Biology subjects

Sun, P.

Publications and source records attributed to Sun, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Decoding Cell-level Circadian Phase and Rhythm-state Remodeling in Single-cell Transcriptomes With scRhythmBayes

Current circadian omics analysis tools have been developed primarily for bulk time-series. However, heterogeneous single-cell datasets require analysis and interpretation of rhythmic programs across different cells, cell types, and biological conditions. In these datasets, cellular circadian phase is usually unobserved, and sample-level zeitgeber time provides temporal information but does not define the exact phase of every cell. Existing methods address only selected aspects of this problem and do not model how cell-level phase evidence informs gene-level rhythmic parameters and rhythm-state remodeling. Here we present scRhythmBayes, a new probabilistic algorithm for phase-resolved circadian analysis in heterogeneous single-cell transcriptomes. scRhythmBayes combines a seed-gene count likelihood with a stratum-aware circular prior to infer cell-level circadian phase, incorporates phase support into gene-level rhythmic modeling, and assigns posterior probabilities to interpretable rhythm-state categories, including rhythm gain, rhythm loss, amplitude remodeling and phase shifts. In heterogeneous simulations, scRhythmBayes achieved higher phase-recovery accuracy than existing phase-inference methods and maintained balanced performance across rhythmic gene detection, parameter recovery, and rhythm-state classification. Stress tests defined practical requirements for seed-gene support, zeitgeber anchoring, temporal sampling density, and cell number. In mouse liver, scRhythmBayes revealed distinct circadian phase occupancy and rhythm-state organization between periportal and pericentral hepatocytes, supporting a temporal dimension of liver zonation. It also identified cell-type-specific rhythmic markers that were largely distinct from conventional static markers, indicating that cellular identity includes temporal programs not captured by average expression. In human heart disease data, phase-coordination and phase-distribution analyses identified cell-type-selective temporal disorganization rather than uniform circadian disruption across the tissue. scRhythmBayes therefore provides a statistically grounded approach for resolving circadian organization across cells, genes, cell types and biological conditions.

bioinformatics↗

bioRxiv2026

VASP Promotes Aortic Valve Calcification by Interacting with FBLIM1 to Activate the Focal Adhesion Pathway

BackgroundCalcific aortic valve disease (CAVD) is the most prevalent valvular heart disease, yet there is no effective pharmacological therapy to halt or reverse its progression. Focal adhesions (FAs) are dynamic structures that connect cells to the extracellular matrix (ECM), serving not only as mechanical anchors but also as critical signalling hubs that regulate cell adhesion, spreading, migration, differentiation, and mechanotransduction. However, their specific role in CAVD pathogenesis remains largely unknown. MethodsTo identify upregulated hub genes, an integrated analysis of proteomics and RNA sequencing was performed on calcified aortic valves. To investigate functional roles in vitro, we utilized genetic knockdown and overexpression of VASP in valvular interstitial cells (VICs), followed by phenotypic evaluations of osteogenic differentiation, calcification, and elastin (ELN) secretion. Downstream mechanisms were explored using RNA-seq in VASP-overexpressing VICs, alongside pharmacological inhibition of the FA pathway. Finally, protein-protein interaction assays were conducted to map and analyze the physical binding between VASP and the structural domains of FBLIM1. ResultsIntegrated omics analysis identified VASP as a significantly upregulated gene in human calcified aortic valve tissues. Functionally, VASP knockdown inhibited, whereas its overexpression promoted, the osteogenic differentiation of VICs. RNA-seq revealed that VASP overexpression activated the FA pathway, and the pharmacological blockade of this pathway successfully suppressed calcification both in vitro and vivo. Mechanistically, we demonstrated a direct physical interaction between VASP and the third LIM zinc-binding domain of FBLIM1, and knockdown of FBLIM1 effectively reversed the pro-calcific effects of VASP. Finally, VASP overexpression was found to promote the secretion of ELN, which subsequently contributed to the calcification process. ConclusionOur study reveals that the interaction between VASP and FBLIM1 drives CAVD progression by activating the FA pathway, which subsequently leads to excessive ELN secretion. These findings reveal a novel mechanistic pathway and may provide a potential therapeutic target for CAVD intervention. What are the Clinical Implications?We have identified the VASP-FBLIM1-FA-ELN axis as a novel molecular pathway involved in CAVD pathogenesis, greatly enriching our understanding of the complex process of aortic valve calcification. This pathway intricately links cytoskeletal dynamics, cell adhesion signalling, and ECM remodelling, providing a new theoretical framework for pathophysiological research in CAVD. In clinical practice, VASP and its downstream pathway components, particularly FBLIM1 and the FA pathway, may serve as potential biomarkers and therapeutic targets for the early diagnosis and treatment of CAVD. For example, the FA pathway inhibitors PF-573228 and Y15 demonstrated significant anti-calcification effects both in vitro and in vivo, suggesting that targeting this pathway may offer a new nonsurgical intervention strategy for patients with CAVD.

cell biology↗

bioRxiv2026

Robust integration of weakly anchored spatial multi-omics

Spatial multi-omics holds great promise for dissecting complex biological processes, though inherent technical constraints continue to limit its widespread adoption. Currently, most studies therefore measure distinct omics features on separate tissue sections, necessitating spatial diagonal integration. An emerging practical solution is to leverage hematoxylin and eosin (H&E) images as an integration anchor, given their ubiquity, low cost, and compatibility across tissue preparations. However, this anchor is frequently compromised in real-world settings by variations in H&E staining style, absence of reliable histological landmarks, and mismatches in spatial resolutions across omics modalities. To address this, we introduce SpaWeaver, a computational framework that couples a pathology foundation model with a graph Transformer and a latent feature aligner module, providing a highly robust solution for weakly anchored spatial omics data diagonal integration. Extensive experiments demonstrate that SpaWeaver exhibits superior robustness against isolated or synergistic weak-anchoring factors. The spatial multi-omics profiles generated by SpaWeaver link molecular features originally separated on two sections, unlocking diverse downstream analyses once exclusive to co-assayed spatial multi-omics data, including niche-aware cell-cell communication inference and multi-omics resolved cell state. In this study, it unveils tumor-distance-dependent fibroblast-CD4{square}T-cell signaling in human colon adenocarcinoma and identifies a hypoxic glycolytic tumor state with pyknotic nuclei in human ovarian cancer. Overall, our approach bridges readily accessible single-omics measurements across weakly anchored tissue sections, enabling unified spatial multi-omics characterization and system-level tissue analysis.

bioinformatics↗

bioRxiv2026

Microfluidic-based high-throughput isolation enhances the recovery of novel strains and diversity from Arctic soil microbiome

Microbial cultivation remains essential for understanding the physiology, ecology, and biotechnological potential of environmental microbes, yet conventional plate-based methods (CPM) recover only a minute fraction of the environmental microbiome. Polar regions, particularly Arctic soils, represent unique reservoirs of "microbial dark matter" that remain challenging to cultivate, owing to oligotrophic conditions, low temperatures and freeze-thaw cycles that impose severe physiological constraints on microbial growth. Here, we report the first systematic application of microfluidic droplet technology (MDT) to Arctic active-layer soil microbiota and benchmark its performance against CPM using identical starting cell numbers, R2A medium, and incubation at 15{degrees}C. MDT achieved 6.5- to 8.1-fold higher recovery rates than CPM and improved isolation throughput by >180-fold. Near-full-length 16S rRNA gene sequencing (PacBio) revealed that MDT recovered significantly higher taxonomic richness across all taxonomic levels, with 256 genera detected in the high-cell-input group (DropAS_H) versus 211 in the corresponding plate group (PlateAS_H). Notably, MDT yielded a more even community distribution, significantly reducing the dominance of fast-growing copiotrophs such as Pseudomonas and Flavobacterium. Moreover, approximately 50% of sequences from MDT were affiliated with potential novel species (<98.46% identity to type strains), and 27% with potential novel genera (<95% identity). Strain verification by Sanger sequencing confirmed 12 of 17 isolates as candidate novel species, among which one strain represented a potential novel genus within Devosiaceae. This study demonstrates that MDT is a powerful platform for accessing the uncultured majority of polar soil microbiota and establishes a pipeline for high-throughput isolation of novel cold-adapted bacteria. IMPORTANCEArctic soils harbor a vast reservoir of microbial diversity that remains largely inaccessible due to the extreme oligotrophic conditions and low temperatures characteristic of polar environments, leading to slow growth rates and extended lag phases in most microbes. Conventional plate-based methods (CPM) inherently favor fast-growing copiotrophs while suppressing rare or slow-growing lineages. Here we demonstrate that microfluidic droplet technology (MDT) overcomes these fundamental constraints, representing its first systematic application to polar microbiology. By physically isolating individual cells into nanoliter-scale bioreactors, MDT mitigates interspecific competition, thereby releasing slow-growing and oligotrophic taxa that are otherwise outcompeted in bulk cultures. The water-in-oil emulsion format further enables extended low-temperature incubation without evaporative loss or airborne fungal contamination, issues that frequently compromise long-term plate-based cultivation of Arctic samples. Relative to CPM, MDT increased recovery rates by >6-fold and isolation throughput by >180-fold, while markedly enhanced both taxonomic richness and evenness. Exclusively recovered by MDT, the oligotrophic genus Caulobacter and numerous cold-adapted genera underscore that MDT accesses physiologically distinct fractions of the cryospheric microbiome. Furthermore, the integration of near-full-length 16S rRNA gene sequencing with MDT cultivation assessment provided substantially improved phylogenetic resolution for species-level identification and novel taxon delineation. Collectively, these findings establish MDT as a transformative platform for cryospheric culturomics, accelerating the construction of comprehensive polar strain collections essential for understanding cold-adaptation mechanisms and exploiting the biotechnological potential of Earths frozen microbiomes.

microbiology↗

bioRxiv2026

Ancestral Musaceae karyotype reconstruction provides insights into chromosome evolution and bract coloration

The banana family (Musaceae) exhibits remarkable diversity in both karyotype structure and bract coloration, yet the evolutionary dynamics of chromosomes and the genomic and regulatory basis underlying color diversification remain poorly understood. Here, we present a telomere-to-telomere (T2T), gap-free genome assembly of Musa exotica, an ornamental species with brightly colored bracts occupying an early-branching lineage within sect. Callimusa (Musa L.). By integrating this high-quality genome with other available Musaceae genomes, we reconstruct the ancestral Musaceae karyotype (AMK) for the first time, inferring a haploid chromosome number of n = 17. Comparative genomic analyses reveal recurrent, highly complex lineage-specific inter-chromosome rearrangements across extant Musaceae lineages, leading to inferred stepwise reductions in chromosome number to n = 11, 10, and 9. Notably, closely related species share similar rearrangement patterns, suggesting conserved evolutionary trajectories shaped by lineage-specific structural remodeling. Strikingly, rearrangement-associated regions are enriched for functionally important genes, particularly structural genes (CHS and F3H) and regulatory transcription factors (MYB and bHLH) involved in the anthocyanin biosynthesis pathway. Integrative transcriptomic and regulatory analyses further demonstrate coordinated activation of anthocyanin biosynthetic genes (CHS, CHI, F3'5'H, and ANS) in bracts, with expression divergence largely decoupled from gene dosage and predominantly driven by transcriptional regulation. Co-expression analyses reveal extensive MYB- and bHLH-enzyme interactions, underscoring their central role in modulating pathway activity and bract coloration diversity. Collectively, our findings suggest a link between genome structural evolution to trait diversification, offering a refined framework for understanding genome evolution and phenotypic diversification in Musaceae and other monocots. SignificanceWe reconstructed the ancestral Musaceae karyotype and revealed extensive lineage-specific chromosome rearrangements underlying karyotype evolution. Rearrangement-associated regions are enriched for anthocyanin biosynthetic and regulatory genes, suggesting that genome structural evolution may have contributed to bract coloration diversification in Musaceae. Integrative transcriptomic analyses further indicate that variation in anthocyanin-mediated bract coloration is more closely associated with transcriptional regulation than with gene dosage alone.

evolutionary biology↗

bioRxiv2026

A High-Fidelity 3D Fluid-Structure Interaction Framework for Predictive Microfluidic Design

The commercial maturation of microfluidics remains bottlenecked by empirical prototyping and an absence of predictive digital design capabilities. Because optimizing advanced technologies such as passive particle separation fundamentally hinges on the precise coupling of fluid dynamics and particle mechanics, conventional two-dimensional or decoupled fluid simulations inherently fail to capture authentic multiscale behaviors. To bridge this gap, we establish a high-fidelity three-dimensional fluid-structure interaction framework combining a high-order Arbitrary Lagrangian-Eulerian mapping-based finite element method with a localized hierarchical dynamic mesh strategy. Engineered to accurately resolve complex multiscale hydrodynamics, this architecture utilizes deterministic lateral displacement structures as a stringent test case. Validated against experimental data for rigid microspheres and tumor cells, the framework predicts transport trajectories and critical separation diameters with sub-micron precision. Crucially, the simulation explicitly resolves the M-shaped spatial fluctuation of local size thresholds alongside the dynamic vertical migration of particles. Unveiling these hidden physical mechanisms provides a deterministic explanation for highly debated phenomena such as mixed-mode transport. By enabling the rigorous in silico evaluation of complex non-periodic architectures, this framework serves as a powerful instrument for predictive structural optimization. Such capabilities establish the essential infrastructure for microfluidic digital design, accelerating the transition from empirical trial-and-error to precision simulation-driven engineering.

bioengineering↗

bioRxiv2026

MEIsensor: a deep-learning method for mobile element insertion discovery

Mobile element insertions (MEIs) are a critical source of structural variation in the human genome, yet their accurate detection remains challenging, particularly within repetitive regions and for structurally complex insertions. While long-read sequencing enables the direct recovery of inserted sequences, current analytical pipelines rely heavily on repeat-library alignment, which can limit both computational efficiency and accuracy. Here, we present MEIsensor, a deep learning framework designed to detect and classify MEIs directly from long-read sequencing data. Unlike conventional methodologies, MEIsensor performs direct, sequence-based annotation of Alu, LINE1, and SVA insertions. Evaluated against HGSVC benchmarks using HiFi long-read datasets, MEIsensor consistently outperformed existing tools across major MEI classes while substantially improving computational efficiency, demonstrating particularly pronounced gains for structurally complex SVA insertions. Furthermore, manual curation confirmed that MEIsensor successfully identifies MEIs hidden in highly repetitive genomic regions, including centromeric higher-order repeats, that were previously absent from benchmark datasets. Together, these advancements establish MEIsensor as an efficient framework for MEI analysis that promises to significantly advance our understanding of human genomic architecture and evolution.

bioinformatics↗

bioRxiv2026

Multi-omics analysis of the potential of MACC1 as a biomarker and therapeutic target for colonic adenocarcinoma

Colonic adenocarcinoma (COAD) is a major cause of cancer-related mortality worldwide. Various tumors are linked to metastasis-associated in colon cancer 1 (MACC1). This study aimed to analyze public datasets to examine MACC1 expression, signaling pathways, copy number variations, and associations with immune cell subsets in COAD employing bioinformatics. MACC1 expression was elevated in COAD, especially in Wnt signaling and chromatin modifier pathways. Analysis of somatic copy number alterations in The Cancer Genome Atlas-COAD dataset revealed a link between MACC1 and DNA damage repair. MACC1 also showed a negative correlation with genes involved in immune cell infiltration in patients with COAD, including cluster of differentiation (CD)8+ T cells, activated dendritic cells, CD8 T cells, and cytotoxic cells. Collectively, these findings suggest MACC1 as a potential prognostic biomarker and therapeutic target for COAD.

cancer biology↗

bioRxiv2026

Chronic exposure to low-concentration urban PM2.5 accelerates maladaptive repair after ischemic injury via mitochondrial dysfunction and lysosomal stress.

BackgroundFine particulate matter (PM2.5), airborne particles with an aerodynamic diameter [≤]2.5 m that can penetrate deep into the lungs and enter the circulation, is increasingly recognized as a risk factor for chronic kidney disease (CKD) with long-term exposure. We previously demonstrated that high-dose PM2.5 exposure prior to ischemia-reperfusion injury (IRI) aggravates acute kidney injury (AKI). Here, we investigated how prolonged, low-concentration urban PM2.5 exposure (<15 {micro}g/m3) affects kidney repair after AKI. MethodsSix-week-old mice underwent bilateral IRI or sham surgery, followed by six months of exposure to either filtered air or ambient PM2.5 exposure in a unique exposome chamber. Kidneys were analyzed using pathomics, electron and super-resolution microscopy, immunohistochemistry, transcriptomics, and LC-MS lipidomics/metabolomics. Complementary in vitro hypoxia-reoxygenation and PM2.5 exposure experiments were performed in proximal tubular epithelial cells. ResultsLong-term PM2.5 exposure had minimal effects in sham-operated mice, including no significant changes in body weight or kidney function. Despite preserved kidney function, IRI+PM2.5 mice exhibited reduced weight gain, a marked expansion of the interstitial area, attributable to enhanced fibrosis and inflammatory responses, microvascular rarefaction, and endothelial-to-mesenchymal transition, consistent with maladaptive repair features. Proximal tubules displayed mitochondrial injury, glycolytic reprogramming, lipid accumulation, and a senescent phenotype. Energy Dispersive X-ray (EDX) microscopy confirmed PM2.5-derived elements within proximal tubules lysosomes, accompanied by lysosomal stress. Transcriptional signature-based drug screening identified nicotinamide as a compound capable of reversing PM2.5-induced metabolic alterations; in vitro validation confirmed restoration of mitochondrial function. ConclusionsTogether, these findings show that chronic post-AKI exposure to PM2.5 at levels currently considered safe by regulatory bodies drives maladaptive repair and accelerates CKD progression through mitochondrial dysfunction, lysosomal stress senescence in proximal tubules, due to local PM2.5 element accumulation. Translational StatementAcute kidney injury frequently progresses to chronic kidney disease due to maladaptive repair, yet environmental drivers of this transition remain underrecognized. Using a controlled exposome chamber, we demonstrate that chronic exposure to low, real-world concentrations of urban PM2.5 during post-ischemic recovery results in the accumulation of PM2.5-derived elements within proximal tubular lysosomes, leading to organelle dysfunction, metabolic reprogramming, lipid accumulation, and a senescence-like phenotype. Importantly, transcriptomics-based drug repurposing identified nicotinamide as a candidate compound capable of reversing metabolic dysfunction in injured proximal tubular cells subjected to hypoxia-reoxygenation and PM2.5 exposure, an effect validated in vitro.

molecular biology↗

bioRxiv2026

Achieving spatial multi-omics integration from unaligned serial sections with DIME

Learning integrated representations from spatial multi-omics data is a fundamental challenge, particularly in the context of "diagonal integration", where data are collected from serial tissue sections across distinct omics modalities. Existing methods typically rely on the assumption of feature intersection to construct a common metric space, a prerequisite that is absent in this setting. To address this, we propose the Diagonal Integration Model for Spatial Multi-omics Embedding (DIME), a novel deep learning framework that couples a graph contrastive learning objective with cross-modal correspondence. This global correspondence is established by a hybrid alignment strategy: it first anchors high-confidence regions using Coherent Point Drift with Linear Assignment, and then extends matching to the entire tissue manifold via an Optimal Transport formulation encoding relative geodesic distances. Designed to balance inter-modal guidance with intra-modal structure preservation, DIME enables robust fusion and denoising. Experiments on simulated and real human tissue datasets demonstrate DIMEs superior robustness and versatility, where its learned representations achieve outstanding clustering accuracy and unlock the identification of biologically meaningful spatial domains. The code is available at: https://github.com/Spyyyyyyy/DIME

bioinformatics↗

bioRxiv2026

Diet-induced macrophage-driven inflammation fuels pancreatic plasticity and aggressiveness

High-fat diet (HFD) and obesity are increasingly recognized as risk factors of pancreatic ductal adenocarcinoma (PDAC), yet the mechanisms by which dietary fat contribute to oncogenic transformation remain elusive. Using an inducible acinar-specific KrasG12V/Trp53-loss genetically-engineered mouse model of PDAC, we established early-and late-onset protocols to assess age-dependent susceptibility to HFD. Specifically, HFD accelerated tumorigenesis with poorer prognosis in early-onset mice and, strikingly, enabled full PDAC development in late-onset adult mice otherwise resistant to oncogenic transformation. Tumors arising under HFD activated a distinct transcriptional and epigenetic state enriched in pathways or genes related to stemness, plasticity, and metastatic competence, which was maintained even in tumor-derived cell lines. Mechanistically, fatty acid-educated macrophages secreted the cathelicidin antimicrobial peptide (CAMP), activating P2X purinoceptor 7 (P2RX7) signaling in tumor cells to drive a highly plastic, immune-evasive phenotype reinforced by the expression of the peptidoglycan recognition protein 1 (PGLYRP1), further shielding tumor cells from macrophage phagocytosis. Functionally, HFD-induced tumors displayed enhanced metastatic potential independent of host context. Analysis of 164 human PDAC samples revealed that elevated body-mass index (BMI) was associated to a conserved CAMP-P2RX7-CXCR4 signature, maintained despite weight loss during disease progression. Together, these findings uncover a diet-imprinted macrophage-tumor cell circuit that promotes transformation and accelerates PDAC progression, positioning it as a therapeutic vulnerability in obesity-associated pancreatic cancer. Statement of significanceHigh-fat diet induces pancreatic tumorigenesis in adult tissue, driving metastatic competence and a plastic state, and ultimately engages a macrophage-derived CAMP-P2RX7 circuit that reinforces immune evasion and accelerates PDAC progression.

cancer biology↗

bioRxiv2026

NORAD orchestrates KLC1-mediated SFPQ transport via liquid-liquid phase separation

Neuronal function requires precise long-distance axonal transport mediated by molecular motors and RNA-binding proteins like SFPQ, though regulatory mechanisms remain poorly defined. We identify long non-coding RNA NORAD as a master regulator of this process through liquid-liquid phase separation (LLPS). While SFPQ and kinesin-1 mediate cargo delivery, the specific RNA coordinating their interaction was unknown. We demonstrate NORAD directly binds kinesin light chain 1 (KLC1) and promotes SFPQ condensation into dynamic LLPS droplets, enabling efficient transport. CRISPR-assisted mapping and functional assays show NORAD depletion disrupts granule dynamics, impairs neuroprotective mRNA localization, and induces axonal degeneration. In vitro reconstitution confirms NORAD-KLC1 synergy enhances SFPQ phase separation, and neuron-specific knockout mice exhibit motor deficits with reduced neuronal density. These findings establish the first evidence of lncRNA NORAD-mediated LLPS in axonal transport, revealing a new paradigm for RNA-guided neuronal maintenance.

molecular biology↗

bioRxiv2025

Oxa1L-Mediated Co-translational Protein Insertion Maintains Mitochondrial Function in Parkinson's Disease Models

Mitochondrial respiratory chain integrity relies on the coordinated synthesis and membrane insertion of mitochondrially encoded proteins. How limitations in this process contribute to mitochondrial dysfunction under stress remains poorly understood. Here, we identify the mitochondrial insertase Oxa1L as a key buffering factor that modulates mitochondrial vulnerability under Parkinsonian stress conditions. Transcriptomic analyses and cellular stress models reveal pronounced disruption of oxidative phosphorylation pathways accompanied by reduced Oxa1L abundance. Functional gain- and loss-of-function analyses demonstrate that Oxa1L actively influences mitochondrial membrane potential, reactive oxygen species levels, and ATP production during stress. Notably, Oxa1L selectively governs the abundance of mitochondrially encoded respiratory chain subunits, indicating that co-translational membrane insertion represents a rate-limiting step in mitochondrial protein biogenesis. Structural analyses position Oxa1L at the mitoribosomal exit site, providing a spatial framework for coupling translation to inner membrane insertion. Together, our findings uncover a critical layer of mitochondrial quality control at the level of co-translational insertion and establish Oxa1L as a determinant of mitochondrial resilience under stress.

cell biology↗

bioRxiv2025

Substrates Coupling and Inhibition of the human Na+- dependent Cl-/HCO3-exchanger

Maintaining pH homeostasis is essential for neuronal excitability and for regulating cerebrospinal fluid (CSF). The Na+-dependent Cl-/HCO3- exchanger, NCBE (SLC4A10), abundant in the choroid plexus, contributes to CSF pH control by mediating bicarbonate flux, yet its molecular mechanism has remained unclear. Here we report cryo-EM structures of human NCBE in multiple functional states, revealing conserved binding sites for Na+, Cl-, and HCO3-, as well as an unexpected K+ site indicating relaxed cation selectivity. The inhibitor DIDS binds above the substrate cavity, locking NCBE in an outward-facing conformation and defining a subfamily-selective inhibitory mechanism. Functional assays and molecular dynamics simulations validate ion coordination and inhibitor effects. Comparison of cryo-EM structures with an AlphaFold3 inward-facing model supports an elevator-like mechanism and completes the conformational cycle of Na+-coupled HCO3- transporters. Together, these findings define the structural basis of NCBE and provide a framework for understanding ion coupling and pharmacological modulation within the SLC4 family.

biophysics↗

bioRxiv2025

Dynamic alterations of DNA methylation and transcriptome in adaptation to and recovery from the space environment

Space exploration presents tremendous health challenges. Here, we report time series of multi-omic and phenotypic profiles of seventeen astronauts from six China Manned Space missions with continuous spaceflight durations ranging from 13 to 180 days. We revealed a key role of DNA methylation regulation in reshaping gene expression patterns to adapt to the space environment. Long-duration spaceflight showed more alterations in epigenetic modifications correlated with alternative splicing and protein acetylation. During recovery, an "overrange rebound" phenomenon was observed, furthermore, a mathematical model was established to describe this implying important phenomenon. Moreover, we revealed the correlations between molecular alterations and phenotypic changes such as coagulation activation and bone intensity loss. Additionally, we performed ground-based simulation experiments to estimate the impacts of individual stressors in the space environment on DNA methylation. In summary, our study highlights the importance and complexity of epigenetic regulation in adaptation to and recovery from the space environment.

genomics↗

bioRxiv2025

OSM-11 modulates salinity-stress tolerance in Caenorhabditis elegans

Most terrestrial animals exhibit narrow salinity tolerance compared to their marine counterparts. Previous studies identified osm-11 (which encodes a Notch co-ligand) mutations as a driver of hyper-saline tolerance in Caenorhabditis elegans, but mechanistic insights remained unclear. This study employs RNA sequencing and CRISPR/Cas-9 genome editing to demonstrate that osm-11 mutations enhance salinity stress resistance through up-regulation of fatty acid metabolism (acdh-12, acs-17) and cytochrome P450 pathways (ugt-15), while suppressing calcium signaling. Furthermore, we demonstrated that acdh-12 mutation impairs salinity-stress tolerance by activating ferroptosis and mitophagy, accompanied by down-regulated oxidative phosphorylation and up-regulated autophagic pathways. Morphological observations show that mitochondrial fragmentation contributes to wild-type nematode mortality under high salinity, while enlarged lipid droplets in wild-types correlate with reduced {beta}-oxidation gene expression (dhs-28, daf-22), whose knockout disrupts tolerance in mutants. These findings unravel the multi-pathway regulatory network of osm-11-mediated salinity tolerance, providing mechanistic insights for developing protective strategies against environmental salinity stressors impacting animal survival.

genetics↗

bioRxiv2025

The O-glycosyltransferase SECRET AGENT Participates in Abscisic Acid-Induced Microtubule Remodeling and Stomatal Closure in Arabidopsis thaliana

Secret Agent (SEC) encodes the major O-GlcNAc transferase in Arabidopsis thaliana and has been implicated in stress and signaling pathways, but its role in stomatal regulation remains unknown. In this study, we investigated the function of SEC in abscisic acid (ABA)-induced stomatal closure and drought responses. Loss of SEC function in the sec-5 mutant delayed stomatal closure and increased water loss under drought, whereas SEC overexpression enhanced stomatal responsiveness and drought tolerance. Pharmacological assays revealed that sec-5 was less sensitive to microtubule-stabilizing and -disrupting drugs during ABA-induced stomatal closing, consistent with a defect in cytoskeletal dynamics. Confocal imaging and quantitative analysis of microtubule rearrangements showed that SEC loss-of-function mutation retarded microtubule reorganization in response to ABA, with abnormal microtubule bundling and density. Mechanistically, SEC physically interacted with -tubulin 4 (TUA4) in both yeast two-hybrid and bimolecular fluorescence complementation assays, suggesting tubulin as a potential substrate of SEC-modified O-GlcNAcylation. Together, these findings establish SEC as a key regulator of ABA-induced microtubule remodeling in guard cells, thereby linking O-GlcNAcylation to stomatal regulation and drought tolerance.

plant biology↗

bioRxiv2025

A TARGETED COMBINATION THERAPY ACHIEVES EFFECTIVE PANCREATIC CANCER REGRESSION AND PREVENTS TUMOR RESISTANCE

Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest cancer survival rates. Recent studies using RAS(ON) inhibitors as single agents have opened the door to more efficacious therapies. Here, we demonstrate that genetic ablation of three independent nodes involved in downstream (RAF1), upstream (EGFR) and orthogonal (STAT3) KRAS signaling pathways leads to complete and permanent disappearance of orthotopic PDACs induced by KRAS/TP53 mutations. Likewise, a combination of RAS(ON) (RMC-6236/daraxonrasib), EGFR family (afatinib) and STAT3 (SD36) selective inhibitors/degraders induced the effective regression of these orthotopic tumors with no evidence of tumor resistance for over 200 days post-treatment. This combination therapy also led to significant regression of genetically engineered mouse tumors as well patient-derived tumor xenografts (PDX) in the absence of tumor relapses. Finally, this combination therapy was well tolerated by the animals. These results should guide the development of clinical trials that could benefit PDAC patients.

cancer biology↗