Biology subjects

Zhang, J.

Publications and source records attributed to Zhang, J..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Fetal MRI Reveals Altered Subplate Development in Congenital Heart Disease

Background: The subplate is a transient fetal brain compartment that provides an early foundation for downstream cerebral development. Congenital heart disease (CHD) alters fetal circulation and cerebral substrate delivery, but its impact on subplate development and whether resulting alterations relate to later neurodevelopmental outcomes remain unclear. Methods: In this retrospective observational cohort study, We used fetal MRI to quantify whole-brain, lobar, and regional (17 bilateral cortical regions) subplate volume and thickness to evaluate group differences between 76 fetuses with CHD and 62 typically developing (TD) fetuses scanned between 21-32 weeks of gestation, and estimated individualized deviations from TD developmental trajectories. Associations with fetal hemodynamic indices (substrate delivery score, cerebroplacental ratio [CPR]) and two-year neurodevelopmental outcomes (Bayley Scales of Infant and Toddler Development, N=46 CHD, N=37 TD) were explored. Results: Whole-brain subplate volume was lower in CHD, corresponding to a 5.7% reduction relative to age- and sex-expected values (p=0.003), but this difference was substantially attenuated after accounting for global brain volume (p=0.090). In contrast, regional analyses identified persistent spatially structured deviations beyond global scaling, most consistently involving posterior parietal, occipital and temporal regions, with a left-hemisphere bias in subplate thickness. Normative modelling demonstrated bidirectional regional deviations and increased inter-individual variability in CHD, with extreme subplate volume deviations enriched across 73% of cortical regions (p=0.009). Higher CPR was associated with lower SP thickness deviations, with the association strengthening after accounting for cerebral substrate delivery (p=0.010), although these analyses were exploratory. In CHD fetuses with postnatal follow-up, prenatal subplate deviations showed modest associations with neurodevelopmental outcomes, with right precuneus subplate thickness associated with receptive ({beta}=-11.87, q=0.017) and expressive ({beta}=-14.50, q=0.039) communication on the Bayley, after correction for multiple comparisons. Conclusions: Fetal subplate alterations in CHD are dominated by global reductions in brain growth but also include spatially heterogeneous and individually variable regional deviations beyond global scaling. Exploratory associations with fetal hemodynamics and postnatal neurodevelopment provide hypotheses for future studies investigating the developmental significance of these prenatal alterations.

neuroscience↗

bioRxiv2026

Auditory attention improves scale-invariant neural fidelity to speech across three EEG datasets

Neural speech tracking is stronger for attended speech, yet its common correlation-based readout is scale invariant, so interpreting this effect only as response gain is incomplete. We tested whether attention improves representational fidelity, defined here as scale-invariant agreement between a speech envelope and its neural reconstruction. A leakage-resistant analysis evaluated held-out trials or story parts in three public electroencephalography datasets (52 participants). Fidelity was Fisher-transformed reconstruction-envelope correlation; projection slope quantified scale-dependent gain. In the spontaneous Auditory Attention Switching Dataset, nine odd- numbered participants were used for discovery and nine even-numbered participants for split- sample validation. Fidelity was higher for attended speech in the validation sample and exceeded 5,000 within-trial circular label shifts. The effect replicated under story-part-disjoint validation in KUL and trial-disjoint validation in DTU. A KUL crossover compared the same clean speech sources in attended and ignored states. Across 4,819 isolated spontaneous switches, fidelity did not differ from baseline before the report but shifted toward the newly reported target 0.25-1 s afterward. Passive keypresses altered nonspecific decoder energy. Gain advantages also occurred in all datasets. Selective attention was therefore evident in the scale-invariant preservation of target dynamics, while gain remained a complementary feature.

neuroscience↗

bioRxiv2026

Brain State Dynamics and Developmental Differences in Reading Comprehension

Reading comprehension is a complex cognitive task that involves dynamic interactions between the brain and external information. Previous studies on reading development primarily focused on localized or static brain activities. However, it remains an enigma how brain state dynamics evolve with development underlying reading comprehension. This study aims to address this issue by combining functional magnetic resonance imaging (fMRI) with Hidden Markov Model (HMM) to explore brain state dynamics. A total of 35 typically developing children and 31 adults were scanned while reading a story. Our results demonstrated a tripartite brain state organization, characterized respectively by high activities in the visual (State #1), language (State #2), and default mode network (DMN, State #3) regions. Children exhibited significantly longer dwell time in the DMN state (State #3) compared to adults, along with a higher probability of transitioning from the language state (State #2) to the DMN state (State #3). In addition, adults exhibited greater flexibility in state transitions during reading comprehension. Finally, the alignment between the dynamic states of children and the average states of adults was a significant positive predictor of their reading comprehension performance. This study provides a novel, intuitive perspective on how brain state dynamics evolve during the development of reading comprehension.

neuroscience↗

bioRxiv2026

A haplotype-based breeding framework for the precise pyramiding of elite QTL alleles: a lettuce case study

The efficient pyramiding of favorable alleles underlying complex traits remains a major challenge in crop breeding as most quantitative trait loci (QTLs) have not been resolved to causal genes, limiting their direct application in marker-assisted breeding. Although haplotypes provide more informative genetic units than individual markers, existing haplotype-based studies have largely focused on genetic interpretation and elite haplotype discovery, whereas computational frameworks for translating haplotypes into breeding decisions remain limited. Here, we developed HAPBDB, a haplotype-guided breeding framework that directly translates regional haplotypes into parental selection, cross design, and elite QTL pyramiding, and applied it to a lettuce genomic breeding panel. HAPBDB accurately reconstructed functional haplotypes at known loci and resolved elite haplotypes for five major QTLs controlling flowering time and yield. Integrating haplotype information across loci enabled systematic identification of accessions carrying complementary elite haplotypes and rational design of crosses that maximized favorable haplotype accumulation while minimizing segregating loci. Experimental validation using QTL-specific molecular markers demonstrated concordance between predicted and observed multi-locus genotypes across all designed F hybrids. Our results demonstrated that regional haplotypes can serve as practical breeding units even when the underlying causal genes remain unknown, thereby enabling the direct utilization of genetically mapped QTLs for precision breeding. By bridging the gap between genomic discovery and practical breeding, HAPBDB provides a practical framework for converting genomic information into breeding decisions and accelerating precision improvement of complex traits.

bioinformatics↗

bioRxiv2026

Port of Protein-Protein Interactomes: An experiment-based protein-protein interactome database for rice

Protein-protein interactions (PPIs) play a crucial role in enabling proteins to carry out their functions within various biological processes (Hui et al., 2003). Since the introduction of the yeast two-hybrid (Y2H) method for PPI detection in 1989 (Fields and Song, 1989), the identification of PPIs has become a significant focus in modern biological research. PPI goes beyond examining individual proteins, allowing researchers to establish a comprehensive network that regulates biological processes. Rice, as a key model organism in plant biological studies, has been at the forefront of PPI research. In 2008, prominent rice scientists in China called for concerted efforts to define a comprehensive protein-protein interaction network experimentally, which aimed to facilitate the prediction of the functional mechanisms operating throughout a plants lifecycle (Zhang et al., 2008). With efforts for 2 decades, the experimentally identified rice PPIs have reached over ten thousand. Several public databases have been established to systematically collate and store PPIs, including STRING (Szklarczyk et al., 2019), BioGRID (Oughtred et al., 2020), IntAct (del Toro et al., 2022), PRIN (Gu et al., 2011), RicePPINet (Liu et al., 2017) and RiceNet v2 (Lee et al., 2015). However, most PPI datasets in rice stem from computational predictions, while experiment-based rice PPI datasets are fragmented due to the lack of systematic profiling at the rice PPIome level, which largely hinders information sharing in the rice research community. To bridge this gap, we constructed the Port of Protein-Protein Interactomes (POPPIN; https://riceome.hzau.edu.cn/poppin/), an integrated database dedicated to sharing experimentally verified PPIs and functional clues in rice. Empowered by high-throughput PPIome profiling technologies and text mining assisted by a large language model (Huang et al., 2025; Liu et al., 2025), POPPIN currently has deposited over 150,451 pieces of rice PPI-related information. Additionally, POPPIN provides detailed protein information, including GO annotations, subcellular localizations, domains, trait ontology (TO) information, and hyperlinks to external biological databases. Through offering a user-friendly web interface for search and dynamic network visualization, POPPIN serves as the first large-scale, experiment-based database for searchable PPIs in rice, and has the potential to be extended to other species under this structural framework.

systems biology↗

bioRxiv2026

From distyly to stigma-height dimorphism: phylogenetic insights into the evolutionary breakdown of distyly in Jasminum

Background and AimsDistylous polymorphisms (distyly) are adaptations for plants to improve efficiency of cross-pollination and reduce pollen wastage. Theoretical models suggest that distyly evolves from stylar monomorphism via an intermediate stage of stigma-height dimorphism (SHD), however, this evolutionary scenario is only observed in few distylous lineages. The genus Jasminum have many species exhibit either distyly or SHD, providing an ideal opportunity to test models of the evolution of distyly. Focusing on the evolution of distyly, we investigated floral morphs and evaluated the occurrence of distyly and SHD in Jasminum using phylogenetic reconstruction and morphological analysis. MethodsWe investigated floral morphs and evaluated the occurrence of distyly and stigma-height dimorphism through morphology observation. To perform phylogenetic analysis, we sequenced plastomes of forty species from Jasminum and Chrysojasminum using Illumina next generation sequencing, and then constructed phylogenetic tree using maximum likelihood method and Bayesian inference. Based on the phylogenetic tree, we inferred the ancestral floral type through ancestral reconstruction. Key ResultsOur results suggest that the distyly originated in the common ancestor of Jasminum and Chrysojasminum. SHD occurs in several Jasminum species scattered in different clades of the phylogenetic tree, suggesting multiple independent reversions from distyly back to SHD. However, this transition is not associated with the loss of ancillary polymorphisms, as all the species examined in this study well retain dimorphic traits for other floral organs such as pollens and stigmas. Moreover, most species maintain strict heteromorphic self-incompatibility, while J. officinale has lost or at least partially lost self-incompatibility, suggesting that distyly is not always linked to self-incompatibility. ConclusionsIn Jasminum, breakdown of distyly resulted in evolutionary transitions to stigma-height dimorphism for multiple times, suggesting that distyly is not a stable floral polymorphism under certain selective forces. These findings advance our understanding on the evolution of distyly and plant reproductive systems.

plant biology↗

bioRxiv2026

PASTRI: Resolving Stage-Specific Cell-State Dynamics from Annotated Cell Lineage Trees

Cellular transitions between phenotypic states are fundamental to development and disease, yet quantitative analysis of their dynamics remains challenging. Here we present PASTRI (Phylogenetic Adjacency-based State Transition Rate Inference), a computational framework that infers transition rates from cell lineages/phylogenies annotated with terminal phenotypic states, such as single-cell transcriptomes. We validate PASTRI using simulated lineages and the Caenorhabditis elegans embryonic lineage. Importantly, by leveraging cell pairs at varying phylogenetic distances, PASTRI accurately resolves stage-specific transition rates, circumventing the issue of developmental changes in dynamics. Applied to three cell phylogeny datasets from our lineage-tracing experiments spanning diverse developmental/disease models and tracing systems, PASTRI uncovers rate-limiting steps in the activation of hepatic stellate cells and the differentiation of primordial lung progenitors, as well as attractor states that support cancer cell proliferation. PASTRI thus opens up a venue for dissecting cell state transition dynamics from annotated cell lineage/phylogeny.

bioinformatics↗

bioRxiv2026

TROP2-targeting chimeras (TRTACs) for tumor-selective membrane protein degradation and enhanced drug delivery

Extracellular targeted protein degradation (eTPD) systems typically utilize lysosome-targeting receptors (LTRs) to mediate internalization and lysosomal degradation of extracellular and membrane proteins. While multiple LTRs have been discovered, there remains a compelling need to seek for new LTRs, particularly those with clear clinical relevance, to expand the therapeutic potential of eTPD. Here we report trophoblast cell surface antigen-2 (TROP2), a clinically validated tumor-associated antigen, as a promising tumor-selective LTR. We engineer TROP2-targeting chimeras (TRTACs) by genetically fusing a TROP2-binding nanobody to nanobodies against specific target proteins. We show that TRTACs can induce tumor cell-selective degradation of diverse membrane proteins, including epithelial growth factor receptor (EGFR), human epithelial growth factor receptor 2 (HER2), and programmed death-ligand 1 (PD-L1). The EGFR-targeted TRTAC significantly inhibits tumor cell proliferation and shows potent antitumor activity in vivo. We further design TRTAC-drug conjugates (TRTAC-DCs) by attaching cytotoxic payloads to TRTACs, enabling targeted protein degradation together with enhanced drug delivery. TRTAC-DCs show significantly enhanced activity against HER2- and EGFR-positive tumors both in vitro and in vivo, with minimal toxicity observed in normal tissues. These findings establish TROP2 as a robust LTR and provide a versatile eTPD platform with profound translational potential for tumor treatment.

cell biology↗

bioRxiv2026

The HES1-SOD1 Antagonism Shapes Senescence Heterogeneity and Impacts Metastatic Relapse of Circulating Tumor Cells

Circulating tumor cells (CTCs) encounter multiple challenges within the blood microenvironment, including oxidative stress, flow shear forces, and immune surveillance, often leading to anoikis. Recently, a transitional state of CTC senescence has been identified, contributing to metastatic inefficiency. However, the molecular mechanisms linking senescent CTCs to disease relapse remain to be defined. By integrating a genetic model of cortactin knockdown-induced CTC senescence with single-cell multi-omic analyses, we revealed two distinct senescent CTC subpopulations marked by HES1 expression levels. These HES1low and HES1high subpopulations exhibited differential evolutionary trajectory dynamics and unique molecular and metabolic signatures, which were significantly correlated with adverse clinical outcome across several patient cohorts. HES1low senescent CTCs displayed enhanced mitochondrial fitness, oxidative phosphorylation, and ROS-detoxifying capabilities, resulting in more efficient tumor regrowth with a pro-inflammatory and thrombotic phenotype when compared to the HES1high group. Mechanistically, HES1 directly bound to the Sod1 promoter and repressed its expression, leading to redox imbalance and mitochondrial dysfunction that were linked to weakened tumor regrowth capacity. Both senescent CTC subpopulations were broadly resistant to cytotoxic and targeted therapies, yet they showed elevated dependency on anti-apoptosis programs that make them susceptible to dual blockade by SOD1 inhibitor and the anti-senolytic drug ABT737 in vivo. Finally, in a prospective cohort of on-treatment melanoma patients, HES1 senescent CTCs were highly enriched in patients with progressive disease. Thus, the HES1-SOD1 antagonism shapes CTC senescence heterogeneity and contributes to differential tumor relapse, which can be therapeutically explored for eliminating residual metastatic disease.

cancer biology↗

bioRxiv2026

Endothelial ANGPT2 insufficiency impairs retinal vascularization with ROP-like neovascular tufts

ANGPT2 is widely recognized as a critical regulator of pathological neovascularization. By analyzing scRNA-seq data from neonatal retinas, we demonstrate that Angpt2 transcripts are highly enriched in tip cells relative to other endothelial subtypes, where Angpt1/4 expression is absent. However, mechanisms underlying ANGPT2 function at angiogenic fronts remain inadequately understood. Here, we show that endothelial Angpt2 deletion severely disrupted retinal vascularization, characterized by neovascular tufts and micro-hemorrhage. Similar angiogenic defects also occurred in the brain, but were less evident in other tissues examined. Mechanistically, ANGPT2 insufficiency attenuated retinal tip cell invasion with aberrant mural cell coverage, compromising sprouting into non-vascularized tissues. Retinal RNA-seq analysis revealed that transcripts associated with endothelial migration and junction assembly were reduced in Angpt2 mutants compared to littermate controls, while upregulated genes were enriched in hypoxia-responsive pathways and mural cell development. Notably, abnormal mural-tip cell associations were detected within 48 hours post-Angpt2 deletion, displaying also a hypoxia-driven transcriptomic signature. These closely resemble the vascular pathologies observed in human retinopathy of prematurity. In contrast, Angpt1 insufficiency or Angpt4 deficiency primarily affected venous morphogenesis. Collectively, our findings imply that ANGPT2 is essential for driving tip cell invasion during sprouting angiogenesis, and that its insufficiency triggers hypoxia-driven vascular anomalies.

developmental biology↗

bioRxiv2026

Sequential division of labor between PAXX and XLF drives NHEJ synaptic complex stability and maturation

DNA double-strand breaks (DSBs) are primarily repaired by non-homologous end joining (NHEJ), which tethers and ligates DNA ends within a synaptic complex. PAXX is an NHEJ accessory factor related to XRCC4 and XLF, but its mechanistic role and genetic interaction with XLF are unclear. Using biochemical assays and single-molecule imaging within Xenopus laevis egg extracts and human cell assays, we show that PAXX bridges DNA ends by using its disordered tails to bind opposing Ku molecules. This PAXX tether substantially extends long-range synaptic complex (LRSC) lifetime and modestly stabilizes the short-range synaptic complex (SRSC). LRSC stabilization increases XLF residence and promotes the LRSC-to-SRSC transition. Using domain-swapped chimeras, we demonstrate that PAXXs tails provide synaptic stabilization, whereas XLFs heads interact with XRCC4 to drive the LRSC-to-SRSC transition: an XLF head-PAXX tail chimera recapitulates the functions of both proteins, revealing complementary, sequential roles for PAXX and XLF in NHEJ.

biophysics↗

bioRxiv2026

Myeloid-targeted RNA nanotherapeutics rewire cholesterol metabolism to unleash anti-tumor immunity in glioblastoma

Tumor-associated myeloid cells (TAMCs) dominate the glioblastoma (GBM) microenvironment and suppress anti-tumor immunity. Here, we identify cholesterol efflux via ABCA1 as a targetable metabolic checkpoint controlling TAMC immunosuppression in GBM. Reprogramming TAMC cholesterol metabolism using TAMC-targeting lipid nanoparticle encapsulating ABCA1 siRNA (ABCA1 LNP) converts TAMCs into potent antigen-presenting cells with enhanced pro-inflammatory activity and antigen-presenting capacity, thereby inducing T cell activation, expansion, and tumor infiltration. Mechanistically, ABCA1 blockade induces cholesterol accumulation in TAMC membranes, promoting lipid raft formation and enhancing MHC-I-mediated antigen presentation. In multiple preclinical GBM models, ABCA1 LNP treatment dramatically induces T cell priming, extends animal survival, and overcomes GBM resistance to radiotherapy and immune checkpoint therapy. This efficacy was well-maintained in stem-like and recurrent GBM models, GBM patient specimens, and a renal cell carcinoma model. Altogether, our work identifies cholesterol efflux as a targetable metabolic vulnerability in TAMCs to overcome therapy resistance in myeloid-rich, immunologically "cold" tumors.

immunology↗

bioRxiv2026

IGF2BP3 amplifies antiviral innate immunity with implications for autoimmune diseases

The insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) is a known N6-methyladenosine (m6A) reader, but its role in antiviral innate immunity is unknown. Here, we identify IGF2BP3 as a critical positive regulator of antiviral responses. Viral infection and interferon (IFN) stimulation upregulate IGF2BP3, establishing a feedforward loop that potentiates virus-induced activation of the TBK1-IRF3 and NF-{kappa}B pathways, thereby amplifying type I interferon (IFN-I) production, and restricting viral replication in human and murine cells and in vivo. Mechanistically, IGF2BP3 directly binds and stabilizes MAVS and TBK1 mRNAs and promotes their translation by facilitating recruitment to the eIF4F/PABP-associated initiation complex. Upon infection, IGF2BP3 relocalizes to antiviral stress granules (avSGs), where it scaffolds the RIG-I-G3BP1 complex to enhance viral RNA sensing. Notably, IGF2BP3 is aberrantly upregulated in patients with systemic lupus erythematosus (SLE) and in Trex1 knockout (KO) mice, and pharmacological inhibition by curcumol suppresses IFN-I-driven pathology and improves survival. Collectively, our findings establish IGF2BP3 as a central feedforward circuit that couples viral RNA sensing to the control of RNA stability and translation of key signaling molecules, and reveals its potential as a therapeutic target in interferon-associated autoimmune diseases. Significance StatementAntiviral immunity demands rapid and coordinated gene expression, yet how RNA-binding proteins link viral recognition to downstream signaling is poorly understood. We reveal that the m6A reader IGF2BP3 acts as a central amplifier of antiviral innate immunity. Induced by both viruses and interferons, IGF2BP3 enhances viral RNA sensing, stabilizes key signaling transcripts, and boosts their translation, creating a self-reinforcing feedforward circuit that strengthens interferon responses. Beyond host defense, IGF2BP3 is aberrantly elevated in interferon-driven autoimmunity, and its pharmacological inhibition reduce disease pathology in vivo. Our findings uncover a previously unrecognized mechanism that integrates RNA metabolism, stress-granule signaling, and translational control to regulate innate immunity, offering new therapeutic perspectives for both infectious and autoimmune disease.

immunology↗

bioRxiv2026

MMMAS: A Mendelian Mismatch Matrix Analysis System for Deterministic Pre-Screening of Germplasm Collections

Pedigree errors, duplicate accessions, and undocumented kinship limit the effective use of large genebank collections. Existing tools such as CERVUS and COLONY require allele-frequency estimates and return relationship-level assignments, providing no collection-wide view of Mendelian consistency. We developed the Mendelian Mismatch Matrix (MMM) framework and its open-source implementation, MMMAS (Mendelian Mismatch Matrix Analysis System). We applied MMM to apple (Malus x domestica; 1,085 accessions, 15 SSRs) and sweet cherry (Prunus avium; 383 accessions, 13 SSRs) datasets from the German Fruit Genebank. MMM converts pairwise Mendelian mismatch numbers (Mmn) into an N x N symmetric matrix, from which we derive four collection-scale indices (Mmin, the Mendelian minimum mismatch number; Mavg, the Mendelian average mismatch number; Mzmp, the Mendelian zero-mismatch partner number; Mmmd, the Mendelian mismatch-mode duplication index) and the Mendelian Exhaustive Stratification (MES) grading system. Apple showed a gradient-type structure (Mendelian Grade-gap Index, MGI = 0.125), sweet cherry a broken-type structure (MGI = 0.545). The Mmin-Mavg strategy identified 20 and 10 distinct accessions in apple and sweet cherry, including the scab-resistance donor Malus x floribunda 821 (Rvi6) and the fire-blight donor M. x robusta 5. The Mmmd index flagged one literature-confirmed pair of duplicate genotypes in sweet cherry. Of CERVUS-confirmed parent-offspring pairs, 97.31% in apple and 100% of high-confidence pairs in sweet cherry fell within Mmn <= 1. Mzmp rankings matched documented breeding history, with 'Cox Orange' (Mzmp = 57) and 'Luebecker Bunte' (Mzmp = 49) ranking first in each species. The complete end-to-end analysis of all 588,070 apple pairwise comparisons took 7.24 s on an ordinary workstation. This deterministic pre-screening framework, with a parameter-free core, supports routine quality assessment in germplasm collections.

genetics↗

bioRxiv2026

Pharmacologic eIF2B Activation Rescues Neuropathy in CMT2 Subtypes by Normalizing the Integrated Stress Response

Among the many subtypes of Charcot-Marie-Tooth (CMT) disease, several result from mutations in genes encoding aminoacyl-tRNA synthetases, enzymes required for tRNA charging during cytoplasmic and mitochondrial translation. We report that activation of the integrated stress response (ISR) pathway is a shared molecular feature of tRNA synthetase-associated and other axonal CMT subtypes. RTX-117, a CNS-penetrant small molecule currently in Phase 1 clinical trials, targets eukaryotic initiation factor 2B (eIF2B), a key modulator of protein synthesis and the ISR pathway. Using cryo-EM studies, we have characterized the binding mode of RTX-117 to the eIF2B decamer. In GarsP278KY/+ mice, which develop early onset motor defects and axonal pathology that recapitulate CMT2D symptoms from tRNA synthetase mutations, RTX-117 treatment started after disease onset reduced chronic ISR activation and produced significant functional and electrophysiological improvement. We further identify ISR targets, including secreted proteins such as GDF15 and FGF21 that may serve as translational biomarkers for treatment response to RTX-117 in CMT disease. Broader surveillance of the ISR pathway across models of neurodegeneration reveals strong activation in several diseases and a correlation with disease progression, particularly in models of Alzheimers disease. These findings identify chronic ISR activation as a recurrent, though not universal, pathological mechanism of neurodegenerative disease models. Overall, our study identifies candidate biomarkers for CMT disease subtypes associated with defects in translational homeostasis and supports eIF2[a]-ATF4 axis modulation as a promising therapeutic strategy for this disease class. One Sentence SummaryRTX-117, a clinical stage eIF2B activator, blunts chronic ISR activation and improves nerve and motor function in a mouse model of Charcot-Marie-Tooth Disease Type 2D.

cell biology↗

bioRxiv2026

Bone Lymphatic Endothelial Cells Form a Distinct Skeletal Population and Drive Skeletal Repair

Bone regeneration relies on specialized vascular niches, yet the contribution of lymphatic vessels across distinct skeletal sites remains poorly understood. Here, we identify bone lymphatics as an essential component of the regenerative microenvironment in the mandible and long bones. We demonstrate that bone lymphatic endothelial cells (LECs) constitute a specialized endothelial population that is transcriptionally and spatially distinct from periosteal LECs. During skeletal repair, bone LECs reactivate a regenerative transcriptional programme, and promote mandibular and fracture healing. In osteonecrosis of the jaw and periodontitis, bone lymphatic-associated signalling is disrupted, identifying impaired lymphatic function as a shared feature of mandibular disease. Therapeutic activation of VEGFC-FLT4 signalling during injury or mandibular disease restores lymphangiogenesis, enhances osteogenesis, and markedly improves bone regeneration. Together, our findings advance the paradigm-shifting role of bone lymphatics positive regulators of bone regeneration and identify lymphatic activation as a promising therapeutic strategy to enhance bone regeneration in mandibular diseases.

cell biology↗

bioRxiv2026

Liriodendrin Targets PFKFB3 to Suppress Inflammatory Phenotypic Transition and Vascular Remodeling in Pulmonary Hypertension

BackgroundPulmonary hypertension (PH) involves progressive vascular remodeling and perivascular inflammation. Despite modest clinical improvements with current therapies, their limited ability to reverse remodeling or restore immune homeostasis highlights the need for novel agents. Liriodendrin (Lidd), derived from Sargentodoxae caulis, exhibits anti-inflammatory and antiproliferative activities, but its efficacy and molecular targets in PH are unknown. MethodsTwo well-established PH animal models - the SU5416/hypoxia (SuHx) mice model and monocrotaline (MCT)-induced rat model - were employed for in vivo assessment of Lidd conducted pharmacological effects. Primary human pulmonary artery smooth muscle cells (hPASMCs) were utilized for mechanistic investigations. RNA-sequencing (RNA-seq) analysis was conducted to identify potential signaling pathways modulated by Lidd treatment. The direct molecular target of Lidd was determined through integrated application of drug affinity responsive target stability (DARTS) assay coupled with western blot validation. To delineate histone lactylation-mediated transcriptional regulation, we combined Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing data analysis followed by chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) verification. Genetic validation was achieved using PFKFB3-deficient murine models to verify the specificity of Lidd-mediated pharmacological actions. ResultsLidd administration attenuated pulmonary vascular remodeling, perivascular macrophage infiltration and PH progression in both SuHx and MCT models. Transcriptomic profiling of Lidd-treated hPASMCs revealed predominant enrichment of downregulated genes in inflammatory and cytokine-associated pathways. Mechanistically, Lidd directly bound PFKFB3 and enhanced its interaction with FZR1, promoting PFKFB3 ubiquitination and degradation, which reduced glycolysis-driven lactate and consequent histone lactylation. This, in turn, diminished transcriptional activation of proliferative and inflammatory mediators, including CCND1, TNC, and CCL2. Notably, exogenous lactate supplementation or endogenous lactate accumulation restored histone lactylation and paradoxically potentiated Lidds inhibitory effects on PASMC proliferation and migration, whereas p300 inhibition abrogated these lactate-mediated effects. Importantly, Lidd failed to confer additional protection in PFKFB3-deficient mice, confirming PFKFB3 as the primary target mediating its therapeutic action. ConclusionOur findings reveal that Lidd selectively targets the PFKFB3-mediated glycolytic-epigenetic axis to suppress PASMC phenotypic transformation and pulmonary vascular remodeling, positioning it as a promising therapeutic candidate for PH.

physiology↗

bioRxiv2026

LightAlign: a lightweight pairwise aligner for memory-constrained HiFi read assembly

IntroductionCurrent de novo genome assembly tools often demand substantial memory resources, and their execution typically relies on high-performance computing (HPC) clusters. This dependency limits their use in resource-constrained settings. Furthermore, mainstream third-generation sequencing assembly and alignment tools usually require explicit detection of overlap regions between reads, a process that often entails significant computational and storage overhead. ResultsTo address this issue, we developed LightAlign, a lightweight alignment tool for HiFi data that innovatively uses sequence-derived fuzzy features and reduces the peak memory usage during overlap detection. ConclusionsWhen combined with miniasm, LightAlign generated bacterial draft assemblies while maintaining peak memory usage below 1 GB and completed overlap generation for the tested eukaryotic datasets within 1.88 GB RAM.

bioinformatics↗