Biology subjects

Ye, L.

Publications and source records attributed to Ye, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Immune-Derived THBS1-CD47 Axis Induces Cellular Senescence and Suppresses Osteogenesis in Diabetic Periosteum

Type 2 diabetes mellitus (T2DM) weakens bone repair and increases fracture risk, but how the periosteal environment contributes to this problem is not fully understood. We found that diabetic mice showed thinning of the periosteum, reduced bone mass, and poor function of bone-forming cells. Using single-cell RNA sequencing, we discovered that immune cells and bone-lineage cells interact more strongly in diabetes through the THBS1-CD47 pathway. THBS1 was mainly produced by macrophages, while its receptor CD47 was abundant in osteogenic cells. Laboratory experiments showed that THBS1 blocked bone gene activity, increased inflammation and cell death, and damaged mitochondria, leading to higher oxidative stress. Knocking down CD47 reversed these effects, restoring bone cell activity and energy balance. In diabetic fracture models, blocking THBS1 improved callus formation and bone healing. These findings identify THBS1-CD47 as a key driver of periosteal dysfunction in T2DM and highlight it as a potential target to improve skeletal repair in diabetic patients.

cell biology↗

bioRxiv2025

METTL3-mediated SOCS3 m6A Modification in Preserving CD4+ T Cell Homeostasis in HIV Infected Long-term Non-progressors

The maintenance of normal CD4+ T cell levels in human immunodeficiency virus (HIV) infected long-term non-progressors (LTNPs) remains elusive. N6-methyladenosine (m6A) regulates RNA metabolism and immune function, but its role in LTNP pathogenesis is unelucidated. This study integrated in vivo analyses of peripheral blood mononuclear cells (PBMCs) from LTNPs, typical progressors (TPs), ART-treated patients, and healthy controls with in vitro experiments using the MT2-HIV-1B model to explored the m6A regulatory role in LTNPs. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified uniquely elevated m6A modification abundance and METTL3 expression in LTNPs vs. TPs. Differential m6A and mRNA analysis bighlighted enrichment of innate immunity/inflammation pathways, particularly the SOCS/IL/JAK axis. Further experiments confirmed that METTL3 mediates m6A modification of SOCS3, which suppresses JAK2/STAT4 phosphorylation to modulate IL-12/IFN-{gamma}/IL-4 expression. These findings uncover a novel m6A-METTL3-SOCS3 regulatory axis underlying HIV long-term non-progression, explaining preserved CD4+ T cell homeostasis in LTNPs. IMPOTANCE LTNPs represent a unique subset of HIV-infected individuals who naturally maintain normal CD4 T cell levels and slow disease progression, offering a valuable model to dissect host protective mechanisms against HIV. mA modification has emerged as a pivotal regulator roles in HIV replication and T cell activation, yet its contribution to LTNP biology has remained unclear. This novel mechanism provides a potential explanation for the maintenance of normal CD4+ T cell levels in LTNPs. Our findings shed light on the molecular basis of HIV-1 long-term non-progression and offered crucial insights for developing functional cure for AIDS and new host immune strategies.

immunology↗

bioRxiv2025

Functional architecture for speed tuning in primary visual cortex of carnivores

Perception of motion critically depends on detecting the speed and direction of moving stimuli. The primary visual cortex (V1) of some mammals, including primates and carnivores, exhibits functional organization for key receptive field properties such as orientation, direction, and spatial frequency; however, less is known about the organization of speed-tuned cells. While individual V1 neurons have been shown to exhibit speed selectivity, functional architecture for speed preference has been primarily reported in higher cortical areas such as primate area MT. Using multi-channel electrophysiology in anesthetized female ferrets, we investigated the joint tuning of V1 neurons for spatial frequency, temporal frequency, orientation/direction, and speed. We found significant clustering of cells tuned for speed and for speed preference within single electrode penetrations. We found that both simple and complex cells can exhibit speed tuning, and no strong variation across cortical layers. In reanalysis of intrinsic signal imaging data from cat V1, we observed repeating "hot spots" of high speed selectivity separated by "cold spots" with low tuning for speed. These findings indicate that a functional architecture for speed tuning is present within V1 itself and transmitted to downstream cortical regions. Significance StatementTo perceive moving objects, the visual system must detect both their direction and speed. The primary visual cortex, the first cerebral visual area to receive visual information from the retina via the lateral geniculate nucleus, plays a key role in this process. Here, we demonstrate that the primary visual cortex in carnivores contains speed-tuned neurons. Moreover, these neurons are organized into clustered "hot spots" that repeat across the cortical surface, suggesting a functional architecture for speed. While speed-tuned functional maps were previously thought to exist only in higher visual areas, such as area MT in primates, our findings reveal their presence at the level of primary visual cortex.

neuroscience↗

bioRxiv2025

scPhoenix: A Contrastive Learning-based Framework with Aux-Core Feature Disentanglement Enhances Sparse Cellular Multi-omics Translation

Recent advances in single-cell multi-omics co-assays and spatiotemporal sequencing technologies have provided unprecedented opportunities for systematically characterizing cellular heterogeneity. However, severe sparsity and pronounced spatial heterogeneity--hallmark features of complex diseases and tumor microenvironment--remain major obstacles in deciphering cellular multi-omics data. Here, we present scPhoenix, a contrastive learning-based framework for single-cell cross-modality translation. scPhoenix adopts a two-stage Aux-Core strategy to disentangle modality-specific feature extraction from cross-modality feature interaction. Across diverse datasets, it preserves cellular heterogeneity during translation and demonstrates significant advantages for data with high sparsity. In addition, the framework integrates a contrastive learning framework with five effective data augmentation methods tailored to single-cell data. Moreover, scPhoenixs design supports extensions to unpaired data training and spatial multi-omics translation, enabling robust performance in scenarios with high spatial heterogeneity. scPhoenix is freely available at https://github.com/liwz-lab/scPhoenix.

bioinformatics↗

bioRxiv2025

Transcriptional dynamics of the oligodendrocyte lineageand its regulation by the brain erythropoietin system

Oligodendrocytes differentiate from oligodendrocyte progenitor cells (OPC) in early postnatal development, but some oligodendrogenesis is maintained throughout adulthood, where oligodendrocyte lineage dynamics may contribute to neuroplasticity, adaptive myelination, and myelin repair. Here, we studied the effect of erythropoietin (EPO) and its receptor (EPOR) on oligodendrocyte lineage dynamics employing murine hippocampus and its myelinated fibers as model region. Using multiple stage-specific markers and single-nuclei-RNA-seq data, we find that EPO stimulates all oligodendroglial lineage cells directly, driving differentiation/maturation. Differential gene expression analysis reveals multiple EPO-regulated mRNAs, including downregulated transcripts for GABA-A receptors, fitting the known inhibition of oligodendrocyte maturation by GABA. Importantly, analogous oligodendrocyte responses are seen when endogenous EPO expression in brain is stimulated by hypoxia. Mice lacking EPOR from mature oligodendrocytes show subtle deficiencies of adult myelination in hippocampal fimbria and mild working memory deficits. These gain- and loss-of-function experiments may further suggest EPO as clinically safe treatment for remyelination therapies.

neuroscience↗

bioRxiv2025

Forebrain-specific loss of erythropoietin provokes compensatory upregulation of different EPO receptors

The procognitive growth factor erythropoietin (EPO) and its canonical receptor, EPOR, have long been recognized to be expressed by most cell types in the brain. Cognitive domains, improved by injections of exogenous EPO or by endogenous, hypoxia-stimulated EPO, include important forebrain functions, namely attention, working memory, drive, and executive performance. To gain mechanistic insight into the involvement of forebrain-expressed EPO, we deleted EPO in mice using as specific cre-driver Emx1. Here, we report that these mutant mice act comparably to their wildtype littermates in a comprehensive behavioral test battery. Importantly, we find that the transcripts of both EPOR and a novel, brain-expressed EPO receptor, EphB4, respond to EPO deletion with compensatory upregulation. EphB4 expression in brain and its increase upon forebrain erasure of EPOR are confirmed by in situ hybridization and immunohistochemistry. The augmented expression of both EPOR and EphB4 and their regulatory intercorrelation may explain why EmxEPO mutants show an even superior performance in the most challenging working memory task. Using the previously published single-nuclei-RNA-seq dataset, we further confirm the suggested compensatory mechanism, wherein EPO loss or reduction drives elevated EPOR expression, adding another layer to the intricate regulation of EPO signaling in hippocampal pyramidal neurons. Collectively, these data may explain the lack of behavioral and negative cognitive consequences upon forebrain-wide EPO elimination.

neuroscience↗

bioRxiv2025

Site- and Structure-Specific Characterization of Glycoproteins of H11: Potent Vaccine Candidates against Parasitic Worm Haemonchus

Parasitic worms (helminths) infections pose significant threats to global health and livestock economies. While mass spectrometry (MS)-based glycomics have revealed that helminths express complex, immunomodulatory N-glycans, site- and structure-specific characterization of intact glycopeptides remain challenging. Here we employed advanced MS-based intact glycoproteomics to explore the N-glycosylation profile of H11 antigen - an important vaccine antigen from pathogenic parasite Haemonchus contortus. We successfully identified seven glycosylated aminopeptidases carrying 19 N-glycosylation sites with 31 distinct N-glycan structures. Notably, 13 N-glycopeptides were significantly enriched by H11-induced protective IgG antibodies. Our findings revealed a high degree of structural heterogeneity and abundant core fucosylation among the identified N-glycopeptides. Additionally, molecular docking studies demonstrated those IgG-recognized N-glycopeptides are situated on the protein surface or adjacent to the substrate-access channels, strongly indicating their potential as antigenic epitopes. Overall, our work represents the first comprehensive glycoproteome of an economically important parasitic worm. These results hold important implications for the rational design of vaccines against H. contortus and other related metazoan parasites.

pathology↗

bioRxiv2025

Developmental expression of risk genes implicates the age of onset for neuropsychiatric disorders

The functional effects of genetic variants associated with complex diseases exhibit pronounced spatiotemporal specificity. Although spatially resolved studies have advanced, their temporal dynamics remain poorly characterized. Here, we present an analytical framework integrating developmental gene expression with genome-wide association studies to decipher age-specific windows during which genetic variants exert their effects and to elucidate underlying mechanisms. Applying this framework to five major neuropsychiatric disorders, we uncover a fundamental principle: the peak incidence of a disease precisely coincides with the developmental window of peak expression of its associated risk genes in the prefrontal cortex. These risk windows are characterized by distinct biological processes; for instance, childhood risk for attention-deficit/hyperactivity disorder aligns with a peak in presynaptic machinery gene expression, whereas late-life risk for Alzheimers disease corresponds to heightened immune-related gene activity. Leveraging this principle of temporal convergence significantly improves the prioritization of disease genes. Our work establishes the developmental basis for the age of onset of complex diseases, providing a temporal roadmap for understanding disease mechanisms and developing age-appropriate therapeutic strategies.

genetics↗

bioRxiv2025

Liquid-Liquid Phase Separation of Sp100-HMG: Driving Biogenesis and Functional Diversity of PML Nuclear Bodies

Promyelocytic leukemia nuclear bodies (PML NBs) are membraneless organelles (0.1-1 m) integral to fundamental cellular processes, yet the molecular logic governing their hierarchical organization is unclear. Contrary to the classical "PML-sole-scaffold" model, we identify Sp100-HMG as the unique isoform that autonomously nucleates into liquid-like condensates. Our findings establish an "inside-out" assembly paradigm, where Sp100-HMG initiates a liquid core that recruits PML and other client proteins (DAXX, ATRX) through three distinct cooperative processes: I. Multimerization domain- and intrinsically disordered region (IDR)-mediated LLPS of Sp100-HMG, nucleating the core; II. C-terminal-dependent protein-protein interactions enriching client components; and III. SUMOylation-directed PML recruitment, facilitating the formation of a stabilizing peripheral shell. This assembly paradigm extends beyond Sp100-HMG, as evidenced by ZBTB16--a PML NB-associated oncoprotein implicated in acute promyelocytic leukemia -- adopting an analogous mechanism to organize PML-positive condensates. Using HEp-2 cells as a main model, we show this hierarchical assembly is critical for orchestrating transcriptional programs and cell-cycle dynamics. Together, our study defines a new biogenesis mode for PML-NBs, where a master liquid nucleator coordinates shell integrity and plasticity for nuclear homeostasis. Significance StatementPML nuclear bodies (PML NBs) serve as essential organizers of the cell nucleus, yet the assembly principles underlying their biogenesis and linking it to functional heterogeneity, spatial positioning, and compositional diversity remain elusive. This study overturns the long-standing "PML-centric" view by establishing an LLPS-driven, hierarchical "inside-out" assembly paradigm. We identify Sp100-HMG as a master liquid nucleator that initiates a core to organize the outer PML shell. This inner-core LLPS-driven assembly logic is shared by other PML NB-associated factors, such as the oncoprotein ZBTB16, providing a unified biophysical framework to explain the structural integrity and plasticity of nuclear condensates. Functionally, this organizational process is critical for shaping the compositional diversity and spatial specificity of PML bodies, thereby modulating transcriptional programs and cell-cycle dynamics in a context-dependent manner. These findings offer broad insights into how organized protein condensation sustains nuclear homeostasis and its dysfunction in diseases such as leukemia.

cell biology↗

bioRxiv2025

Oncogenic drivers shape the tumor microenvironment in human gliomas

Gliomas are aggressive and heterogeneous brain tumors with limited treatment options. While oncogenic mutations in gliomas have been well-characterized, their impact on the tumor microenvironment remains poorly understood. To investigate how genomic alterations may influence the glioma microenvironment, we performed an integrative multiomic and spatial transcriptomic analysis of 93 glioma samples (46 IDH-mutant gliomas and 47 IDH-wildtype glioblastoma) from 69 patients representing both primary and recurrent stages. Using whole-genome sequencing, chromatin conformation capture (Hi-C), RNA-seq, and single-cell spatial transcriptomics (Xenium), we defined how major driver mutations influence spatial tumor organization. We found that IDH-mutant gliomas frequently harbored inflammatory microglia expressing CX3CR1 specifically within their astrocyte-like malignant neighborhoods. In contrast, glioblastomas demonstrated relatively higher T-cell infiltration and enrichment of immunosuppressive myeloid cell populations. We further compared glioblastomas harboring EGFR amplifications due to extrachromosomal DNA (ecDNA) amplifications versus linear chromosomal 7 gains. Tumors with EGFR ecDNA displayed increased presence of mesenchymal-like malignant cells, and higher interactions between pericytes and mesenchymal-like malignant cells, likely driven by hypoxia-associated vascular proliferation. Our findings reveal that the mode of oncogene amplification--linear versus ecDNA--shapes distinct tumor architectures and transcriptional dynamics. Taken together, our study highlights the role of oncogenic drivers in shaping the glioma microenvironment, revealing subtype-specific cellular ecosystems that could inform targeted therapeutic strategies.

genomics↗

bioRxiv2025

A CARF-HAD phosphatase effector provides immunity during the type III-A CRISPR-Cas response

CRISPR-Cas systems provide adaptive immunity against phage infection in prokaryotes using an RNA-guided complex that recognizes complementary foreign nucleic acids. Different types of CRISPR-Cas systems have been identified that differ in their mechanism of defense. Upon infection, Type III CRISPR-Cas systems employ the Cas10 complex to find phage transcripts and synthesize cyclic oligo-adenylate (cOA) messengers. These ligands bind and activate CARF immune effectors that cause cell toxicity to prevent the completion of the viral lytic cycle. Here we investigated two proteins containing an N-terminal haloacid dehalogenase (HAD) phosphatase domain followed by four predicted transmembrane helices and a C-terminal CARF domain, which we named Chp. We show that, in vivo, Chp localizes to the bacterial membrane and that its activation induces a growth arrest, leads to a depletion of ATP and IMP and prevents phage propagation during the type III CRISPR-Cas response. In vitro, the CARF domain of Chp binds cyclic tetra-adenylates and the HAD phosphatase domain dephosphorylates dATP, ATP and IMP. Our findings extend the range of molecular mechanisms employed by CARF effectors to defend prokaryotes against phage infection.

microbiology↗

bioRxiv2025

Mapping cellular targets of covalent cancer drugs in the entire mammalian body

As our understanding of biological systems reaches single-cell and high spatial resolutions, it becomes imperative that pharmacological approaches match this precision to understand drug actions. This need is particularly urgent for the targeted covalent inhibitors that are currently re-entering the stage for cancer treatments. By leveraging the unique kinetics of click reactions, we developed volumetric clearing-assisted tissue click chemistry (vCATCH) to enable deep and homogeneous click labeling across the 3D mammalian body. With simple and passive incubation steps, vCATCH offers cellular resolution drug imaging in the entire adult mouse. We combined vCATCH with HYBRiD imaging and virtual reality to visualize and quantify in vivo targets of two clinical cancer drugs, afatinib and ibrutinib, which recapitulated their known pharmacological distribution and revealed previously unreported tissue and cell type engagement potentially linked to off-target effects. vCATCH provides a body-wide, unbiased platform to map covalent drug engagements at unprecedented scale and precision.

pharmacology and toxicology↗

bioRxiv2025

A monophyletic origin of domesticated barley

The origin of domesticated barley has been debated extensively over the past century. Early botanical and comparative morphological research and recent genetic research supported a polyphyletic origin. A monophyletic origin was proposed after the discovery that a single genetic locus controls the presence of hull-less grains in all domesticated barley. Interpreting the origin of domesticated barley is further complicated by the archaeological record showing that the first domesticates had two rows of grain on the inflorescence, as does its wild progenitor. However, these two-rowed types effectively disappeared from the record for thousands of years, and they were replaced by derived six-rowed types that dominated barleys cultivation history and only reappeared in the record around one thousand years ago. Here, we used two independent datasets with large sample sizes and genome-wide genetic markers to re-evaluate barley cultivation history. We unequivocally demonstrate that modern domesticated barley has a monophyletic origin. Phylogenetic reconstruction and examination of current archaeological records suggests that the west Fertile Crescent was most likely where barley was first domesticated. Modern two-rowed types were likely derived from six-rowed domesticated types not earlier than 3,500 years ago in modern Turkiye and Iran. We conclude that the two distinct non-brittle rachis haplotypes, coinciding with distinct row types in cultivated barley, are likely the results of two chronological events along the same evolutionary line. Our results provide a reconcilable framework for explaining genetic and phytogeographic patterns and pave the way for a consensus on the origin of barley domestication.

evolutionary biology↗

bioRxiv2025

Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

Chimeric antigen receptor-engineered macrophages (CAR-Ms) hold great promise for solid tumor immunotherapy. The intracellular domains (ICDs) of CARs determine the phenotypic output of therapeutic macrophages but remain largely unexplored. Here, we constructed a CAR library containing 131 unique signaling domains derived from native immune receptors and identified 17 ICDs that enhance macrophage phagocytosis, inflammatory responses, or tumor infiltration in vitro and in vivo. We further developed a scalable 3 barcode technology, CARode, to uniquely label and trace ICD variants within large-scale combinatorial CAR library and applied it to single-cell RNA sequencing and single-cell CAR analysis to assess the synergetic effects of ICD combinations on macrophage activation. Our approach uncovered a novel CD40-LY9-FCRL1 chimeric receptor that modulates the tumor microenvironment and improves solid tumor clearance. In conclusion, our findings demonstrate that pooled screening can accelerate the discovery of complex ICD constructs, providing a powerful platform for engineering macrophage-based immunotherapies.

bioengineering↗

bioRxiv2025

DNA repair functions are essential for bacterial stress defense but render antibiotic tolerant sub-populations susceptible to ciprofloxacin and gentamicin upon prolonged treatment

The unresponsiveness of bacterial tolerant subpopulations to antibiotics has been attributed to physiological dormancy triggered by environmental stresses. In this work, we showed that protein and DNA synthesis activities in tolerant subpopulations that formed during nutrient starvation remained at a high level and only dropped gradually during the course of six days-starvation. Interestingly, upon decline of these activities, the tolerant subpopulations became susceptible to antibiotics that target protein and DNA synthesis, which was found to be required to support DNA repair functions essential for prolonged survival of the tolerant subpopulation. The increasing susceptibility of the bacterial tolerant subpopulation to antibiotics was also due to diminishing energy production, antioxidant defense and efflux functions, which resulted in weakening defense and further inhibition of synthesis and functions of DNA repair and other defense proteins. These findings confirm that bacterial tolerant subpopulations remain physiological active, and open new opportunities for combating bacterial tolerance with existing antibiotics.

microbiology↗

bioRxiv2024

A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation

Compared to the well-established functions of sympathetic innervation, the role of sensory afferents in adipose tissues remains less understood. Recent work revealed the anatomical and physiological significance of adipose sensory innervation; however, its molecular underpinning remains unclear. Here, using organ-targeted single-cell RNA sequencing, we identified the mechanoreceptor PIEZO2 as one of the most prevalent receptors in fat-innervating dorsal root ganglia (DRG) neurons. We found that selective PIEZO2 deletion in fat-innervating neurons phenocopied the molecular alternations in adipose tissue caused by DRG ablation. Conversely, a gain-of-function PIEZO2 mutant shifted the adipose phenotypes in the opposite direction. These results indicate that PIEZO2 plays a major role in the sensory regulation of adipose tissues. This discovery opens new avenues for exploring mechanosensation in organs not traditionally considered mechanically active, such as the adipose tissues, and therefore sheds light on the broader significance of mechanosensation in regulating organ function and homeostasis.

neuroscience↗

bioRxiv2024

Genome-wide CRISPRi-seq identified ferredoxin-NADP reductase FprB as a synergistic target for gallium therapy in Pseudomonas aeruginosa

With the rise of antibiotic-resistant bacteria, non-antibiotic therapies like gallium are increasingly gaining attention. Gallium ions exhibit potent activity against multidrug-resistant bacteria and intravenous gallium nitrite is under phase 2 clinical trials to treat chronic Pseudomonas aeruginosa infections in cystic fibrosis patients. However, its clinical efficacy is constrained by the achievable peak concentration in human tissue. To address this limitation, we applied a genome-wide CRISPR interference approach (CRISPRi-seq), to identify potential synergistic targets with gallium. Through the systemic screening, we classified the essential genes by response time and growth reduction, pinpointing the most vulnerable therapeutic targets in this species. In addition, we identified a highly conserved gene fprB, encoding a ferredoxin-NADP+ reductase, the downregulation of which dramatically sensitized the cells to gallium. Using a null mutant, we confirmed the loss of fprB lowers the minimum inhibitory concentration of gallium from 320 {micro}M to 10 {micro}M and shifted galliums mode of action from bacteriostatic to bactericidal. Further investigation revealed that FprB plays a critical role in modulating oxidative stress induced by gallium, via control of the iron homeostasis and reactive oxygen species accumulation. Deleting fprB also enhanced galliums efficacy against biofilms formation and improved outcomes in murine lung infection model of P. aeruginosa, suggesting FprB as a promising drug target in combination with gallium. Overall, our data showed CRISPRi-seq as a powerful tool for systematic genetic analysis of P. aeruginosa, advancing identification of novel therapeutic targets.

microbiology↗

bioRxiv2024

The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth

During the process of secondary growth, the vascular cambium produces the conductive xylem and phloem cells, while the phellogen (cork cambium) deposit phellem (cork) as the outermost protective barrier. Although most of the secondary tissues is made up by parenchyma cells which are also produced by both cambia, their diversity and function are poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories of the cell types in the Arabidopsis root undergoing secondary growth. By analysing 93 reporter lines, we were able to identify 20 different cell types or cell states, many of which have not been described before. We additionally observed distinct transcriptome signatures of parenchyma cells depending on their maturation state and proximity to the conductive cell types. Our data shows that both xylem and phloem parenchyma tissues are required for normal formation of conductive tissue cell types. Furthermore, we showed that mature phloem parenchyma gradually obtains periderm identity, and this transition can be accelerated by jasmonate or wounding. Thus, our study reveals the remarkable dynamic and diverse nature of parenchyma cells during secondary growth.

plant biology↗