Biology subjects
Publications and source records attributed to Zhang, N..
Our study has for the first time identified H5N1 strains (clade 2.3.4.4b, genotype B3.2) in brown skuas from the Fildes Peninsula, South Shetland Islands, Antarctica. These findings indicate that highly pathogenic avian influenza H5N1 viruses is now actively circulating in Antarctic ecosystems, representing a significant expansion of its geographic range.
Stem cell-based therapy holds great potential for substituting degenerated motor neurons (MNs) in amyotrophic lateral sclerosis (ALS). Missing protocols for advanced differentiation of transplanted cells into MNs, immune rejection, and the lack of suitable ALS models for preclinical trials have slowed the development of effective therapies. Here, we employed multiplex genetic-editing to generate a novel human pluripotent stem cell line containing doxycycline (Dox)-inducible MNs-specific transcription factors and comprehensively modified immunomodulatory genes. We transplanted these cells into the spinal cord of ALS large animal models (SOD1G93A pigs and TIA1P362L rabbits), which faithfully recapitulate pathologies and symptoms observed in ALS patients. The transplanted cells could efficiently differentiate into functional MNs upon Dox treatment in vivo, distribute throughout the spinal cord and motor cortex via extensive migration, survive long-term without the need for immunosuppression. Notably, these MNs integrated into host neural circuits, as evidenced by their long projection of peripheral axons to target muscle and reformation of neuromuscular junctions. As result, pathologies and motor deficits were substantially ameliorated in both animal models. One Sentence SummaryHypoimmunogenic human motor neurons induced from iPSCs in vivo reform neuromuscular junctions and ameliorate ALS disease in pig and rabbit models.
Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.
Root-knot nematodes (Meloidogyne spp.) are obligatory plant root parasites whose effector proteins play a critical role in suppressing plant immunity. However, the effectors direct host targets and underlying molecular mechanisms remain poorly understood. Using TurboID-mediated proximity labeling in tomato (Solanum lycopersicum) hairy roots, we identified an interaction between the nematode effector Mj-MSP18 and the tomato BRASSINOSTEROID-SIGNALING KINASE 7 (Sl-BSK7). Yeast two-hybrid (Y2H) assays confirmed that this interaction is conserved in Arabidopsis thaliana and Nicotiana benthamiana. Additionally, yeast three-hybrid and luciferase complementation assays demonstrated that Mj-MSP18 disrupts the interaction between BSK7/8 and FLS2 in both yeast and in planta. Given that the BSK7/8-FLS2 interaction is essential for flg22-induced pattern-triggered immunity (PTI), this disruption likely accounts for the suppression of reactive oxygen species (ROS) production and callose deposition observed upon transient expression of Mj-MSP18 in flg22-treated N. benthamiana leaves. Correspondingly, Arabidopsis and tomato bsk7 mutants exhibited increased susceptibility to root-knot nematode infection. Furthermore, RNA-seq analysis of tomato hairy roots expressing Mj-MSP18 revealed extensive transcriptional reprogramming, including the downregulation of defence-related genes and hydrogen peroxide response pathways. In addition, Y2H screening identified Sl-MYB and Sl-MYC2 as additional interactors, linking Mj-MSP18 to phytohormone biosynthesis, particularly the brassinosteroid (BR) and salicylic acid (SA) pathways, as validated by targeted metabolite analysis. The conservation of Mj-MSP18 across Meloidogyne species suggests a broadly conserved mechanism for host immune suppression and phytohormone modulation.
Sequencing an entire spatial transcriptomics slide can cost thousands of dollars per assay, making routine use impractical. Focusing on smaller regions of interest (ROIs) based on adjacent routine H&E slides offers a practical alternative, but there is (i) no reliable way to identify the most informative areas from standard H&E images alone; and (ii) limited solutions for clinicians to prioritize the microenvironment of their own interests. Here we introduce SpatialFinder, a framework that combines a biomedical vision-language model (VLM) with a human-in-the-loop optimization pipeline to predict gene expression heterogeneity and rank high-value ROIs across routine H&E tissue slides. Evaluated across four Visium HD tissue types, SpatialFinder consistently outperforms baseline VLMs in selecting regions with high cellular diversity and tumor presence, achieving up to 89% correlation with ground truth rankings. These results demonstrate the potential of human-AI collaboration to make spatial transcriptomics more cost-effective and clinically actionable.
Inhibitory control, or the ability to withhold action in certain situations, is behaviorally essential. Disrupted inhibitory control is linked to various neuropsychiatric symptoms, making it critical to understand the underlying neural basis. We examined how the tail of the striatum (TS), a major basal ganglia sensory hub, regulates actions to sensory stimuli. Mice performed an auditory Go/NoGo task where we recorded cell-specific activity of TS neurons. Both major striatal types were active during target sounds, but non-target sounds preferentially engaged indirect pathway neurons. Temporarily silencing this activity increased errors to non-target stimuli, indicating a role in suppressing inappropriate action. In mice deficient for the synaptic adhesion molecule Neurexin1, a gene linked to autism spectrum disorder and ADHD, TS indirect pathway recruitment was reduced, and these mice demonstrated auditory-specific inhibitory control deficits. Altogether, these findings highlight a subcortical target to potentially improve attentional and behavioral regulation in neurodevelopmental disorders. TeaserPosterior striatal circuits control sensory-guided actions and are disrupted in a rodent model of neurodevelopmental disorders.
Spatial transcriptomics (ST) has revolutionized biological research by enabling the joint profiling of gene expression and spatial context, along with histological images. However, current existing ST technologies remain high-cost and time-consuming, hindering their broader clinical applications. Although computational methods have been developed to infer gene expression directly from histology images, these methods still suffer from limited accuracy and spatial resolution due to insufficient training data and model capacity. Here, we introduce SpaFoundation, a large-scale histology foundation model designed to accurately predict spatial gene expression from tissue images. SpaFoundation employs a teacher-student Vision Transformer (ViT) architecture to learn generalizable histological representations by modeling potential dependencies among image patches. Notably, we incorporated self-distillation and masked image modeling (MIM) jointly to capture high-level semantic representations and fine-grained structural features, enriching spots representations. The model is pretrained on 1.79 million patches spanning 26 tissue types, with 80 million parameters. We validated SpaFoundation using 117 samples, demonstrating its flexibility across different spatial resolutions and superior performance in spatial gene expression prediction, as well as strong transferability to downstream tasks such as tumor detection and spatial domain clustering. Our results highlight the potential of large-scale foundation model to learn informative histological representations and underscore the benefits of domain-specific pretraining in extracting task-relevant representations, paving the way for foundation model-driven spatial gene expression inference. The implementation and pre-trained weights of SpaFoundation are publicly available at https://github.com/NingZhangCSUBio/SpaFoundation.
The plasticity-first hypothesis posits that phenotypic plasticity emerges first in novel environments, followed by (epi)genetic changes that stabilize adaptive phenotypes. Whether tumor evolution follows this model, and how non-genetic mechanisms sustain long-term therapeutic resistance, remain unclear. Here, we develop eTRACER, an endogenously targeted, high-resolution and spatially-resolved CRISPR-Cas9 lineage-tracing system, to study tumor adaptation during longitudinal CD8+ T cell-mediated immunotherapy. Integrated clonal and single-cell transcriptomic analyses show that tumor immune evasion is governed by clonal state composition rather than clonal identity, arguing against selection from pre-existing genetic heterogeneity. Spatiotemporal lineage tracing reveals highly reversible state transitions prior to therapy, followed by consolidated epithelial-mesenchymal transition (EMT) during therapy. Single-cell multiomics identifies AP-1 as a key regulator of EMT stabilization and its inhibition enhances tumor sensitivity to immune killing. Together, these findings show that tumor plasticity precedes stable immune evasion, revealing an AP-1-centered mechanism underlying plasticity-first tumor evolution.
Posterior cortical impairments in visuospatial/perceptual function are common non-motor symptoms of the Lewy Body Dementias (LBD) and are relatively specific for LBDs compared to other dementias. Across populations, cognitive impairments correlate with the presence of -synuclein (-syn) pathology in limbic and neocortical brain regions. However, the specific role that -syn pathology plays in driving cortical circuit dysfunction and cognitive impairment remains controversial. We hypothesized that inducing -syn pathology in primary visual cortex (V1) in mice would impair neuronal activity and encoding of visual information, leading to visuoperceptual impairments. To test this, we injected -syn pre-formed fibrils (PFF) into V1, causing the formation of sparse Lewy-like pathology. Using longitudinal in vivo two-photon (2P) calcium imaging over 6 months, we recorded visually evoked activity of pyramidal cells in layer 2/3 (L2/3) and quantified -syn pathology using C05-05, a fluorescent ligand that binds aggregated -syn. Measuring population activity, we found a greater percentage of neurons in PFF-injected mice were responsive to visual stimuli with lower direction selectivity compared to controls at 4-5 months post-injection (MPI). Neurons with somatic Lewy-like inclusions showed reduced activity compared to neighboring neurons without inclusions. Conversely, neurons without somatic inclusions showed increased activity, positively correlated with the local burden of -syn pathology. Using a coherent motion discrimination task, we found no impairments in visuoperceptual ability in PFF-injected mice. Our results demonstrate that -syn pathology leads to reductions in neuronal activity in cells with somatic inclusions and reciprocal changes in local population activity but does not impair visuoperceptual function. Reflecting the early stages of neocortical -syn pathology, our model provides a framework for future studies to better understand the heterogeneity of cognitive symptoms and -syn pathology across patients.
The lateral hypothalamus (LH) is a highly heterogeneous brain region regulating hunger and motivated behaviors. In zebrafish, the LH shows distinct neural activity across hunger, feeding, and satiety states. However, the functional and evolutionary conservation of relevant neural circuits remain unclear. Using integrative transcriptomics of zebrafish and mouse LH, we identify conserved cellular clusters with shared molecular markers, particularly within GABAergic neurons. We highlight a conserved GABAergic population expressing tachykinin and growth hormone receptors, which is responsive to food cues and modulated by hunger and feeding states. This cluster may mediate acute appetite-enhancing effects of growth hormone. In both species, feeding elevates growth hormone receptor and tachykinin expression and activates these neurons, while human growth hormone increases their activity and food intake in zebrafish. These findings suggest a conserved neural mechanism by which metabolic hormones influence feeding behavior. Our comparative LH atlas highlights the evolutionary biology of appetite regulation and the integration of hormonal and neural signals driving energy homeostasis.
Mitochondrial bioenergetic competency in cells is frequently assessed by the Mito Stress Test protocol, which includes uncoupler addition for evaluating respiratory capacity. The uncoupled oxygen consumption rate (OCR) is usually defined as maximal respiration, with little consideration of whether the measured rate is restricted by substrate supply. In this study, we show that the uncoupled OCR is substrate-limited in rat primary cortical neurons and isolated mouse forebrain synaptosomes. We use a different respirometry protocol we name CRABS-ROC (Complex Respirometry Assay Bypassing Substrate-Restricted Oxygen Consumption) that enables evaluation of individual electron transport chain (ETC) complex capacity using saturating levels of substrate to bypass this restriction. Applying CRABS-ROC to primary cortical neurons reveals >2-fold excess Complex I capacity beyond the uncoupled OCR of cells metabolizing glucose and pyruvate. Furthermore, we demonstrate that CRABS-ROC can expose a Complex I deficit in isolated harlequin mutant brain mitochondria that display wild-type levels of Complex I-substrate-linked respiration despite having about half the normal level of Complex I. Thus, CRABS-ROC should be broadly useful for studies on mitochondrial function because it can both reveal excess ETC capacity and unmask ETC alterations that may be missed by the most widely used methods.
Huntingtin (HTT) function is enigmatic, as the native protein plays critical roles in neuronal health, while mutant HTT (mHTT), carrying an expanded polyglutamine stretch, triggers neurotoxicity and contributes to the pathogenesis of Huntingtons disease (HD). We recently found that HTT is part of a nuclear transcription-coupled DNA repair (TCR) complex with DNA repair enzymes including polynucleotide-kinase-3-phosphatase (PNKP). This complex resolves DNA lesions during transcription to maintain genome integrity, while in HD, mHTT impairs the activity of this complex, resulting in accumulation of DNA lesions. Using molecular, cellular biology and computational methods, we find that HTT has a role in assembling a functional DNA repair complex in mitochondria. Together with mitochondrial RNA polymerase and transcription factors, HTT resolves mitochondrial DNA lesions to preserve mitochondrial genome integrity and function. Pathogenic mHTT impairs this activity, resulting in persistent DNA lesions and reduced mitochondrial function in HD. Importantly, restoring activity of this complex in a Drosophila HD model through ectopic HTT or PNKP expression significantly improves mitochondrial genome integrity and ameliorates motor deficits. HIGHLIGHTSO_LIHTT organizes a functional, multifactorial mitochondrial DNA repair complex C_LIO_LIMutant HTT impairs the mitochondrial DNA repair complex causing DNA damage accumulation C_LIO_LIHTT-associated repair complex resolves mitochondrial DNA lesions and DNA integrity C_LIO_LIRestoring repair activity in HD flies rescues mitochondrial DNA integrity and motor defects C_LI
Subcellular imaging transcriptomics has offered unprecedented resolution of spatial mapping of gene expressions at subcellular level. However, accurate and robust cell type annotation at cellular level remains a challenge. Here we present SpatialMap, a deep weakly supervised cell typing framework that combines graph neural networks (GNN) with transfer learning to annotate cellular identities in subcellular spatial transcriptomics (ST). SpatialMap consistently outperforms state-of-the-art annotation methods on both simulated and real-world ST datasets. It demonstrates strong scalability across diverse tissue types and platforms, including NanoString CosMx, MERFISH and 10x Genomics Xenium. When applied to a mouse primary motor cortex dataset, SpatialMap successfully identified Micro, L4/5 IT, and L6 IT Car3 absent from the reference data, showcasing its capability to discover novel cell types. Furthermore, SpatialMap accurately annotated malignant cells in human liver cancer samples. Its design also enables seamless extension to cross-omics cell typing and cross-platform annotation within proteomics.
Cell-cell interactions play a pivotal role in organ development, yet these communications have previously been studied one interaction at a time in model organisms, leaving a gap in our understanding of the cellular interplay in human development. To address this, we investigated human kidney development using single-cell RNA sequencing and spatial transcriptomics, analyzing over 500,000 cells. By mapping gene expression and differentiation trajectories in histologic space, we define the spatial organization of kidney development. Our analysis revealed newfound plasticity, showing that nephron progenitor cells undergo an early fate decision between renal corpuscle and tubular lineages. However, this choice is later reversed with some mature tubule cells transitioning back to a renal corpuscle fate. Further, through a genome-wide, spatially-aware cell-cell interaction analysis, we identified specific ligands and neighboring cell signals that create biologically meaningful cellular neighborhoods and mediate cell fate choices, offering a blueprint to understand the coordination of human development at scale.
Pathogen adaptations to the intracellular macrophage environment remain poorly understood. We performed a high-resolution structural analysis of the lipid A purified from intracellular Klebsiella pneumoniae (KP). In both mouse and human macrophages, KP produces hexa- and hepta-acylated lipid A species modified with palmitate and 2-hydroxylated. LpxL1, PagP, and LpxO enzymes govern the intracellular lipid A in a PhoPQ-dependent manner triggered by the acidic pH of the KP-containing vacuole (KCV). Absence of LpxO and PagP lipid A modifications impairs intracellular survival and heightens NF-{kappa}B and IRF3-mediated inflammation, though KCV maturation remains unaffected. Instead, these modifications fortify the bacterial membrane. Absence of TLR4-TRAM-TRIF signalling increases KCV pH, impairing the production of the intracellular lipid A. KP intracellular survival is reduced in tlr4-/- macrophages, highlighting the critical role of this signalling pathway in KP immune evasion and how the pathogen has evolved to rely on innate immune system cues for virulence.
The prefrontal cortex (PFC) is one of the last brain regions to fully mature, making it particularly sensitive to drug use early in life. Both human and rodent studies find long-lasting behavioral changes after adolescent alcohol exposure that implicate underlying disruptions in PFC development, including structural abnormalities and altered brain functional connectivity. Few rodent studies have been conducted to understand the network-level implications of these disruptions. We assessed how adolescent binge-like alcohol consumption in a drinking in the dark (DID) model affected adult alcohol consumption, behavioral exploration, and brain-wide functional connectivity in mice. Approximately one month after the conclusion of DID, only female mice exposed to alcohol during adolescence exhibited aversion-resistant alcohol preference in adulthood. Adult females exhibited additional sex-specific changes in exploratory behavior in the elevated plus maze after adolescent alcohol consumption. Resting state neuroimaging revealed sex-specific changes in prefrontal cortical connections with sensory motor, hippocampal, striatal, and other networks, providing insights into the putative systems underlying deficits caused by adolescent alcohol exposure. Critically, our data corroborate a growing body of literature in human and rodent studies demonstrating that adolescent alcohol use may increase risk for adult alcohol use more strongly in females. Finally, we identify neural correlates of this effect that include both known and novel neural networks and tie these back to human datasets, allowing biological and mechanistic targets to be further explored for future study and interventions.
The gut microbiome generates a diverse array of metabolites that actively shape host immunity, yet the pro-inflammatory potential of microbial metabolites remains poorly understood. In this study, we identified hippuric acid, an aromatic gut microbe-derived metabolite, as a potent enhancer of pro-inflammatory responses using a murine bacterial infection model and a non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. Administering hippuric acid intraperitoneally in murine models of Escherichia coli infection or LPS-induced inflammation significantly heightened pro-inflammatory responses and innate immune cell activation. In vitro, hippuric acid selectively potentiated M1-like macrophage polarization (LPS + IFN{gamma}) but had no effect on M2-like polarization (IL-4). Hippuric acid further enhanced responses to diverse MyD88-dependent TLR ligands, but not TRIF-dependent TLR3, implicating a possible mechanism of action via activation of TLR-MyD88 signaling. Genetic deletion of MyD88 abrogated the pro-inflammatory effects of hippuric acid both in vitro and in vivo, confirming its dependence on the MyD88 pathway. Transcriptomic and lipidomic analyses revealed that hippuric acid promoted cholesterol biosynthesis and lipid accumulation, linking microbial metabolism to lipid-driven immune activation. Notably, hippuric acid similarly enhanced pro-inflammatory responses in human macrophages, and its elevated levels correlated with increased sepsis mortality, highlighting its potential clinical relevance. These findings establish hippuric acid as a previously unrecognized microbial-derived inflammatory modulator, bridging gut microbial metabolism, lipid remodeling, and innate immune signaling, and offer new insights into its role in infection and inflammation.
Immunity is generally considered critical for plant health against pathogen infection. Citrus Huanglongbing (HLB) caused by the phloem colonizing bacterial pathogen Candidatus Liberibacter asiaticus (CLas) was suggested to be a pathogen triggered chronic immune disease. However, the genetic evidence and mechanistic understanding for such a disease model is lacking. Here, we show CLas triggers phloem cell death, reactive oxygen species (ROS) production and callose deposition in photosynthesis tissues, but little or none in non-photosynthesis tissues of citrus. We further demonstrate that CLas triggers ROS production in chloroplasts. Overexpression of flavodoxin (Fld), an electron shuttle, in chloroplasts reduced ROS production, cell death and HLB symptoms, but not phloem callose deposition induced by CLas. Knockout, silencing, and overexpression of phloem callose synthase genes CsCalS7a, CsCalS7b, or CsCalS7c demonstrated that phloem callose deposition also caused phloem cell death. Trunk injection with 2-deoxy-d-glucose, a callose deposition inhibitor, reduced fruit drop and increased fruit yield of HLB symptomatic trees in field trials. Using tomato-Ca. L. psyllaurous (Lpsy) as a model, knockout of Eds1 and Pad4 but not RbohB, Bik1 and Sobir1 abolished ROS production, phloem callose deposition, cell death and disease damages caused by Lpsy. This study provides genetic evidence for Ca. Liberibacter-triggered immune disease and reveals that tuning plant immune responses converts Ca. Liberibacter into a benign endophyte, providing a promising strategy for precision breeding to enhance resistance/tolerance against HLB.