: Kim Gyuhyeon , Siprashvili Zurab , Yang Xue , Meyers Jordan M. , Ji Andrew , Khavari Paul A. , Ducoli Luca 
Published: October 2024

AbstractCutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer deaths globally, making it the second-highest subtype of skin cancer. The prevalence of cSCC in humans, as well as the poor capacity for an efficient prognosis, highlights the need to uncover alternative actors and mechanisms at the foundation of skin cancer development. Significant advances have been made to better understand some key factors in cSCC progression. However, little is known about the role of noncoding RNAs, particularly of a specific category called long noncoding RNA (lncRNA). By performing pseudobulk analysis of single-cell sequencing data from normal and cSCC human skin tissues, we determined a global portfolio of lncRNAs specifically expressed in keratinocyte subpopulations. Integration of CRISPR interference screens in vitro and the xenograft model identified several lncRNAs impacting the growth of cSCC cancer lines both in vitro and in vivo. Among these, we further validated LINC00704 and LINC01116 as proliferation-regulating lncRNAs in cSCC lines and potential biomarkers of cSCC progression. Taken together, our study provides a comprehensive signature of lncRNAs with roles in regulating cSCC progression.
Genetic instrumental variable framework for assessing relevance of in-vitro cellular phenotypes to organism-level phenotypes
Authors: Howe Laurence J , Aulchenko Yury , Cortes Adrian , Gordillo Jorge Esparza , Johnson Toby , Richardson Tom G , Sanseau Philippe , Scott Robert A , Seaton Daniel D 
Published: October 2024

AbstractGene perturbation screens (e.g. CRISPR-Cas9) assess the impact of gene disruption on cellular phenotypes (e.g., proliferation, anti-viral response, transcriptomics). Cellular phenotypes can be useful in-vitro models for understanding the aetiology of organism-level (in-vivo) phenotypes (e.g., anti-viral response in immune cells and infectious disease outcomes). However, demonstrating relevance between cellular and organism-level phenotypes is non-trivial.If a cellular phenotype is relevant, then we should observe that perturbed genes impacting the cellular phenotype also impact the organism-level phenotype with mechanism-consistent directionality. We propose a framework, loss-of-function instrumental variable analysis (LoF-IV), to evaluate relevance between cellular and organism-level phenotypes using estimates of gene effects on cellular phenotypes from perturbation screens and estimates of gene effects on human-level phenotypes from loss-of-function burden tests.Using data from four published genome-wide CRISPR-Cas9 screens and UK Biobank whole-genome sequence burden tests, we evaluated relevance of four in-vitro cellular phenotypes (chondrocyte proliferation, insulin content, adipocyte differentiation, lysosomal cholesterol accumulation) to human-level phenotypes. We found evidence that higher lysosomal cholesterol accumulation lowers LDL-cholesterol measured in human blood plasma (P = 0.0006), consistent with the known role of lysosomes in lipid biosynthesis. However, we did not find strong evidence for phenotypic relevance of the other cellular phenotypes, illustrating the complexities of developing disease-relevant in-vitro models. LoF-IV enables systematic evaluation of the relevance of cellular phenotypes to the human phenome informing assay prioritization and supporting novel hypothesis generation.
Generalization and extinction of platform-mediated avoidance in male and female rats
Authors: López-Moraga Alba , Luyten Laura , Beckers Tom 
Published: October 2024

AbstractBackgroundUnderstanding the basis of anxiety-related disorders can be advanced by studying the fear learning mechanisms implicated in the transition from adaptive to maladaptive fear. Individuals with anxiety disorders typically exhibit impaired fear extinction, pervasive avoidance, and overgeneralization of fear. While most research has examined deviations in these fear learning characteristics in isolation, their potential interactions remain understudied. Here, we introduce a modification of the platform-mediated avoidance task and use it to chart avoidance, generalization, and extinction using a single procedure in male and female rats.ResultsIn the first experiment, we demonstrated that male rats readily acquire avoidance, show a gradient of generalization in a two-day generalization test, and gradually reduce avoidance and fear responding under extinction. In the second experiment, female rats likewise exhibited successful avoidance learning, showed gradual generalization and extinction of defensive behaviors. Across both experiments, interesting sex differences emerged. The third experiment aimed at corroborating these sex differences but showed that they were subtler than expected from the prior separate experiments. Finally, we present an open-source automated system to facilitate the processing of DeepLabCut and SimBA output and obtain reliable results for scoring avoidance and freezing behavior.ConclusionsThe modified platform-mediated avoidance task can effectively probe avoidance, generalization, and extinction of fear in male and female rats in a single procedure. Our automated behavioral scoring approach offers researchers an efficient and reproducible method to quantify the defensive behaviors of avoidance, freezing and darting in rats.
Neutrophils exhibit distinct migration phenotypes that are regulated by transendothelial migration
Authors: Schwartz Amy B. , Kandasamy Adithan , del Álamo Juan C. , Yeh Yi-Ting 
Published: October 2024

AbstractThe extravasation of polymorphonuclear neutrophils (PMNs) is a critical component of the innate immune response that involves transendothelial migration (TEM) and interstitial migration. TEM-mediated interactions between PMNs and vascular endothelial cells (VECs) trigger a cascade of biochemical and mechanobiological signals whose effects on interstitial migration are currently unclear. To address this question, we cultured human VECs on a fibronectin-treated transwell insert to model the endothelium and basement membrane, loaded PMN-like differentiated HL60 (dHL-60) cells in the upper chamber of the insert, and collected the PMNs that crossed the membrane-supported monolayer from the lower chamber. The 3D chemotactic migration of the TEM-conditioned PMNs through collagen matrices was then quantified. Data collected from over 50,000 trajectories showed two distinct migratory phenotypes, i.e., a high-persistence phenotype and a low-persistence phenotype. These phenotypes were conserved across treatment conditions, and their existence was confirmed in human primary PMNs. The high-persistence phenotype was characterized by more straight trajectories and faster migration speeds, whereas the low-persistence one exhibited more frequent sharp turns and loitering periods. A key finding of our study is that TEM induced a phenotypic shift in PMNs from high-persistence migration to low-persistence migration. Changes in the relative proportion of high-persistence and low-persistence populations correlated with GRK2 expression levels. Inhibiting GRK2 hindered the TEM-induced shift in migratory phenotype and impaired the phagocytic function of PMNs. Overall, our study suggests that TEM-mediated GRK2 signaling primes PMNs for a migration phenotype better suited for spatial exploration and inflammation resolution. These observations provide novel insight into the biophysical impacts of TEM that priming PMNs is essential to conduct sentinel functions.
Human Astrocytes Synchronize Neural Organoid Networks
Authors: Patel Megh Dipak , Lavekar Sailee Sham , Jaisalmeria Ronak , Oji Suki , Jayasi Jazmine , Cvetkovic Caroline , Krencik Robert 
Published: October 2024

AbstractBiological neural networks exhibit synchronized activity within and across interconnected regions of the central nervous system. Understanding how these coordinated networks are established and maintained may reveal therapeutic targets for neurodegeneration and neuromodulation. Here, we tested the influence of astrocytes upon synchronous network activity using human pluripotent stem cell-derived bioengineered neural organoids. This study revealed that astrocytes significantly increase activity within individual organoids and across long distances among numerous rapidly merged organoids via influencing synapses and bioenergetics. Treatment of amyloid protein inhibited synchronous activity during neurodegeneration, yet this can be rescued by propagating activity from neighboring networks. Altogether, this study identifies critical contributions of human astrocytes to biological neural networks and delivers a rapid, reproducible, and scalable model to investigate long-range functional communication of the nervous system in healthy and disease states.
Coordinated Division of Selective Stationary-Phase Yeast Cells Expands the Population Survivorship in Quiescence
Authors: Hsiao Kai-Ching , Lin Hsin-Ying , Hazbun Tony R. , Kuo Min-Hao 
Published: October 2024

SummaryBudding yeast employs a variety of survival strategies in response to starvation, including pseudohyphal development, invasive growth, and sporulation. Here we report an innate pathway of “viability resurgence in quiescent time” (VRQT) by aged cultures to preserve and expand the population survivorship. Without additional nutrients, a few stationary-phase cells synchronously enter mitosis, increasing the population viability that does not likely result from mutations. VRQT is a population density-dependent collective behavior that can be triggered by quorum sensing aromatic alcohols. Genetic analyses demonstrate that VRQT is independent of many canonical pathways for cell growth, development, or stress responses. This community survival program allows yeast to proactively extend vitality amidst a common nutritional crisis. Wild strains isolated from clinical samples exhibit VRQT, suggesting that this survival mechanism must be considered when treating human infections.