Biology subjects

Zhao, Y.

Publications and source records attributed to Zhao, Y..

At least 253 records · Page 14Linked to original sources

bioRxiv2025

EHMT2 Controls Neural Crest-Derived Craniofacial Development but is Dispensable in Limb Development

Post-translational modifications of histones, such as methylation of histone H3 at lysine 9 (H3K9), play critical roles in regulating chromatin structure and gene expression. EHMT2 (also called G9A), a histone methyltransferase, mediates H3K9 mono- and dimethylation and has been implicated in both transcriptional repression and context-specific gene activation. Although global knockout of the mouse Ehmt2 gene results in early embryonic lethality, tissue-specific knockouts have uncovered diverse roles in organ development. However, how EHMT2 contributes to skeletal development in a lineage-specific manner remains to be fully elucidated. Here, we investigated the role of EHMT2 in skeletal development by conditionally inactivating Ehmt2 in neural crest-derived and mesoderm-derived progenitors using Wnt1-Cre and Prx1-Cre mouse lines, respectively. Loss of Ehmt2 function in neural crest cells led to postnatal growth failure and craniofacial defects, including delayed intramembranous ossification and malformations of the jaw and cranial base. Transcriptomic analysis of neural crest cells revealed disrupted chromatin regulatory networks, reduced expression of proliferation-associated genes, and upregulation of inflammatory pathways. In contrast, inactivation of Ehmt2 in Prx1-expressing mesodermal progenitors had minimal impact on limb and cranial bone development, with no significant alterations in bone mass or osteoblast function. Together, these results reveal a lineage-specific requirement for EHMT2 in neural crest-derived skeletal tissues, suggesting that distinct progenitor populations exhibit differential dependency for bone development.

cell biology↗

bioRxiv2025

Hypoimmunogenic human motor neurons induced from iPSCs in vivo substantially ameliorate ALS disease in large animal models

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.

neuroscience↗

bioRxiv2025

Enhancers mediate euchromatin hopping at chromatin contact points

Enhancer-mediated gene activation involves the recruitment of chromatin modifiers and RNA polymerase to target promoters, but it is unknown if enhancers influence chromatin beyond their target genes. Euchromatin and heterochromatin associated histone modifications separate the genome into opposing nuclear compartments. Whereas heterochromatin marks are known to spread from one modified nucleosome to another, no such ability has been ascribed to euchromatin. Using mono-allelic enhancer deletions, native ChIP-seq, and an engineered interaction between an enhancer and transcriptionally inert DNA, we show that enhancers mediate the acquisition of euchromatin features at distal regions through chromatin looping. We term this phenomenon euchromatin hopping and found it occurring on average [~]270kb bidirectionally from enhancers, redefining our understanding of enhancer-mediated chromatin architecture with implications on enhancer identification using chromatin features. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/674255v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@12c6e9aorg.highwire.dtl.DTLVardef@1165feorg.highwire.dtl.DTLVardef@3f08c8org.highwire.dtl.DTLVardef@598bd3_HPS_FORMAT_FIGEXP M_FIG C_FIG Euchromatin hopping modelFigure showing the proposed euchromatin hopping model. TFs recognize and bind to their binding sites in an active enhancer region. Upon activation enhancers recruit coactivators and RNAPII forming a condensate that supports gene activation. After an abundance of transcriptional machinery and coactivators are recruited, adjacent TF bound sites acquire euchromatin features through physical proximity to the active compartment, we call these regions "bystanders". Upon enhancer deletion, condensate formation is lost and active euchromatin marks are not acquired at the gene promoter or other enhancer chromatin contacts. TFs are displayed in yellow, coactivators in green, RNAPII in pink, and histone modifications in red.

molecular biology↗

bioRxiv2025

Prior photon measurement density function constructed in a standard channel space for functional near-infrared spectroscopy

Photon measurement density function (PMDF) determines the measurement locations and their associated sensitivity to the hemodynamic fluctuations of an fNIRS channel, which is essential for pre-experiment optode arrangement and post-experiment signal analysis/results interpretation in fNIRS studies. However, obtaining the exact PMDF relies on individual MR images, which are unavailable in common fNIRS studies. Previous studies alternatively adopt the PMDF derived from single head templates, i.e., template-PMDF, which ignores the anatomical difference between the template and the participants, as well as the anatomical variability across participants. Here, we propose a methodological framework using a standard channel space to construct a prior-PMDF from a structural MRI database for arbitrarily given channel locations. We demonstrate the utility of the prior-PMDF in estimating channel-wise fNIRS imaging parameters, such as subject-specific PMDF, sensitivity in intracerebral and extracerebral tissue compartments, and sensitivity to regions defined by brain atlas. The performance of the prior-PMDF tested on an independent dataset was compared with the template-PMDF. The results show that the prior-PMDF significantly surpasses the template-PMDF.

bioengineering↗

bioRxiv2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

Tumor evolution is driven by various mutational processes, ranging from single-nucleotide vari- ants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alter- ations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational frame- work for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by indepen- dent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods.

genomics↗

bioRxiv2025

Structural insights and engineering of deep-sea halophilic PET hydrolytic enzymes

Pervasive use of polyethylene terephthalate (PET) poses tremendous challenges for global waste management and environmental sustainability, fueling growing interests in enzymatic degradation as an eco-friendly solution. While PET hydrolases hold significant promise, their industrial deployment is hindered by insufficient performance, particularly under high-salinity conditions raised from high substrate loads. Building on our previous discovery of three deep-sea PET hydrolases (dsPETase01, dsPETase05 and dsPETase06) with exceptional halophilicity and PET-degrading activity, we here present their three-dimensional structures and mechanistic characterization. Structural comparison, site-directed mutagenesis, and domain swapping reveal key structural features and the essential role of C-terminal acidic residues in salt tolerance. Integrating semi-rational protein design, Transformer-based modeling, and disulfide bond engineering, we synergistically enhance the thermostability and catalytic efficiency of dsPETase05. These findings elucidate the unique structural features and salt adaptation mechanisms of deep-sea halophilic PET hydrolases, and inform the future engineering of biocatalysts for application in harsh industrial environments.

molecular biology↗

bioRxiv2025

Contrasting patterns of interleukin signalling in LRRK2 and idiopathic Parkinson's

Sporadic PD and LRRK2-associated Parkinsons Disease (PD) present with similar features although the familial form of disease is classically associated with less cognitive impairment, better REM sleep behaviour, and reduced incidence of hyposmia but more freezing gait and postural instability. Although being classified as the same disease from a clinical perspective there is an ongoing debate on whether these 2 conditions are linked to different causative molecular mechanisms. In this work we analysed the transcriptomics and proteomics profile of sporadic and LRRK2 PD patients to contrast and compare inflammatory markers in blood and CSF. Analyses showed molecular differences in the burden of inflammatory signals clearly differentiating the sporadic and the familial forms of disease. Finally, a cluster of closely connected proteins whose expression levels were changed in the familial forms of disease was highlighted. The levels of these inflammatory markers were associated with tau pathology suggesting this protein cluster might be a system model to evaluate the control of tau metabolism in the presence of LRRK2 mutations.

neuroscience↗

bioRxiv2025

Mapping the impact of microplastics exposure on enteric viral infections in intestinal organoid models

Micro- and nanoplastics (MNPs) are pervasive environmental pollutants increasingly detected in human tissues, yet their long-term health consequences remain poorly understood. The intestinal epithelium, continuously exposed to ingested MNPs and serving as a primary entry site for enteric viruses, provides a critical context to study pollutant-pathogen interactions. We used human intestinal organoids to model chronic exposure, found that prolonged NPs exposure potentially triggered mitochondrial stress and broad metabolic disruption without overt toxicity. This reprogramming altered the host-virus response and also reduced sensitivity to the antiviral treatment. These findings suggest that chronic plastic exposure may subtly but persistently reshape mucosal physiology in ways that alter host-pathogen response and therapeutic efficacy, highlighting an urgent need to address environmental pollutants in infectious disease and public health research.

cell biology↗

bioRxiv2025

Endothelial LRRC8C associates with LRRC8A and LRRC8B to regulate vascular reactivity and blood pressure

Vascular tone is impacted by the endotheliums ability to detect mechanical and chemical stimulation. Leucine-Rich Repeat-Containing protein 8A, (LRRC8A), was previously identified as a required component of the mechanoresponsive endothelial LRRC8 complex regulating AKT-endothelial nitric oxide synthase (eNOS) signaling and vascular function. While LRRC8A is broadly expressed, LRRC8B, C, D and E have tissue-restricted expression. Here, we identified 2 single nucleotide polymorphisms (SNPs) in LRRC8C highly associated with elevated diastolic and systolic blood pressure in human genetic studies, implicating LRRC8C as a regulator of vascular function. While LRRC8A/B/C/D/E are expressed in endothelium, co-immunoprecipitation experiments from lung endothelium using Lrrc8a-3xFlag knock-in mice, Lrrc8c-HA knock-in mice and endothelium-specific Lrrc8a-3xFlag overexpression mice demonstrate the endothelial LRRC8 complex to be composed largely of LRRC8A/B/C heteromers. Lrrc8a/b/c knock-out studies in mice and knock-down studies in human umbilical vein endothelial cells show co-dependent expression of LRRC8A/B/C proteins, but not LRRC8D. Functionally, LRRC8A and LRRC8C depletion reduces endothelial volume regulatory anion channel (VRAC) currents, inhibits AKT-eNOS signaling, increases myogenic tone, impairs eNOS dependent vasodilation, and exacerbates angiotensin-induced hypertension. These data identify LRRC8A, LRRC8B and LRRC8C as components of the endothelial LRRC8 complex and reveal LRRC8C as having a non-redundant role in regulating endothelial AKT-eNOS, vascular relaxation and susceptibility to hypertension.

cell biology↗

bioRxiv2025

Detection of prostate cancer in 3D pathology datasets via generative immunolabeling

Recent advancements in nondestructive 3D pathology offer a complement to standard histology by enabling comprehensive volumetric analyses of intact clinical specimens (e.g. biopsies). Prior studies have demonstrated the added prognostic value of 3D pathology for prostate cancer risk stratification by correlating 3D microarchitectural features with long-term patient outcomes. However, these analyses relied on coarse manual annotations of cancer-enriched regions for downstream analysis without fine-grained delineation between often-intermixed cancerous and benign glands. To address these limitations, we have developed a 3D computational pipeline: Synthetic Immunolabeling for Generative Heatmaps of Tumor (SIGHT). SIGHT relies on deep learning-based 3D image translation models, trained in a fully supervised fashion, to convert H&E-analog 3D pathology datasets into multiplexed 3D immunofluorescence datasets that facilitate tumor detection. Our implementation of SIGHT synthetically labels two cytokeratin markers that are differentially expressed in cancerous and benign prostate glands, which are used to generate explainable 3D heatmaps of cancer-enriched regions in prostate tissues. Validation of SIGHT against ground-truth annotations from a panel of genitourinary pathologists yields an average F1 score of 0.88 which is comparable to the average inter-pathologist agreement F1 score of 0.90. To demonstrate the value of SIGHT, we developed machine classifiers of recurrence risk based on 3D glandular histomorphometric features from 75 patients. Volumetric glandular analysis in SIGHT-identified cancer-enriched regions vs. all tissue regions yields an average Kaplan-Meier hazard ratio of 3.57 (1.6 - 7.9 CI) vs. 0.92 (0.45 - 1.89 CI).

pathology↗

bioRxiv2025

A population-scale atlas of blood and tissue in lupus nephritis

One Sentence SummaryA single-cell atlas of paired blood and tissue samples from Lupus Nephritis patients and healthy controls identified stromal and immune populations within renal tissue, including the scar-associated macrophage populations, which correlate with and may drive renal disease activity. Lupus nephritis (LN), a severe manifestation of Systemic Lupus Erythematosus (SLE), is a heterogeneous disease driven by diverse immune and tissue cell types. We obtained 538K single-cell and 140K single-nuclear profiles from kidney biopsies of 155 LN patients and 30 pre-implantation transplant biopsy controls, along with 325K single-cell blood profiles overlapping many of these patients. We identified key tissue cell types and cell states, and immune cell states; we were able to determine cell states that were tissue specific, and those that were present in the blood. We observed that LN pathological features are significantly associated with cell states using differential gene expression and Covarying Neighborhood Analysis (CNA). These analyses revealed broad changes in cell states associated with irreversible chronic tissue damage. After controlling for the effects of ongoing tissue damage, we observed that expansion of key glomerular and Scar Associated Macrophages (SAMs) populations tracked with increasing inflammatory disease activity. SAMs appear to drive LN fibrosis and, in active disease, infiltrate the glomeruli more than other myeloid cells. These observations strongly support that therapeutic targeting of myeloid populations may offer an as-of-yet unproven strategy to prevent renal inflammation and ongoing kidney damage in LN.

molecular biology↗

bioRxiv2025

The antioxidant networks act as a firewall in maintenance of genomic integrity

Reactive oxygen species (ROS) threatens genomic integrity by both destruction of DNA metabolic enzymes and oxidative DNA damage. We find a negative correlation between oxidative DNA damage and activity of antioxidant enzymes. An antioxidant network formed by interactions between the antioxidant enzymes and the proteins involved in maintenance of genomic integrity was indentified in the nucleus by multi-proteomic investigations. The protein-protein interactions in the antioxidant network are up-regulated under oxidative stress, as proved by quantitative proximity ligation assays in situ within single cells. The antioxidant network catalyzes the ROS dismutation cascade before ROS attacks DNA-processing enzymes, thereby preventing DNA and DNA metabolic enzymes from oxidative damage and dysfunction. Therefore, the antioxidant network plays a firewall role in maintenance of genomic integrity.

biochemistry↗

bioRxiv2025

BioScientist Agent: Designing LLM-Biomedical Agents with KG-Augmented RL Reasoning Modules for Drug Repurposing and Mechanistic of Action Elucidation

Drug discovery is protracted, resource-intensive, and afflicted by attrition rates exceeding 90 %, which leaves most diseases, particularly rare or neglected indications, without effective therapies. Drug repurposing offers a cost effective alternative, yet systematic identification of novel drug indication pairs and mechanistic rationales remains hindered by the scale and heterogeneity of biomedical knowledge. We present BioScientist Agent, an end to end framework that unifies a billion-fact biomedical knowledge graph with (i) a variational graph auto-encoder for representation learning and link prediction driven drug repurposing, (ii) a reinforcement learning module that traverses the graph to recover biologically plausible mechanistic paths, and (iii) A large language model (LLM) multi-agent layer that orchestrates these components, enabling inference of target pathways for a drug disease pair, and automatic generation of coherent causal reports. In all downstream tasks, the BioScientist Agent surpasses existing state of the art baseline models across various metrics and provides mechanistic explanations consistent with the literature. Its open and modular design accelerates hypothesis generation and reduces experimental overhead in early stage discovery.

bioinformatics↗

bioRxiv2025

Hyaluronic Acid-Modified Mesoporous Manganese Dioxide Combined with Carboplatin Synergistically Enhances Ovarian Cancer Therapy

Ovarian cancer (OC) is a prevalent malignant tumor that poses a significant threat to womens health. Conventional chemotherapeutic agents, such as carboplatin, are associated with several limitations, including notable side effects and the emergence of drug resistance. Carboplatin (CBP) and hyaluronic acid (HA) were subsequently loaded into nanoparticles through incubation to construct targeted nanoparticles (210.3 nm, -31.2 mV) capable of delivering both chemotherapy and chemodynamic therapy. In vitro experiments demonstrated that these nanoparticles enhanced ROS generation through enzyme-like activity and induced immunogenic cell death (ICD) by releasing damage-associated molecular patterns (DAMPs), such as ATP and HMGB1. In vivo animal studies revealed that the nanoparticles predominantly accumulated at the tumor site within 24 hours and significantly suppressed tumor growth by activating the cGAS-STING pathway. These findings indicate that the CBP@HMnO2@HA nanoparticles exhibit potent chemotherapeutic and chemodynamic properties, along with strong catalytic activity. This study presents a promising nanotechnology-based strategy for cancer therapy. HighlightsO_LIThe CBP@HMnO2@HA nanoparticles integrate chemotherapy with chemodynamic therapy, thereby enhancing anti-tumor efficacy. C_LIO_LIThese nanoparticles induce ROS-mediated immunogenic cell death, leading to the release of DAMPs, including ATP and HMGB1. C_LIO_LIThrough HA-mediated targeting, the nanoparticles demonstrate preferential accumulation within tumor tissues, resulting in significant tumor growth inhibition in vivo while reducing off-target toxicity. C_LI

cancer biology↗

bioRxiv2025

Betrixaban Activates cGAS and ERVs to Promote Dual Nucleic-Sensing Antiviral Immunity

Broad-spectrum host-directed antivirals are urgently needed, as virus-targeted drugs often suffer from narrow specificity and rapid resistance. Here, we reported that Betrixaban (BT), an FDA-approved oral Factor Xa inhibitor, induced a robust antiviral state through dual innate immune pathways. Mechanistically, we identified BT directly bound and activated the DNA sensor cGAS to induce cGAMP production, representing BT as the first small-molecule cGAS agonist. Concurrently, BT inhibited histone deacetylases (HDACs), leading to chromatin de-repression of endogenous retroviruses (ERVs) and production of immunostimulatory double-stranded RNA (dsRNA) that engaged RIG-I/MDA5. These combined signal cascades triggered strong type I interferon responses and conferred broad-spectrum antiviral protection against RNA and DNA viruses in vitro and in vivo. These findings unveil a unique host-directed antiviral strategy wherein a small molecule drug engage dual nucleic acid-sensing pathway, and suggest repurposing BT as an orally broad-spectrum antiviral. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/669242v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@aa153dorg.highwire.dtl.DTLVardef@585d43org.highwire.dtl.DTLVardef@152ec59org.highwire.dtl.DTLVardef@11ada33_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Diverse microbial communities assemble on both recalcitrant and labile carbon sources

Microbial community assembly is shaped by the nature of available resources, with labile carbon sources such as glucose often expected to support low diversity due to rapid growth and competitive exclusion. In contrast, recalcitrant substrates like cellulose are thought to support higher diversity through slower growth and increased niche partitioning. In previous work, we showed that compost-derived microbial communities propagated on cellulose maintained high diversity over nearly a year. To determine whether such diversity is specific to recalcitrant substrates or reflects more general features of assembly, we tracked community dynamics in three environments--cellulose paper, cellulose broth, and glucose--using daily 16S rRNA profiling over eight weeks. Communities were maintained through bi-weekly serial transfers, with five replicates per treatment, yielding a high-resolution dataset of over 800 samples. Despite originating from the same inoculum, communities diverged sharply in both taxonomic and functional composition. Cellulose environments yielded stable communities enriched in specialists, while glucose environments exhibited rapid succession and dominance by generalists. Surprisingly, all environments sustained comparably high levels of taxonomic diversity. Functional inference suggested extensive cross-feeding and resource salvaging in both cases. While the mechanisms maintaining diversity on glucose remain unresolved, our results reveal distinct assembly trajectories under simple carbon regimes and provide a foundation for future mechanistic study.

ecology↗

bioRxiv2025

RESM: Capturing sequence and structure encoding of RNAs by mapped transfer learning from ESM (evolutionary scale modeling) protein language model

RNA sequences exhibit lower evolutionary conservation than proteins due to their informationally constrained four-letter alphabet, compared to the 20-letter code of proteins. More limited information makes unsupervised learning of structural and functional evolutionary patterns more challenging from single RNA sequences. We overcame this limitation by mapping RNA sequences to pseudo-protein sequences to allow effective transfer training from a protein language model (protein Evolution-Scale Model 2, protESM-2). The resulting RNA ESM (RESM) outperforms 12 existing RNA language models in zero-shot prediction, not only in sequence classification but also in RNA secondary structure and RNA-RNA interaction prediction. Further supervised fine-tuning demonstrates RESMs generalizability and superior performance over the existing models compared across multiple downstream tasks, including mRNA ribosome loading efficiency and gene expression prediction, despite RESM being trained exclusively on noncoding RNAs. Moreover, RESM can generalize to unseen sequences beyond its 1,024-nucleotide training limit, achieving 81.3% improvement over state-of-the-art methods in supervised secondary structure prediction for RNAs up to 4,000 nucleotides, limited only by the available GPU memory, while providing >1000-fold speedup compared to MSA-based approaches. RESM provides a robust foundation for deciphering RNA sequence-structure-function relationships, with broad implications for RNA biology.

bioinformatics↗

bioRxiv2025

Serotonin shapes the temporal window for associative fear learning

Fear learning is a critical adaptive mechanism that enables the association of an environmental cue (the conditioned stimulus, CS) with a potential threat (the unconditioned stimulus, US), even when these events are temporally discontiguous. When associations are instead formed between unrelated cues and threats, the maladaptive learning process can give rise to neurological disorders. Therefore, maintaining accurate temporal boundaries for forming such associations is crucial for distinguishing real threats from irrelevant stimuli. Despite its importance, the mechanisms defining this precise time window remain poorly understood. Here, we report that serotonin plays a crucial role in modulating the associable interval in trace fear conditioning. Specifically, we show that serotonergic projections from the dorsal raphe nuclei (DRN) to the CA1 region of the ventral hippocampus (vCA1) dynamically regulate the association of discontiguous CS and US. Mechanistically, we demonstrate that sustained serotonin release in the vCA1 maintains the ensemble activity of 5-HT2C receptor-expressing pyramidal neurons, facilitating the association between temporally separated events. In contrast, when the trace interval exceeds the associable window, transient serotonin release fails to drive vCA1 neuronal ensemble activity, thus preventing maladaptive learning. These findings highlight a key role for serotonin in regulating the temporal precision of fear learning and reveal the DRN-vCA1 serotonergic pathway as a potential therapeutic target for related disorders.

neuroscience↗