Biology subjects

Huang, S.

Publications and source records attributed to Huang, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

The pore-forming protein APOL7C ruptures Leishmania major-containing parasitophorous vacuoles in dendritic cells to promote IL-12 production and the induction of T helper type 1 immunity

Classical dendritic cells (cDCs) are required for the efficient priming of T helper type 1 (Th1) immunity against Leishmania major infections in mice. They do so by producing large quantities of IL-12 in response to L. major infection. IL-12 in turn supports the generation of protective CD4+ Th1 cells. However, the mechanism(s) by which L. major instigates robust IL-12 production by cDCs has not been addressed. Here we show that expression of a pore-forming protein called APOL7C is induced in cDCs by L. major infection. APOL7C is expressed in the cytosol of host cells and, remarkably, upon infection is recruited to L. major parasitophorous vacuoles (PVs) where it induces PV rupture. PV rupture leads to the exposure of L. major-derived pathogen-associated molecular patterns (PAMPs) to cytosolic pattern recognition receptors (PRRs). Cytosolic PRR signaling then drives IL-12 production by cDCs. Consequently, L. major challenge of APOL7C-deficient mice results in reduced numbers of IL-12 producing cDCs as well as a diminished Th1 response. In sum, our data indicate the presence of pore-forming proteins in the cytosol of cDCs that interfere with the intracellular niche of Leishmania to modulate immunity to these parasites.

cell biology↗

bioRxiv2025

Active zone remodeling by Bruchpilot couples synaptic architecture to Kv1/Shaker excitability control

Presynaptic active zones are known to undergo state-dependent remodeling across sleep, circadian, and experience-dependent conditions, yet how such structural changes influence synaptic computation and excitability has remained unclear. Here, we address this gap by examining the functional consequences of physiological upscaling of the active zone scaffold Bruchpilot (BRP), within the range previously observed during natural state-dependent plasticity. We show that moderate BRP elevation expands the number of functional release sites while surprisingly reducing vesicle release probability, thereby establishing a presynaptic operating mode with selectively enhanced transmission at intermediate firing frequencies. This remodeled mode depends on Kv1/Shaker potassium channels, which normally constrain the increased structural capacity generated by BRP; accordingly, perturbation of Shaker abolishes BRP-dependent reductions in release probability and unmasks an enlarged synaptic output capacity. To test the functional relevance of this coupling, we examined sleepless mutants, in which Kv1/Shaker channels are destabilized and presynaptic remodeling is compromised. We show that direct, physiological-level BRP upscaling selectively restores the Shaker/Hyperkinetic channel complex from near-undetectable levels toward normal abundance without inducing global proteomic changes, and correspondingly rescues excitability balance, oxidative stress resistance, lifespan, and mid-term memory. Together, these findings identify a mechanistic coupling between active zone architecture and intrinsic excitability control and demonstrate how presynaptic structural plasticity shapes frequency-dependent transmission and functional robustness under stress.

neuroscience↗

bioRxiv2025

Local tolerance and innate immune activation of primary human respiratory cells exposed to flagellin

Antibiotic-resistant respiratory infections can lead to treatment failure, highlighting the need for alternative strategies. FLAMOD, a recombinant flagellin, stimulates innate immunity via Toll-like receptor 5 when delivered intranasally. In mice, FLAMOD protects against bacterial pneumonia. The protection is associated with activation of airway epithelial cells. This study aimed to assess the tolerance of human primary respiratory epithelium to FLAMOD administered apically as liquid droplets or by nebulization, to measure the innate immune response, and the pharmacokinetics of FLAMOD. We used epithelia reconstituted from human nasal and bronchial (MucilAir), small airways (SmallAir) and alveolar (AlveolAir) primary epithelial cells, cultured at the air-liquid interface. We report that daily administration of escalating doses of FLAMOD for 5 days was well tolerated by epithelia as barrier integrity, cilia motion and cell viability were not affected. FLAMOD was rapidly degraded without leakage into the basal compartment. Each epithelial model exhibited responses involving pathways of innate defense and immune cell infiltration, which were dose-dependent, with an effective concentration of FLAMOD in the picomolar range. Similar tolerance profile and immune responses were obtained with airway epithelium from cystic fibrosis and chronic obstructive pulmonary disease patients. In conclusion, this study supports the stimulation of epithelial Toll-like receptor 5 signaling to fight against infections of vulnerable patients.

cell biology↗

bioRxiv2025

Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity

Glycans modify nucleic acids, proteins and lipids in fundamental biological processes, but have long been considered confined to the secretory pathway and cell surface. Here, we challenge this view with evidence that N-glycosylation, a ubiquitous glycan modification, occurs within cell nuclei across tissues and species, exhibiting cell type-dependent abundance and localization patterns. Using a multi-faceted approach, we show that numerous classical membrane and secreted glycoproteins localize to the nucleus with N-glycan modifications, exemplified by the cell adhesion molecule L1CAM. Mechanistically, we show that the N-glycosylated L1CAM is transported to the nucleus by KPNB1, where it transcriptionally modulates neuronal differentiation. Moreover, this nuclear N-glycosylation event contributes to neurodevelopmental disorders and is pharmacologically reversible. These findings revise the cellular geography of N-glycosylation and expand the known routes of protein trafficking, and highlight nuclear N-glycosylation pathways as potential therapeutic entry points for developmental disorders.

cell biology↗

bioRxiv2025

Multi-Timescale Neural Adaptation Failure as a Mechanistic Signature of Major Depression

Major depression (MD) is usually characterized in terms of momentary abnormalities, such as negative bias or emotional blunting, derived from paradigms that measure only the first response to a stimulus. Yet depressive experience in daily life is repetitive and cumulative. Here we test the hypothesis that a failure of neural adaptation across repetitions is a core feature of MD. Using a repeated negative-stimulus paradigm, we quantified adaptation at micro (within-trial) and macro (across-session) scales via electroencephalography in 28 MD patients and 34 healthy controls, measuring both conventional event-related potentials and large-scale traveling-wave propagation. MD patients exhibited pervasive maladaptation: neural rigidity at the micro scale (absent repetition suppression) and progressive regulatory depletion at the macro scale (escalating emotional reactivity with declining cognitive control). Across analyses, adaptation-based metrics revealed larger group differences than single-shot indices, and classifiers built on adaptation features--especially traveling-wave dynamics--outperformed single-shot models (task AUC = 0.83 vs 0.78) and generalized to two independent datasets (up to AUC = 0.91). These findings challenge conventional symptom-based characterizations of MD, establishing adaptation failure--not initial reactivity--as the mechanistically primary pathological signature. This reframing provides a unified mechanistic explanation for rumination and cognitive inflexibility while offering a standardized, low-cost biomarker requiring minimal electrodes ([≤]8 channels), enabling large-scale screening in resource-limited settings.

neuroscience↗

bioRxiv2025

The FERM Guild: A Differentially Correlated Microbial Module Drives Hypertension via Metabolic Flux Perturbations

BackgroundHypertension is a major risk factor for cardiovascular diseases, with changes in gut microbiota composition and function being closely associated with its onset and progression. However, the high inter-individual variability in gut microbiota complicates the identification of pathogenic mechanisms using traditional methods. In contrast, the smaller variability in gut microbial metabolites offers a more reliable and consistent basis for cross-individual comparisons. ResultsParsimonious Flux Balance Analysis (pFBA), integrated with Double Machine Learning (DoubleML), identified 17 metabolites significantly associated with hypertension (p < 0.05, RobustnessV alue > 0.1). These included meso-2,6-diaminoheptanedioate, p-hydroxyphenylacetic acid, cellobiose, dextran 40 (1,6--D-glucan), L-glutamic acid, kestopentaose, among others. Differential microbial correlation network analysis identified a key microbial sub-network, the FERM guild, consisting of 19 species, with prominent genera including Faecalibacterium,Enterobacter,Roseburia, and Methanobrevibacter. Using GSEA, the dysregulation of this guild was found to be strongly associated with a set of 17 hypertension-related metabolites(p = 0.017). Further analysis revealed that the contribution of FERM genus to key metabolites is significantly associated with blood pressure (p < 0.05), even without significant differences in their abundance; additionally, an imbalance exists between FERM genus and other species. ConclusionsOur findings reveal that hypertension is associated with a disruption of gut microbial diversity, structure, and metabolic function. Seventeen key metabolites related to blood pressure regulation were identified, exhibiting pro- or anti-hypertensive potential and linked to functional microbial modules. These results highlight the gut microbiota and its metabolites as promising targets for therapeutic intervention in hypertension.

bioinformatics↗

bioRxiv2025

Decoding Neoantigen-encoding Tumor-Specific Transcripts Unveils a Shared Target Reservoir for Immunotherapy in Hepatocellular Carcinoma

Background and AimsPrimary liver cancer, predominantly hepatocellular carcinoma (HCC), has limited therapeutic options. While mutation-derived neoantigen vaccine holds promise, its success is hindered by low antigen availability. This study explores transcriptome-derived neoantigens (neoantigen-encoding tumor-specific transcripts, neoTSTs) in HCC, characterizing their features, generation mechanisms, and therapeutic potential. Approach and ResultsWe analyzed RNA-seq data from 1,013 liver cancer patients and constructed a multi-layered reference dataset. Using a customized pipeline, we identified an average of 60 neoTSTs per patient, significantly surpassing mutation-derived neoantigens (neoMuts). NeoTSTs exhibited higher population frequencies, with 73.1% providing multiple epitopes, and were validated through mass spectrometry and HLA transgenic mouse models. Mechanistically, neoTSTs were generated via retained introns, transposable element activation, HNF4A-regulated alternative promoters, and de novo transmembrane domain (TMD) generation. Single-cell analysis revealed neoTSTs cover >75% of tumor cells and identified antigen-presenting cancer-associated fibroblasts (apCAFs) that enriched in immunotherapy responders and amplified CD4 T-cell responses via MHC-II presentation. In murine HCC models, neoTST vaccination outperformed neoMuts, inducing dual MHC-I/II activation and significant tumor growth inhibition. ConclusionsNeoTSTs represent a superior neoantigen source in HCC, compensating for the limitations of mutation-derived targets. Their abundance, sharedness, and dual MHC pathway activation highlight their potential for personalized immunotherapy, particularly in low-TMB tumors. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/692877v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1bedfedorg.highwire.dtl.DTLVardef@5f6c95org.highwire.dtl.DTLVardef@d1deb5org.highwire.dtl.DTLVardef@743e85_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Early-Life Commensal Lung Bacteria Shape Immune Responses and RSV Susceptibility in Neonatal Mice

The lung mucosa during the neonatal period and early infancy is especially susceptible to respiratory syncytial virus (RSV) infection. Respiratory disease severity is strongly influenced by the age at first exposure, which may also affect the trajectory of airway function. Early life represents a critical window for lung development and initial microbiota colonization, both of which shape mucosal immune responses to RSV. The contribution of early lung-colonizing bacterial strains to the establishment of the lung microbiota and susceptibility to RSV infection in neonatal mice remains poorly characterized. In the present study, we showed that early-life primo-colonizing bacterial strains in the mouse lung differentially induce innate immune responses and influence RSV susceptibility in ex vivo models using lung explants and alveolar macrophages (AMs). We identified a specific bacterial strain (strain 17) whose prior exposure enhances type I interferon (IFN-I) responses in AMs upon RSV infection and reduces viral replication both ex vivo and in vivo in lung tissues. Intranasal administration of this strain during early life prevented the development of immunopathological responses upon RSV reinfection in adult mice. Finally, using a translational human airway epithelium model, we demonstrated that pre-exposure to strain 17 restricts RSV spread without cytotoxicity, likely via enhanced {beta}-defensin 2 production. These findings highlight the potential of early-life microbiota modulation as a promising intervention for preventing RSV disease and its long-term respiratory consequences. Author summaryRespiratory syncytial virus (RSV) is a major cause of severe respiratory infections in newborns and infants, a period during which the lungs and immune system are still maturing. Simultaneously, the respiratory tract undergoes its first microbial colonization by so-called primo-colonizing bacteria -- the first bacterial species to establish themselves on neonatal lower respiratory mucosal surfaces. These early microbial pioneers may play an unsuspected role in shaping how the immature immune system responds to viral threats. In this study, we investigated whether these early lung-colonizing strains influence RSV susceptibility. Using neonatal mouse models, lung explants, and alveolar macrophages, we found that distinct bacterial strains trigger markedly different innate immune responses. Prior exposure to one strain in particular, strain 17, was associated with enhanced type I interferon responses, reduced viral replication, and protection against harmful inflammation upon RSV reinfection later in life. In a human airway epithelium model, pre-exposure to strain 17 also restricted RSV spread without tissue damage, potentially through increased {beta}-defensin 2 production. These findings provide proof-of-concept that the bacterial strains establishing in the neonatal lung can influence future immune reactivity and antiviral responses, and suggest that early-life respiratory microbiota modulation could represent a promising strategy to prevent severe RSV disease.

immunology↗

bioRxiv2025

MCA1 mechanosensitive channels enable fast communication of wound signals between lateral roots

Although plant roots are hidden in soil, they are vulnerable to damage by insect herbivory, just as like aerial tissues. Yet wound signalling in roots is poorly understood. Here, we examined how damage signals spread locally and over long distances between Arabidopsis lateral roots. Using intracellular membrane potential recordings, calcium imaging, and optogenetics, we show that mechanical injury triggers immediate local membrane depolarization and cytosolic Ca2+ elevations whose magnitude and duration scale with wound severity. Depolarizations were also detected in neighbouring lateral roots within milliseconds, demonstrating the presence of a rapid inter-root signalling pathway. Through mutant analyses, we highlight the roles of glutamate-like receptors and MCA1 mechanosensitive channels in mediating this long-distance communication. Our results demonstrate that a wound-induced decrease in root cell turgor pressure rapidly spreads across the root network, where neighboring roots decode this signal via MCA1. This work underscores fundamental differences between root and shoot wound responses and uncovers a mechanosensory basis for fast communication between lateral roots.

plant biology↗

bioRxiv2025

Tumor cell-specific loss of GPX4 reprograms triacylglycerol metabolism to escape ferroptosis and impair antitumor immunity in NSCLC

Glutathione peroxidase 4 (GPX4) is a master regulator of ferroptosis, a process that has been proposed as a potential therapeutic strategy for cancer. Here we have unexpectedly found that inducible knockout of GPX4 in tumor cells significantly promotes non-small cell lung cancer (NSCLC) progression in the autochthonous KrasLSL-G12D/+Lkb1fl/fl (KL) and KrasLSL-G12D/+Tp53fl/fl (KP) mouse models, whereas inducible overexpression of GPX4 in tumor cells exerts the opposite effect. GPX4-deficient tumor cells evade ferroptosis by upregulating the expression of DGAT1/2 to promote the synthesis of triacylglycerol (TAG) and oxidized TAG (oxTAG) and the formation of lipid droplets in cells. In addition, GPX4-deficient tumor cells secrete TAG and oxTAG into the extracellular space to induce dysfunction of antitumor CD8+ T cells, thereby coordinating an immunoinhibitory tumor microenvironment (TME). Consistently, treatment with DGAT1/2 inhibitors or inducible overexpression of GPX4 in tumor cells significantly resensitizes tumor cells to ferroptosis and ignites the activation of T cells in the TME to inhibit NSCLC progression. These findings highlight a previously uncharacterized role of tumor cell-specific GPX4 in NSCLC progression and provide potential therapeutic strategies for NSCLC.

cell biology↗

bioRxiv2025

Impact of N6-methyladenosine (m6A) machinery on HIV-1 replication in primary CD4+ T cells

N6-methyladenosine (m6A) is the most prevalent internal modification of cellular and viral RNA and is critical to the regulation of its localization, stability, and translation. Previous studies on the role of m6A during HIV-1 replication have produced conflicting results. Since m6A function can vary dramatically by cell type and state, here we aimed to clarify the role of the m6A machinery during HIV-1 replication in primary CD4+ T cells. Using CRISPR-Cas9 we targeted 46 cellular genes implicated in m6A or 5-methylcytosine (m5C) regulation and measured subsequent HIV-1 replication in primary CD4+ T cells. Only knockout of the m6A writer complex auxiliary proteins VIRMA and WTAP, and the m6A reader YTHDF2 were validated as significantly decreasing HIV-1 replication. In contrast, knockout of METTL3 or METTL14, which form the catalytic core of the writer complex, resulted in only marginal changes in HIV-1 infection, despite significant decreases in total cellular m6A levels. Chemical inhibition of METTL3 led to a dose-dependent decrease in HIV-1 infection, coupled with an increase in protein levels of METTL3 and other writer complex members. Expression of writer proteins was also co-dependent, revealing complex regulatory feedback mechanisms. Overall, these results clarify the role of epitranscriptomic machinery during HIV-1 replication in primary CD4+ T cells and suggest regulation by auxiliary members of the m6A writer complex is more influential than the function of the catalytic core itself on HIV-1 infection in primary CD4+ T cells. IMPORTANCEm6A is the most common chemical modification on cellular and viral RNA and regulates its stability, localization, and translation. m6A modification and its regulation varies dramatically between cell types and cell states. In this study, we investigated the role of m6A factors during HIV-1 infection of physiologically relevant primary CD4+ T cells. Using CRISPR-Cas9 to knockout 46 cellular genes implicated in RNA modification, we found only the m6A writer complex auxiliary members WTAP and VIRMA, and the reader YTHDF2, significantly affected HIV-1 replication in these cells. In contrast, knockout of METTL3 or METTL14, which form the catalytic core of the writer complex, resulted in marginal changes in HIV-1 infection, despite larger reductions in total cellular m6A levels. Our findings suggest regulation by auxiliary members of the m6A writer complex is more influential than the function of the catalytic core itself on HIV-1 infection in primary CD4+ T cells.

microbiology↗

bioRxiv2025

R-loops orchestrate the maternal-to-zygotic transition by harnessing RNA polymerase II pause release

R-loops, ubiquitous three-stranded nucleic acid structures abundant in the mammalian genome, play pivotal roles in diverse biological processes1-3. However, the dynamics and functions of R-loops during mammalian preimplantation embryonic development remain poorly understood. Here we optimized an innovative, ultra-sensitive RIAN-seq method capable of mapping genome-wide R-loop landscape using ultra-low cell numbers to investigate R-loop dynamics in mouse gametes and early embryos. Our findings reveal the widespread presence of AT-rich R-loops during early mouse embryonic development and highlight their critical roles in orchestrating transcription machinery during zygotic genome activation (ZGA). We demonstrate that the stability and inheritance of R-loops through developmental stages are governed by their sequence composition, with GC-rich R-loops exhibiting greater stability. Notably, R-loops, particularly AT-rich R-loops, inhibit DDX21 helicase activity on the 7SK/HEXIM1 snRNP complex, thereby reducing CDK9 release. This, in turn, modulates the phosphorylation of Ser2 at C-terminal domain (CTD) of RNA polymerase II (RNAPIIS2p) at the promoters of major ZGA and maternal genes. Furthermore, R-loops promote RNAPII accumulation at major ZGA gene promoters, preventing RNAPII from premature release and ensuring timely activation of major ZGA genes. Conversely, R-loops enhance the retention of stalled RNAPII at maternal gene promoters, effectively repressing their expression and facilitating the maternal-to-zygotic transition. In summary, our study unveils a key role for R-loops in regulating the maternal-to-zygotic transcription transition and early embryonic development in mice.

developmental biology↗

bioRxiv2025

Xanthomonas type III effector XopN targets scaffold protein OsRACK1B to suppress rice immunity

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a major bacterial disease that poses a substantial threat to rice production. Although Xoc deploys a variety of effectors to subvert host defenses, the mechanistic basis of how these effectors modulate plant immune signaling remains largely unclear. Here, we show that XopN suppresses rice immune responses and physically interacts with the rice scaffold protein OsRACK1B. Notably, OsRACK1B expression is induced following Xoc infection in a type III secretion system (T3SS)-independent manner. Functional analyses indicate that OsRACK1B overexpression enhances Xoc resistance, whereas loss-of-function mutants exhibit heightened susceptibility. This increased susceptibility is characterized by compromised immunity, including reduced callose deposition, diminished reactive oxygen species (ROS) accumulation, and attenuated expression of defense-related genes such as OsPBZ1 and OsPAL1. Furthermore, we demonstrate that XopN competes with OsRap2.6 for binding to OsRACK1B, thereby disrupting the formation of the OsRACK1B-OsRap2.6 immune complex. These findings reveal a novel virulence strategy in Xoc and identify promising gene targets for developing disease-resistant rice varieties.

plant biology↗

bioRxiv2025

Engineering Linear Cap-independent mRNA Vaccines with Intrinsic Adjuvanticity for Potent Cancer Immunotherapy

mRNA cancer vaccines have shown promising efficacy in early-phase clinical trials, but existing platforms struggle to boost antitumor efficacy without added cost or complexity. Here, we present a streamlined linear cap-independent RNA (LciRNA) cancer vaccine platform that achieves stable expression in vivo without 5 capping or ribonucleotide modification, and innately stimulates immune responses to enhance antitumor immunity. By fusing a UPA protective sequence, composed of a viral exoribonuclease-resistant RNA (xrRNA) and a poly(A) binding protein (PABP) motif, with an optimized Enterovirus A internal ribosome entry site, LciRNA resists 5 exonuclease decay and drives superior in vivo expression. Mechanistically, UPA sequence not only impedes exonuclease-mediated decay but also recruits RNA-binding proteins to stabilize LciRNA. Moreover, LciRNA robustly activates dendritic cell pattern-recognition receptor pathways, promotes dendritic cell maturation, and upregulates proinflammatory signals. In murine melanoma and HPV-associated tumor models, it elicits strong systemic and intra-tumoral T cell responses and superior tumor control, demonstrating how immune stimulation-translation synergy underpins its efficacy. This work establishes a next-generation cost-effective mRNA cancer vaccine platform with simplified production and enhanced efficacy, highlighting immuno-translation coupling as a paradigm for future mRNA cancer vaccines.

bioengineering↗

bioRxiv2025

Spatially-resolved Photoproximity Profiling of MYC Identifies a MYC-BAF Liability in Cancer Cells

The c-MYC transcription factor is aberrantly expressed in most human cancers to enhance expression of proliferative gene programs. Owing to its pseudo-ordered structure and reliance on extensive and dynamic protein-protein interactions in distinct transcriptional regulatory complexes, defining context-specific MYC interactors has remained challenging. Therefore, mapping MYC-centered complex topologies in disease relevant models could identify components critical for its function which may serve as therapeutic targets in MYC-driven cancers. Here, we present a matched pair of photoproximity probes coupled with quantitative proteomics which enable context-dependent mapping of protein complex topology inside cells. We applied this spatially resolved, intracellular photoproximity (siPROX) profiling workflow to map MYC interactomes across temporal, spatial and disease-relevant contexts. Basal and inhibitor-treated profiles confirmed interactions with a wide range of known chromatin-associated transcriptional regulatory factors that define the extended MYC transcriptional bubble in live cells. Time-resolved mapping of inhibitor treated cells identified dynamic remodeling of numerous transcriptional regulatory factors and identified several BAF complex members (e.g., PBRM1 and SMARCC1)1 that persist in the presence of bromodomain inhibition. Furthermore, spatial MYC topology maps in small cell lung cancer cells confirmed the presence of BAF complex members under conditions where MYC induced target gene expression, altered cell morphology and enhanced proliferation. Lastly, loss of BAF function via inhibition of SMARCA2/4 ATPase activity resulted in rapid loss of chromatin-bound and nuclear MYC levels, downregulation of MYC-dependent transcripts and MYC-specific cell growth in several cancer cell models. Together, these data highlight the potential for siPROX to identify spatially resolved, dynamic TF interactors and highlight MYC-proximal BAF interactions as a targetable liability to regulate MYC-dependent transcription and proliferation.

cancer biology↗

bioRxiv2025

Cytosolic Ca2+ as a universal signal for rapid root growth regulation

Roots must continuously adapt their growth and have evolved the ability to rapidly respond to diverse environmental and hormonal cues, including the phytohormone auxin. Auxin-induced cellular responses involve membrane depolarization, cytosolic calcium (Ca{superscript 2}) elevation, and extracellular pH increase, but how these processes lead to rapid growth regulation remains unclear. Here, we show that cytosolic Ca{superscript 2} acts as a universal signal integrating diverse cues for rapid regulation of root growth. Using live imaging, microfluidics, and optogenetics in Arabidopsis, we demonstrate that a swift rise in cytosolic Ca{superscript 2} is the primary target of auxin signaling affecting growth inhibition. Disruption of Ca{superscript 2} influx abolishes these responses, whereas light-gated Ca{superscript 2} influx from the apoplast or endoplasmic reticulum stores inhibits growth. Multiple unrelated stimuli--including auxin, extracellular ATP, RALF peptides, and hydrogen peroxide--converge on this Ca{superscript 2}-dependent mechanism. Cytosolic Ca{superscript 2} elevation thus represents a necessary and sufficient step for rapid growth inhibition, revealing a unifying principle of root signaling.

plant biology↗

bioRxiv2025

Clinical Interventions and Inflammatory Signaling Shape the Transcriptional and Cellular Architecture of the Early Postnatal Lung

The early postnatal period in human development is characterized by extensive remodeling of the distal lung to support gas exchange, but this critical period remains poorly understood. Here, we constructed a comprehensive cellular atlas of the early postnatal human lung (0 to 2 years) using single-nucleus RNA sequencing of histologically normal specimens from 23 individuals. Our analysis identified two previously unknown and mutually exclusive transcriptional states of alveolar type 2 (AT2) cells, one defined by upregulation of genes involved in lipid metabolism and identified by unique expression of FMO5, and the other defined by upregulation of inflammatory response genes and identified by unique expression of CFTR. Using spatial transcriptomics, we discovered that AT2 cell states reside in specific niches and interact with distinct alveolar fibroblast subtypes. Clinical data and organoid experiments further suggest that the environment dictates which state prevails as the pro-inflammatory/pro-regenerative signals TNF- and IL-1{beta} promoted the CFTR+ state in vitro, while patients treated with the anti-inflammatory drug dexamethasone (Dex) had more abundant FMO5+ AT2 cells, and Dex induced the FMO5+ state in vitro. These observations link inflammatory signaling and anti-inflammatory clinical interventions to shifts in transcriptional state of the alveolar epithelium. We benchmarked two neonatal lung diseases, bronchopulmonary dysplasia and pulmonary interstitial glycogenosis, revealing a profound disruption in the balance of AT2 states, a broad arrest of postnatal cellular development, and impaired cellular maturation. Our work uncovers a fundamental new understanding of early postnatal human lung biology, linking pro- and anti-inflammatory signaling to AT2 transcriptional phenotypes and providing a new framework for understanding lung disease.

developmental biology↗

bioRxiv2025

Presynaptic Release Probability Determines the Need for Sleep

Sleep is universal among animals with synapses, yet the synaptic functions determining the need for sleep remain elusive. By directly measuring synaptic transmission at anatomically defined synapses in Drosophila, we found that synaptic strength remained stable or declined after sleep deprivation in a circuit-specific manner. In contrast, presynaptic release probability (Pr) consistently decreased with sleep loss across circuits and species, stemming from reduced Ca2+ influx or weakened vesicle-channel coupling at presynaptic terminals, and recovered after sleep. Bidirectional manipulations of Pr altered sleep pressure, establishing a causal relationship between presynaptic function and sleep need. Non-synaptic sleep-regulatory signaling pathways consistently modulate Pr but not synaptic strength. Thus, our findings identify Pr, rather than synaptic strength, as the conserved synaptic substrate underlying sleep need.

neuroscience↗