Biology subjects

Hu, K.

Publications and source records attributed to Hu, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

The human parasite, Toxoplasma gondii, is paralyzed without two components of the apical polar ring

The phylum Apicomplexa contains [~] 6000 known species of unicellular eukaryotic parasites. A unifying feature among the apicomplexans is the apical complex, which varies in complexity in different lineages, but always contains an annulus (a.k.a. the apical polar ring) into which the minus ends of an array of cortical microtubules are embedded. In Toxoplasma gondii, the apical complex also includes the conoid, which contains several signaling and structural proteins critical for parasite motility. The conoid extends and retracts through the apical polar ring in a calcium-dependent manner. Here we report the identification of several new apical polar ring components, including APR9, which is highly conserved among the apicomplexans and their free-living relative Chromera velia. The loss of APR9 alone has only a moderate impact on the parasite lytic cycle. However, the knockout of both APR9 and KinesinA (another apical polar ring component) paralyzes parasite and drastically impairs invasion, egress and the lytic cycle. The double-knockout displays multiple subcellular abnormalities, including the formation of an apical actin concentration, impaired conoid extension, and significantly reduced secretion of a major adhesin (MIC2) upon stimulation with a calcium ionophore. These findings reveal that the apical polar ring plays a critical role in parasite motility and contributes to multiple subcellular processes.

cell biology↗

bioRxiv2026

Exploring differences across pangenome-graph representations using Escherichia coli O157:H7 as a model

Pangenome graphs are increasingly used to represent population-scale bacterial diversity, yet construction methods span fundamentally different representation paradigms whose outputs and sensitivities to assembly quality remain poorly quantified. We systematically reviewed microbial pangenome graph tools and benchmarked six representative methods spanning gene-cluster, compacted coloured de Bruijn graph (ccDBG), multiple sequence alignment, and hybrid approaches. Using a repeat-rich Escherichia coli O157:H7 dataset with complete genomes and matched short-read data, we constructed graphs from identical inputs and observed orders-of-magnitude differences in graph size and fragmentation, indicating that global topology is driven by representation strategy. Varying completeness composition revealed that assembly fragmentation is a first-order determinant of graph structure: gene-cluster graphs contracted as draft assemblies replaced complete genomes, whereas unitig graphs expanded, with distinct degree-prevalence fingerprints across tools. Computational cost mirrored these shifts and depended strongly on completeness composition, including a pronounced runtime penalty for one ccDBG implementation on all-draft inputs. Finally, analysis of Shiga toxin loci showed that pangenome-level reconciliation does not reliably correct assembly artefacts at challenging multi-copy genes and that performance varies by locus. Together, these findings show that pangenome graphs are representation-dependent models of bacterial diversity, and that assembly completeness is a primary determinant of their topology, scalability, and locus-level accuracy. Authors SummaryBacterial populations are often described using "pangenome graphs," which aim to capture all genetic variation across many genomes in a single structure. However, different tools build these graphs in fundamentally different ways, and little is known about how those differences affect the results. In this study, we systematically compared several widely used approaches using a clinically important strain of Escherichia coli that is rich in repeated and mobile DNA. We found that the size, connectivity, and overall structure of the resulting graphs varied dramatically depending on the method used. Importantly, we also show that incomplete genome assemblies (common in large sequencing studies) strongly alter graph structure, and that different tools respond to incomplete data in different ways. In some cases, this affects the detection of medically relevant genes, including Shiga toxin genes linked to severe disease. Our results demonstrate that pangenome graphs are not interchangeable representations of bacterial diversity. Instead, their structure depends on both the method and the quality of the input data. We argue that researchers should choose graph-building tools carefully and report structural properties explicitly to ensure reproducible and interpretable results.

bioinformatics↗

bioRxiv2026

Development of Integrin α5β1-targeted PET/NIR imaging probes for glioblastoma intraoperative navigation and intracavity targeted radionuclide therapy

Incomplete extent of tumor resection is the major factor of glioblastoma recurrence, leading to its poor prognosis. Developing therapies that enable the minimal tumor cell remnant during surgical resection is a major challenge to combat this aggressive cancer. This study develops a glioblastoma integrin 5{beta}1-selective peptide binder through series strategy screening and labeling it with 68Ga, indocyanine green (ICG), or 177Lu for efficacious multimodal treatment. This strategy combines positron emission tomography (PET) imaging for preoperative diagnosis, intraoperative NIR-II fluorescence-guided surgery for maximal tumor resection, and followed by intracavity targeted radionuclide therapy for elimination of residual tumor cells. We identified GR, with five arginine mutation, exhibiting superior integrin 5{beta}1 binding affinity and brain penetration. [68Ga]GR demonstrated substantial tumor uptake and prolonged retention time in both mouse models and tissues from glioblastoma patients. The guidance of ICG-GR achieved accurately intraoperative tumor imaging and maximal tumor resection in orthotopic mouse glioblastoma models. Notably, combining intracavity administration of [177Lu]GR following ICG-GR guiding resection markedly inhibited tumor growth and reduced possibility of tumor recurrence compared with surgery alone (unguided or ICG-GR-guided) or unguided surgery followed by [177Lu]GR. Therefore, we have reported the integrin 5{beta}1-targeted radionuclide and optical agents for maximal elimination of tumor cells during surgical resection in glioblastoma patients. HIGHLIGHTSO_LIGR is a glioblastoma-specific peptide with both favorable binding affinity superior brain penetration. C_LIO_LIICG-GR is a glioblastoma-targeted NIR probe enabling maximal surgical resection. C_LIO_LIICG-GR-guided surgery with [177Lu]GR-based adjuvant therapy allows robust elimination of tumor cells. C_LI

cancer biology↗

bioRxiv2026

Ac-FAPI-04 Promotes Anti-tumor Immunity via IL-27 Activation and Tnfaip3 Inhibition

BackgroundAccumulating evidence substantiates the capacity of targeted radionuclide therapy (TRT) to potentiate tumor immunotherapy responses. However, combining TRT and immunotherapies exhibits substantial varying efficacy, underscoring the importance of investigating mechanisms through which TRT remodels the tumor microenvironment (TME). Despite recent advancements, the specific signaling molecules mediated by TRT that regulate the functions of cytotoxic T lymphocytes (CTLs) remain unclear. MethodsGiven the demonstrated potential of -radionuclides targeting the fibroblast activation protein (FAP) in TRT, this study employed [225Ac]Ac-FAPI-04 to investigate the mechanisms of TRT-induced TME remodeling. The cytotoxic effects were first evaluated in the B16F10 cell line, followed by an assessment of its in vivo therapeutic efficacy in tumor-bearing mice. RNA-sequencing analysis was utilized to elucidate underlying signaling pathways involving immune responses. Results[225Ac]Ac-FAPI-04 significantly induced DNA double-strand breaks, further elevated ROS levels, and apoptosis in tumor cells. Transcriptomic profiling revealed that [225Ac]Ac-FAPI-04 activates the IL-27/JAK-STAT pathway to amplify interferon-mediated responses, indicating IL-27 serves as a critical regulatory signal for CTLs during TRT. A concomitant observation was the downregulation of Tnfaip3 following [225Ac]Ac-FAPI-04 treatment. Tnfaip3 is implicated in modulating CTLs behavior and intratumoral infiltration, while its downregulation was associated with the upregulation of cytotoxic effector molecules, as confirmed in this study. ConclusionThis study identifies a TRT-induced pattern of synergistic signaling mediated by IL-27 and Tnfaip3, which collectively enhances CTL recruitment and potentiates their cytotoxic function. These findings provide a detailed mechanistic rationale for strategies aimed at augmenting the therapeutic efficacy of TRT and immunotherapy combinations.

molecular biology↗

bioRxiv2025

Structural and Functional Insights into HBx-Smc6 Targeting for HBV Inhibition

The hepatitis B virus (HBV) X protein (HBx) is a multifunctional regulator essential for HBV replication and HBV-associated hepatocarcinogenesis. Despite its central role, the molecular basis of HBx function has remained elusive. Here, we present the first cryo-electron microscopy structure of the human HBx-CRL4-Smc5/6 complex at 3.1 [A] resolution. In this reconstituted ten-subunit assembly, HBx adopts a Zn2 {square}-stabilized Y-shaped architecture that simultaneously engages the DDB1 and the Smc6 subunit. A composite helix-turn-helix (HTH) pocket in HBx accommodates a conserved "Leucine Key" motif (LRCKL) on Smc6, forming a critical interface essential for complex stability and function. Molecular docking and biochemical validation reveal that the compound Tranilast binds this HTH pocket, disrupts the HBx-Smc6 interaction, and suppresses HBV replication. These findings define the structural mechanism by which HBx counteracts host restriction and establish the HBx-Smc6 interface as a previously unrecognized and druggable target for antiviral intervention.

cell biology↗

bioRxiv2025

Targeted Intestinal Cooling Offers Superior Brain Protection in the Mouse Stroke Model

BackgroundIntestinal immune and inflammatory response plays a detrimental role following a stroke. This study aims to evaluate the brain protective efficacies of a novel intestinal cooling (CC) technique relative to the body surface cooling (SC) and the normothermic (NT) condition in a mouse stroke model. MethodsMice were randomly assigned to CC (n=13), SC (n=15), or NT (n=11) groups. They underwent 60 min of middle cerebral artery occlusion (MCAO) followed by 7-day reperfusion. Both head and intra-colon temperatures were maintained at 37{degrees}C for 30 min before, during, and 30 min after MCAO. At 30 min reperfusion, a cooling catheter was placed to maintain intra-colon at 37{degrees}C in NT or 12{degrees}C in CC. The head temperature was maintained at 37{degrees}C in NT and 30{degrees}C in CC. In SC, both intra-colon and head temperatures were maintained at 30{degrees}C. Cooling lasted 3 hours. Bodyweight, behavioral deficits (nesting and pole test), and survival rate were assessed post-MCAO. At day 7 post-MCAO, mice were perfusion-fixed for histopathological analysis. ResultsPost-stroke histopathological brain injury areas and volume were significantly reduced in CC, and appeared reduced though not statistically significant in SC, relative to NT. Compared with NT, body weight, nest building activity, and pole test were all significantly recovered in CC post-MCAO. In SC, only nest building improved significantly, while body weight and pole test showed marginal, nonsignificant trends. Consistent with functional recovery, survival was significantly improved in CC but not in SC, compared with NT. ConclusionIn a murine model, our novel CC technique successfully achieved targeted intestinal cooling while preserving safe upper-body temperatures necessary for normal cardiopulmonary function. Targeted intestinal cooling provides significant benefits superior to SC and NT, including smaller stroke volume, fewer functional deficits, and lower mortality rates, thus supporting the novel concept that the intestines are potential therapeutic targets for stroke management. Graphical Abstracts O_FIG O_LINKSMALLFIG WIDTH=131 HEIGHT=200 SRC="FIGDIR/small/681764v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1aa07cdorg.highwire.dtl.DTLVardef@1e64569org.highwire.dtl.DTLVardef@d6f178org.highwire.dtl.DTLVardef@1871862_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPost-stroke body surface cooling-induced hypothermia demonstrated marginally neuroprotective effects compared to normothermic conditions in the mouse model. C_LIO_LITargeted deep cooling of the intestine after a stroke resulted in a significantly greater reduction in stroke injury areas and volume, as well as lower mortality rates and fewer functional deficits, compared to body surface cooling-induced hypothermia and normothermic conditions. C_LI

neuroscience↗

bioRxiv2025

Transfection of the free-living alga Chromera velia enables direct comparisons with its parasitic apicomplexan relative, Toxoplasma gondii

Chromera velia is a photosynthetic, free-living alga that is closely related to the apicomplexans, a phylum of intracellular parasites responsible for many devastating diseases, including malaria, cryptosporidiosis, and toxoplasmosis. With molecular and cellular landmarks that are clearly related to but distinguishable from those found in apicomplexan parasites, Chromera provides a fantastic opportunity to investigate the evolutionary origin of the structures and processes needed for intracellular parasitism. However, tools for defining localization and functions of gene products do not exist for Chromera, which creates a major bottleneck for exploring its biology. Here we report two major advances in exploring the cell biology of this free-living relative of a large group of intracellular parasites: 1) successful cell transformation and 2) the implementation of expansion microscopy. The initial analysis enabled by these tools generated new insights into subcellular organization in different life stages of Chromera. These new developments boost the potential of Chromera as a model system for understanding the evolution of parasitism in apicomplexans.

cell biology↗

bioRxiv2025

Intracranial Insights into the Developing Neural Basis of Moral Punishment

Third-party punishment (TPP) is a critical component of social regulation and justice, in-tegrating moral reasoning and emotional salience. However, the neural developmental basis underpinning this complex process remains largely unknown. Using rare intracranial stereo-electroencephalography (SEEG) in 14 children and 17 adults, we investigated the developing neural circuits of TPP. We found that broad-band gamma activity in the amygdala and ventromedial prefrontal cortex (vmPFC) encodes inferred intentions, with different patterns across age groups. Furthermore, the vmPFC, insula, and inferior parietal lobule (IPL) integrate punishment efficacy, also showing significant developmental differences. Combining task and resting state functional connectivity analyses, we further found age-dependent interactions among the amygdala-insula and IPL-vmPFC neural couplings during decision-making. These findings provide valuable intracranial evidence that the maturation of moral decision-making stems from the developmental refinement of subcortical-cortical circuits that integrate emotional and cognitive evaluations, explaining the shift from intuitive decisions in children to context-sensitive judgments in adults.

neuroscience↗

bioRxiv2025

Functional impact of pathogenic Runt domain mutations in Runx2 in vivo: Insights into the skeletal and dental anomalies of cleidocranial dysplasia

Runt-related transcription factor 2 (RUNX2) is essential for skeletogenesis, and mutations in its gene cause cleidocranial dysplasia (CCD), an autosomal dominant skeletal disorder. The evolutionarily conserved 128-amino acid Runt homology domain (RHD) of human RUNX2 is essential for DNA binding and heterodimerization, and serves as a mutation hotspot associated with severe CCD phenotypes. To elucidate the functional impact of pathogenic RHD mutations in vivo, we generated two novel mouse lines: one carrying a missense mutation, c.695G>A (p.R232Q) (Runx2m/+), corresponding to the human RUNX2 c.674G>A (p.R225Q), and the other harboring a frameshift mutation, c.697_698delGA (p.E233TfsTer9) (Runx2112/+), causing a premature stop codon. Homozygous Runx2m/mand Runx2112/112 mice lacked membranous ossification, whereas heterozygous Runx2m/+ and Runx2112/+ mice displayed typical CCD-like skeletal features, including an open anterior fontanelle and clavicle hypoplasia. Unexpectedly, heterozygotes carrying pathogenic mutations in RHD developed an accessory root-like protrusion at the furcation of three-rooted maxillary first molars, representing a previously unrecognized dental phenotype during root development. Dual luciferase assays revealed impaired transactivation of the p.R232Q mutant Runx2 on the osteocalcin enhancer/promoter. Wild-type Runx2 was robustly expressed in osteoblasts and hypertrophic chondrocytes during bone formation, but the mutant Runx2 exhibited reduced expression in hypertrophic chondrocytes and partially impaired nuclear localization, resulting in arrested osteoblast and chondrocyte maturation. Our mutant mouse model provides a valuable in vivo platform to study CCD pathogenesis, mechanisms of tooth root furcation, and therapeutic interventions targeting dysfunctional RHD.

genetics↗

bioRxiv2025

Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex

Single-cell spatial transcriptomes have demonstrated molecular and cellular diversity in the brain1, 2, 3, 4, 5, 6, 7, 8, but gene regulatory mechanisms underlying transcriptomic profiles and disease pathogenesis remain largely unknown in primates. Here we performed single-nucleus Assay for Transposase-Accessible Chromatin followed by sequencing (snATAC-seq) for [~]1.6 million cells from 142 cortical regions of two male cynomolgus monkeys (Macaca fascicularis), and identified distinct chromatin accessibility profiles of cis-regulatory elements (CREs) for various cell types. By integrative analysis with large-scale spatial transcriptome data, we found that these CREs showed laminar and regional preferences, with their regional accessibility exhibiting striking dependence on the regions hierarchical level. Cross-species comparison of snATAC-seq data revealed human/macaque-enriched layer-4 glutamatergic neurons and LAMP5/LHX6-expressing GABAergic neurons as well as human/macaque-biased CREs for genes related to neurodevelopment and psychiatric diseases. Importantly, risk single-nucleotide polymorphisms for many brain disorders strongly associated with human/macaque-biased CREs in glutamatergic neuronal types and those for Alzhemers disease strongly associated with CREs exclusively in microglia. Our results provided the basis for understanding the spatial gene regulatory mechanisms underlying cellular diversity and disease pathogenesis in the primate cortex.

neuroscience↗

bioRxiv2025

Developing a versatile technology for agroinfiltration in multiple plants

Agrobacterium-mediated transient transformation methods are widely used in plant science and molecular pharming. However, plant immune response and post-transcriptional gene silencing (PTGS) can compromise gene expression, limiting the adaptability of these methods across plant species. The lack of a robust reporter system further hinders advancements in agroinfiltration technology. To address these challenges, we developed a fungal bioluminescence pathway (FBP)-based reporter system that utilizes caffeic acid to generate self-sustained luminescence. By incorporating NahG and P19, our FBP assay enhances transient transformation efficiency in over 20 plant families, including major crops, vegetables, ornamental plants, and trees. Furthermore, we demonstrate its utility for assessing protein localization, interactions, and transcriptional regulation in multiple plant species, thereby broadening our understanding of gene function throughout the plant kingdom.

plant biology↗

bioRxiv2025

Mapping Architecture of Protein complexes in Arabidopsis using XL-MS

Capturing molecular machines in action is essential for understanding protein complex architecture, cellular regulation, and gene function. Here, we present a large-scale structural proteomics resource for Arabidopsis thaliana generated using an optimized cross-linking mass spectrometry (XL-MS) workflow. Using the trifunctional cross-linker PhoX, whose phosphonic acid moiety enables immobilized metal affinity chromatography (IMAC)-based enrichment, we selectively enriched cross-linked peptides from whole-cell lysates, chloroplasts, and nuclei. Analysis with pLink 3.2 identified 52,944 unique cross-linked peptide pairs, corresponding to 37,531 residue-level contacts across 5,064 proteins. These data define 3,083 protein-protein interactions, including 2,385 heteromeric and 698 homomultimeric interactions. Comparison with the STRING database showed that 676 interactions are supported by STRING scores [≥]0.9. Structural mapping to Protein Data Bank (PDB) and AlphaFold models showed that most cross-links were within the expected 35 [A] distance constraint. The dataset further enabled the analysis of protein connectivity and complex topology across diverse molecular assemblies, including the Rubisco holoenzyme, chloroplast 70S ribosome, photosystem complexes, and the cytosolic 80S ribosome together with associated biogenesis and regulatory factors. We also identified histone-associated complexes, including interactions involving an O-acyltransferase. By providing residue-level structural constraints for a substantial portion of the Arabidopsis proteome, this study provides a resource for exploring plant molecular machines and their spatial organization. Significance StatementUnderstanding how proteins interact within living cells is essential to deciphering cellular architecture and function. However, capturing native protein-protein interactions (PPIs) on a global scale has proven technically challenging. Here, we present a proteome-wide cross-linking mass spectrometry (XL-MS) platform that can systematically map direct PPIs in plant cells without requiring transgenic manipulation. This approach identifies thousands of interactions spanning major subcellular compartments and characterizes the in situ organization of critical protein assemblies, such as photosystems, ribosomes, and chromatin-associated connectivity. By mapping both established and less-characterized interactions, this work advances our understanding of the plant protein interactome and provides a valuable resource for investigating the structural organization of the plant proteome.

molecular biology↗

bioRxiv2025

Harnessing Generative Pre-trained Transformer for Antimicrobial Peptide Generation and MIC Prediction with Contrastive Learning

Antimicrobial peptides (AMPs) have garnered considerable attention due to their reduced likelihood of inducing resistance in pathogens compared to traditional antibiotics, which has spurred the interest in de novo design of AMPs. Despite the availability of various methods, accurately generating AMPs and predicting their inhibitory effects remains a challenging task. In this work, we introduce AMPCLGPT, a novel approach that leverages contrastive learning and generative pre-training for AMP design and minimum inhibitory concentration (MIC) prediction. First, AMPCLGPT is pre-trained on a large-scale unlabeled peptide dataset to learn peptide sequence patterns and enhance its ability to extract powerful representations. Second, the pre-trained AMPCLGPT is fine-tuned on AMP data with contrastive learning to increase the distance between antimicrobial and non-antimicrobial peptides in the latent space, improving its ability to accurately generate AMPs. Additionally, the pre-trained AMPCLGPT is fine-tuned to predict MIC values based on the learned peptide features. Empirical results demonstrate that our model can effectively generate AMPs and accurately predict their MIC values. By integrating these two capabilities, AMPCLGPT enables fully automated design of AMPs with low MIC values. AMPCLGPT represents a significant advancement in the field of AMP research, potentially accelerating the development of potent AMP-based therapeutics.

bioinformatics↗

bioRxiv2025

panHiTE: a comprehensive and accurate pipeline for TE detection in large-scale population genomes

Transposable elements (TEs) are key drivers of genomic variation and species evolution. Advances in high-throughput sequencing have enabled whole-genome sequencing of individuals or subspecies, facilitating the identification of population-specific variations. Detecting population-specific TE insertions at scale is crucial for understanding species-specific phenotypic traits. However, tools for constructing comprehensive pan-TE databases remain limited. To address this gap, we develop panHiTE, a population-scale TE detection and annotation tool with several core innovations. panHiTE features a deep learning-based long terminal repeat retrotransposon (LTR-RT) detection algorithm, outperforming existing tools in both sensitivity and precision. It also introduces a novel de-redundancy algorithm, which eliminates highly divergent redundant TE instances, significantly reducing the size of the TE library. Additionally, panHiTE can detect low-copy TEs, which are overlooked in individual genome analyses and absent from existing databases due to their rarity. Furthermore, panHiTE allows for TE-gene association analysis, enabling comprehensive insights into TE-driven phenotypic variation. panHiTE, powered by a Nextflow pipeline, enables efficient and scalable TE detection in large plant genomes and has successfully been applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

genomics↗

bioRxiv2025

APV-Sankey: A Comprehensive Toolbox for Aptamer Screening and Visualization

Aptamers, short single-stranded DNA or RNA molecules, have gained prominence as molecular recognition elements in diagnostics and therapeutics. Screening high-performance aptamers from SELEX process is tough due to limited library diversity, PCR bias, and low library enrichment efficiency. The enriched highest frequency sequences often do not have the highest affinity or specificity. Thus, we developed APV-Sankey, a novel and versatile toolbox designed for the rapid aptamer screening and visualization of the enrichment process. Its key feature is the innovative use of Sankey charts for interactive and informative visualizations. These charts facilitate tracing the evolution of K-mers (K-mer is just a sequence of k characters in a string) across SELEX rounds, aiding in the identification and selection of high-affinity sequences containing K-mers while excluding high-frequency sequences without affinity. Besides integrating essential functions for aptamer analysis, we also developed advanced methods including K-mer concatenation and K-mer evolution, combined with Sankey chart visualizations. Using this toolbox to analyze experimentally screened sequences, we successfully identified high-performance candidate aptamers of rapamycin and thrombin.

bioinformatics↗

bioRxiv2025

Pyruvate and Related Energetic Metabolites Modulate Resilience Against High Genetic Risk for Glaucoma

A glaucoma polygenic risk score (PRS) can effectively identify disease risk, but some individuals with high PRS do not develop glaucoma. Factors contributing to this resilience remain unclear. Using 4,658 glaucoma cases and 113,040 controls in a cross-sectional study of the UK Biobank, we investigated whether plasma metabolites enhanced glaucoma prediction and if a metabolomic signature of resilience in high-genetic-risk individuals existed. Logistic regression models incorporating 168 NMR-based metabolites into PRS-based glaucoma assessments were developed, with multiple comparison corrections applied. While metabolites weakly predicted glaucoma (Area Under the Curve=0.579), they offered marginal prediction improvement in PRS-only-based models (P=0.004). We identified a metabolomic signature associated with resilience in the top glaucoma PRS decile, with elevated glycolysis-related metabolites--lactate (P=8.8E-12), pyruvate (P=1.9E-10), and citrate (P=0.02)--linked to reduced glaucoma prevalence. These metabolites combined significantly modified the PRS-glaucoma relationship (Pinteraction=0.011). Higher total resilience metabolite levels within the highest PRS quartile corresponded to lower glaucoma prevalence (Odds Ratiohighest vs. lowest total resilience metabolite quartile=0.71, 95% Confidence Interval=0.64-0.80). As pyruvate is a foundational metabolite linking glycolysis to tricarboxylic acid cycle metabolism and ATP generation, we pursued experimental validation for this putative resilience biomarker in a human-relevant Mus musculus glaucoma model. Dietary pyruvate mitigated elevated intraocular pressure (P=0.002) and optic nerve damage (P<0.0003) in Lmx1bV265D mice. These findings highlight the protective role of pyruvate-related metabolism against glaucoma and suggest potential avenues for therapeutic intervention.

genomics↗

bioRxiv2024

Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

Why mammals cannot regenerate limbs, unlike amphibians, presents a longstanding puzzle in biology. We show that exposing ex vivo amputated embryonic mouse limbs to subatmospheric oxygen environment, or stabilizing oxygen-sensitive HIF1A enables not only rapid wound healing, but alters cellular mechanics, and reshapes the histone landscape to prime regenerative fates. Conversely, regenerative Xenopus tadpole limbs display low oxygen-sensing capacity, robust wound healing, a regenerative histone landscape, and glycolytic programs even under high oxygen. This reduced oxygen-sensing capacity, in stark contrast to mammals, associates with decreased HIF1A-regulating gene expressions. Our findings thus uncover species-specific oxygen sensing as a unifying mechanism for limb regeneration initiation across vertebrates, reveal how aquatic subatmospheric habitats may enhance regenerative capabilities, and identify targetable barriers to unlock latent limb regenerative programs in adult mammals.

developmental biology↗

bioRxiv2024

Single-Cell full-length Isoform Sequencing Unveils Transcriptional Dysregulation in Autism Spectrum Disorder During Cerebral Cortex Development

Regulation of RNA splicing is pivotal in neural development, with established gene isoform expression patterns (1, 2). However, the specific roles of isoform diversity across cell types in both healthy and diseased brains warrant further investigation. Here, we employed a combination of metabolic RNA labeling using 4-thiouridine (4sU) and long-read sequencing based single-cell full-length transcriptome sequencing to capture newly synthesized transcripts within the developing mouse cortices. This approach allowed us to identify predetermined cell states supported by new RNAs and the driving isoforms of transcription factors that regulate the development of deep-and upper-layer neurons. Through detailed single-cell isoform expression analysis, we discovered novel cell type-specific isoforms and uncovered isoform switch events that modulate neuron differentiation. Additionally, we investigated isoform regulation associated with Autism Spectrum Disorder (ASD) during embryonic development of BTBR T+ Itpr3tf (BTBR) mice. Notably, our findings indicate a premature emergence of cortical projection neurons (CPNs) with an immature identity in ASD-affected cortices. These CPNs exhibit the highest degree of differential transcript usage (DTU), significantly overlapping with their cell type markers and being enriched in RNA splicing processes. Exon inclusion was significantly enriched in ASD and the related RNA binding proteins (RBPs) were extracted, nearly 60% of which have been reported as ASD risk genes. Lastly, we revealed a reduction in isoform diversity in ASD, potentially linked to H3K27ac dysregulation in the associated genes. Collectively, our study marks a substantial advancement in understanding the molecular basis of cortical development and function, paving the way for future studies on neurodevelopmental disorders.

developmental biology↗