Biology subjects

Zhou, H.

Publications and source records attributed to Zhou, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

SARS-CoV-2 NSP14 inhibitor exhibits potent antiviral activity and reverses NSP14-driven host modulation

The emergence of SARS-CoV-2 variants and drug-resistant mutants highlights the urgent need for novel antiviral therapeutics. SARS-CoV-2 NSP14, an N7-guanosine methyltransferase, plays a critical role in viral RNA capping, enabling viral replication and immune evasion. While NSP14 has emerged as a promising drug target, its role in host-virus crosstalk and the cellular consequences of NSP14 inhibition remain poorly understood. Here, we present the identification and characterization of C10, a highly potent and selective first-in-class non-nucleoside inhibitor of the NSP14 S-adenosylmethionine (SAM)-binding pocket. C10 demonstrates robust antiviral activity against SARS-CoV-2, including its variants, with EC50 values ranging from 64.03 to 301.9 nM, comparable to the FDA-approved drug remdesivir in our cell-based assays. C10 also exhibits broad-spectrum activity against other betacoronaviruses and inhibits SARS-CoV-2 at the replication stage. C10 suppresses viral translation and exhibits immunostimulatory effect. Additionally, C10 specifically reversed NSP14-mediated alterations in host transcriptome. The antiviral efficacy of C10 was further validated in a transgenic mouse model of SARS-CoV-2 infection. Our findings highlight C10 as a promising candidate for the development of effective treatments against SARS-CoV-2 and its emerging variants. This study also uncovers a novel mechanism of NSP14 in SARS-CoV-2 pathogenesis and its therapeutic potential, providing insights that may extend to other viral capping methyltransferases.

microbiology↗

bioRxiv2025

Functional recovery by transplantation of human iPSC-derived A2B5 positive neural progenitor cell after spinal cord injury in mice

Human induced pluripotent stem cells (hiPSCs) hold great potential for patient-specific therapies. Transplantation of hiPSC-derived neural progenitor cells (NPCs) is a promising reparative strategy for spinal cord injury (SCI), but clinical translation requires efficient differentiation into desired neural lineages and purification before transplantation. Here, differentiated hiPSCs--reprogrammed from human skin fibroblasts using Sendai virus-mediated expression of OCT4, SOX2, KLF4, and C-MYC--into neural rosettes expressing SOX1 and PAX6, followed by neuronal precursors ({beta}-tubulin III/NESTIN) and glial precursors (GFAP/NESTIN). Both neuronal and glial precursors expressed the A2B5 surface antigen. A2B5+ NPCs, purified by fluorescence-activated cell sorting (FACS), proliferated in vitro with mitogens and differentiated into mature neurons and astrocytes under lineage-specific conditions. NOD-SCID mice received a T9 contusion injury followed by transplantation of A2B5+ NPCs, human fibroblasts, or control medium at 8 days post-injury. At two months, grafted NPCs showed robust survival, progressive neuronal maturation ({beta}-tubulin III [->] doublecortin [->] NeuN), and astrocytic differentiation (GFAP), particularly in spared white matter. Transplantation significantly increased spared white matter volume and improved hindlimb locomotor recovery, with no teratoma formation observed. These results demonstrate that hiPSC-derived, FACS-purified A2B5+ NPCs can survive, differentiate into neurons and astrocytes, and enhance functional recovery after SCI. This approach offers a safe and effective candidate cell source for treating SCI and potentially other neurological disorders.

neuroscience↗

bioRxiv2025

Splicing Retention and Enhancer Divergence Govern the Evolutionary Fate of Ohnologues Following Whole-Genome Duplication in Rainbow Trout

Whole-genome duplication (WGD) produces gene duplicates--known as ohnologues--that expand evolutionary potential while posing challenges for regulatory coordination and functional balance. While divergence in gene expression has been widely studied post-WGD, the long-term evolutionary dynamics of alternative splicing (AS) and its regulatory basis remain unresolved. Here, we investigate the evolution of AS in rainbow trout (Oncorhynchus mykiss), a species that underwent a salmonid-specific WGD [~]100 million years ago. Using a high-quality genome assembly, transcriptome data across six tissues, and ChIP-seq profiling of histone modifications, we classify ohnologue pairs based on their expression divergence, splicing complexity, and epigenetic signatures. We find that most ohnologues are retained through conservation, with a gradual reduction in AS diversity over time. Contrary to earlier models, a substantial fraction of ohnologues follows an independent splicing model, maintaining splicing complexity similar to their unduplicated ancestors. Strikingly, we show that enhancer-associated histone marks, particularly H3K27ac, diverge significantly between neofunctionalized and independently splicing gene pairs, implicating enhancer rewiring as a key driver of regulatory and functional divergence. These findings reveal that AS evolution after WGD is shaped by both selective pressures and epigenetic modulation, challenging assumptions of rapid splicing loss and highlighting the independent model as a dominant long-term fate. Our results provide a unified framework for understanding how splicing and regulatory landscapes evolve following genome duplication, with broad implications for vertebrate genome evolution and functional innovation.

genomics↗

bioRxiv2025

Putative long-range mossy fiber sprouting and regional hypermetabolic capacity in the hippocampus of patients with mesial temporal lobe epilepsy

Mesial temporal lobe epilepsy (MTLE) is pathologically characterized by neuronal loss in the dentate hilus, CA3 and CA1 regions, and mossy fiber (MF) sprouting into the inner molecular layer (iML). The latter forms aberrant excitatory circuities that are considered to facilitate recurrent seizures, with the subiculum also being related to epileptogenic activation. We recently identified a distinct expression of -smooth muscle actin (SMA) at the MF terminals in human hippocampus. This prompted us to explore MF sprouting in resected hippocampi (n=20) from patients with MTLE relative to postmortem control (n=20) using SMA along with reference markers for pathological cross-validation. Compared to control, neuronal loss assessed with neuron-specific nuclear antigen and sortilin immunolabeling reached CA1 in all resected hippocampi. SMA, zinc transporter 3 and {beta}-secretase 1 immunolabeling in the iML tended to be increased. The MF-related markers also revealed a preserved fibrous band extending across CA1 to subiculum. Cytochrome c oxidase immunolabeling also increased in iML and subiculum in the MTLE group. Taking together, the current findings point to the existence of long-range MF sprouting and a regional hypermetabolic compacity in the hippocampal formation of patients with drug resistant MTLE.

neuroscience↗

bioRxiv2025

A Paracrine-to-Autocrine Shunt of GREM1 Fuels Colorectal Cancer Metastasis via ACVR1C

Tumor cells typically rely on paracrine stromal signals to guide malignant behaviors, but whether they acquire signaling autonomy to support metastasis remains unclear. We elucidate this in colorectal cancer (CRC) by uncovering a paracrine-to-autocrine shunt of Gremlin1 (GREM1), a canonical stromal-secreted antagonist of bone morphogenetic proteins (BMPs). We demonstrate that while GREM1 remains restricted to stromal cells in earlier-stage (I-III) CRC, its ectopic expression in tumor epithelium increases markedly in stage IV. Mechanistically, we identify ACVR1C as a novel, high-affinity epithelial receptor for GREM1. Their interaction activates SMAD2/3 signaling, which upregulates SNAI1 and GREM1, establishing a feedback loop that amplifies epithelial-mesenchymal transition (EMT). Disrupting this loop impairs CRC metastasis in vivo. Clinically, epithelial GREM1 or ACVR1C expression predicts metastasis and poor survival. These findings define a paradigm in which tumor cells hijack stromal GREM1 to establish a GREM1-ACVR1C autocrine loop that sustains EMT and metastasis, marking a shift toward signaling autonomy and revealing a targetable vulnerability in advanced CRC.

cancer biology↗

bioRxiv2025

In Silico Screening of Peptide Inhibitors of PHLDA1-Encoded Protein Targeting Cardiovascular Diseases

The PHLDA1-encoded protein (PEP) is a pivotal regulator of cardiomyocyte apoptosis and a promising therapeutic target for cardiovascular diseases. Leveraging in silico approaches, we characterized PEPs structure using AlphaFold3 (AF3) and refined it via molecular dynamics (MD) simulations with various force fields. Kinetic and thermodynamics analysis further confirmed revealed that the Amber99 force field induced the most significant structural change, with the most significant decrease in radius of gyration and lowest potential energy. High-throughput screening of 20 phenylalanine-based dipeptides (FA-FY) revealed sequence-dependent binding to PEP, with FF, FH, FP, and FY exhibiting the maximum count of binders (11, 7, 6, and 6, respectively). Key residues (e.g., L55, C60, E142, E89) formed a continuous binding groove, while FF dipeptides demonstrated cooperative aggregation-enhanced binding. Notably, low-pLDDT regions (< 50) frequently participated in ligand interactions, challenging the rigid "lock-and-key" paradigm and underscoring the role of intrinsic disorder in binding. this work establishes PEP as a tractable target for dipeptide inhibitors and provides a computational framework for designing peptide-based therapeutics against cardiac injury.

pharmacology and toxicology↗

bioRxiv2025

Towards the Development of Isoenergetic Peptide Nucleic Acid Based Probes Targeting Double-Stranded RNAs Through Enhancing Sequence-Specific Stacking Interactions

Peptide nucleic acid (PNA), a synthetic nucleic acid analog, exhibits substantial potential in biotechnology and therapeutic applications due to its high binding affinity and nuclease/protease resistance. Chemically modified PNAs capable of forming stable triplex structures with double-stranded RNAs (dsRNAs) under near-physiological conditions further expand their utility by enabling sequence-specific precise targeting and probing of functional RNA structural motifs. However, the presence of inverted Watson-Crick pairs (C-G and U-A) may significantly weaken the triplex formation of the dsRNA-binding PNAs (dbPNAs). Our previous work demonstrated that dbPNA P3 (composed of L, T, and Q monomers for the recognition of G-C, A-U, and C-G base pairs, respectively) can stimulate ribosomal frameshifting by binding to rHP2, a model RNA hairpin structure in an mRNA, albeit with suboptimal efficiency, due to its significantly weakened Q*C-G triple formation. We hypothesize that incorporating s2U adjacent to Q may offer unique stacking and hydrogen bonding interactions facilitating the development of isoenergetic dbPNA-based probes binding toward dsRNAs with varied sequences. In this study, we investigate how incorporating s2U adjacent to Q residues in P3 influences its binding to rHP2. Bio-layer interferometry (BLI) and non-denaturing polyacrylamide gel electrophoresis (PAGE) analyses demonstrate that substituting T with s2U at the N-terminal position adjacent to Q (P3-2QT) enhances binding affinity by [~]10-fold compared to unmodified P3, whereas C-terminal substitution (P3-TQ2) yields only a 2-fold improvement. Consistent with these findings, a cell-free dual-luciferase reporter assay reveals that P3-2QT significantly increases ribosomal frameshifting efficiency compared to P3 and P3-TQ2. Molecular dynamics simulations further indicate that P3-2QT maintains enhanced PNA-PNA stacking stability, particularly between s2U3 and Q4, suggesting a structural basis for its superior activity. Intriguingly, analogous s2U substitution in the P5 oligomer with the Q replaced by L does not confer a comparable enhancement in binding to the target RNA (rHP1) and frameshifting stimulation, highlighting the context-dependent nature of this modification. To assess the broader applicability of the s2U-Q motif, we examined its effect in dbPNAs targeting the RNA panhandle structure of influenza virus A and precursor microRNA-21, respectively. Both PAGE and BLI data confirm that s2U incorporation improves binding affinity, reinforcing the generality of this strategy. These findings underscore the potential of sequence-dependent uracil thiolation in optimizing triplex-forming dsRNA-binding PNAs, warranting further exploration of modified nucleobase designs to enhance their binding and functional properties. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/662161v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@15d86aborg.highwire.dtl.DTLVardef@1347369org.highwire.dtl.DTLVardef@852040org.highwire.dtl.DTLVardef@84b0a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThiolation of uracil upstream of Q base in PNA markedly enhances triplex binding affinity and enables isoenergetic and orthogonal targeting/activation. C_LIO_LIN-terminal s2U modification adjacent to Q residues increases PNA-dsRNA binding by [~]10-fold and significantly boosts ribosomal frameshifting efficiency. C_LIO_LIBiophysical assays and molecular dynamics simulations reveal that thiolation improves PNA stacking stability and slows dissociation, thereby enhancing functional activity toward structured RNA targets. C_LIO_LIThe general applicability of s2U modification is demonstrated with influenza A virus RNA panhandle structure and precursor micoRNA-21 targets, underscoring its broad potential for optimizing PNA-based therapeutics and biotechnological tools. C_LI

biochemistry↗

bioRxiv2025

Computational Design of Next-Gen Peptide Biopesticides: Targeting the Nicotinic Acetylcholine Receptor in Rice Pests Class

The brown planthopper (Nilaparvata lugens) threatens global rice production, and conventional pesticides face resistance and environmental challenges. We present a computational framework integrating AlphaFold3-predicted structure of the nicotinic acetylcholine receptor 3 subunit (nAChR-3) with multi-force-field molecular dynamics (MD) refinements to design peptide biopesticides. Crucially, we introduce "Dipeptide Probing", a high-throughput MD-based screening strategy employing 20 phenylalanine-containing dipeptides (F-X) to map dynamic binding sites. Unlike rigid docking or static free energy calculations, this approach captures transient interactions and cooperative binding phenomena, identifying Phe-Met (FM) as the top binder through hydrophobic contacts and multiple hydrogen bonding, while{pi} -stacking contributed minimally to complex stability, contradicting conventional paradigms. Additionally, MD simulations revealed an unexpected Aggregation-Induced Hydrophobicity Binding (AIHB) mechanism: FM dipeptides self-assemble via hydrogen bonds, orienting hydrophilic groups toward solvent and exposing hydrophobic surfaces to the target, thereby stabilizing complex formation to the helix bundle surface of nAChR-3. This cooperative behavior, undetectable by docking (e.g., AutoDock Vina failed to predict FM binding) or static energy methods, resolves limitations of reductionist approaches. Our work establishes "Dipeptide Probing" as a generalizable paradigm for dynamic binding-site mapping and underscores AIHBs potential to revolutionize peptide-based agrochemical design by leveraging emergent intra-/intermulti-molecule interactions.

plant biology↗

bioRxiv2025

Targeting ZNRF3 and RNF43 to Restore Regeneration and Reverse Metabolic Dysfunction-Associated Steatotic Liver Disease

Liver regeneration and hepatocyte metabolic identity are disrupted in metabolic dysfunction-associated steatotic liver disease (MASLD) and its advanced form, metabolic dysfunction-associated steatohepatitis (MASH), yet the mechanisms of restore liver regeneration and reprogram metabolism for disease reversal remains poorly understood. Here, we show that {beta}-Catenin activity progressively declines in hepatocytes during MASH in both humans and mice, coinciding with impaired regeneration and defective lipid clearance. Targeted deletion of the endogenous WNT pathway inhibitors ZNRF3 and RNF43 in hepatocytes after MASH onset reactivates {beta}-Catenin signaling, leading to robust regression of steatosis, inflammation, and fibrosis, and restoring regenerative capacity across multiple fatty liver disease models. Mechanistically, this therapeutic effect is driven by {beta}-Catenin-dependent induction of the alternative bile acid synthesis pathway without disrupting systemic lipid homeostasis. Importantly, both short-and long-term deletion of ZNRF3/RNF43 restores liver function without triggering tumorigenesis or hepatotoxicity, indicating a safe therapeutic window. These findings reveal that physiological activation of WNT/{beta}-catenin signaling via ZNRF3 and RNF43 offers a viable regenerative and metabolic strategy for reversing fatty liver disease.

cell biology↗

bioRxiv2025

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses

Characterizing viral strategies for circumventing cellular defenses is critical to understanding the biology and therapeutic application of bacteriophages as antimicrobials. Many bacteriophages synthesize complex modifications (i.e., hypermodifications) to the nucleobases of their virion DNA in order to circumvent the endonuclease-based defenses of their hosts. To date, most hypermodified pyrimidines in viruses are synthesized via group transfer to a pre-existing hydroxyl moiety in DNA during the later stages of lytic development leading up to packaging of the viral chromosome into the capsid. Typically, these occur at hydroxymethylcytosine or hydroxymethyluracil. We find mono- and poly-arabinosylated cytidines completely replacing canonical cytidine in the native DNA of the Escherichia phage RB69 and Acinetobacter baumannii phage DLP3. In both cases, an arabinosyl moiety is connected directly to the pyrimidine through an ether linkage with the bridging oxygen originating from 5-hydroxycytosine (5hoC) in DNA. The 5hoC is synthesized as a mononucleotide by a virally encoded thymidylate synthase homolog. We find diverse virally encoded thymidylate synthase homologs, including the Rhizobium phage RL38J1, are capable of producing 5hoC suggesting this base modification is a starting point for glycodiverse cytosine derivatives. Characterizing these cytosine derivatives adds to our understanding of viral anti-defense mechanisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/659550v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@fcc165org.highwire.dtl.DTLVardef@1fced2aorg.highwire.dtl.DTLVardef@369ceaorg.highwire.dtl.DTLVardef@177df60_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Selective vulnerability of cerebral vasculature to NOTCH3 variants in small vessel disease and rescue by phosphodiesterase-5 inhibitor

NOTCH3 variants cause CADASIL the most common genetic form of small vessel disease (SVD) and vascular dementia (VaD) and increase the stroke and SVD/VaD risk. CADASIL is a systemic vasculopathy but predominantly manifests in the brain. The molecular mechanisms of CADASIL remain largely unclear with no specific available treatments. NOTCH3 is primarily expressed in vascular smooth muscle cells (VSMCs). Using human induced pluripotent stem cell (iPSC) models and developmental lineage-specific VSMC differentiation, we revealed a selective vulnerability of cerebral but not peripheral VSMC mimics to NOTCH3 variants. Transcriptomic, protein and functional analyses demonstrated a switching of CADASIL iPSC-VSMCs from a contractile to a synthetic phenotype, accompanied with extensive extracellular matrix accumulation and impairment of cell adhesion leading to anoikis. Importantly, we describe an endothelial independent nitric oxide signalling in VSMCs which was dysregulated in the CADASIL iPSC-VSMCs, and posphodiesterase-5 (PDE5) inhibition successfully rescued the abnormal VSMC function, suggesting a novel therapeutic strategy. Our findings offer new mechanistic insights into brain specific phenotype in NOTCH3-associated SVD/VaD and support patient-specific iPSCs to be a valuable model for identifying targeted treatment for NOTCH3-associated SVD/VaD.

neuroscience↗

bioRxiv2025

The evolution of interdisciplinarity and internationalization in scientific journals

There is a widely-held perception that science is becoming increasingly international -- both in terms of collaborations involving authors from multiple countries and in terms of publications from authors from a broader group of countries -- and more interdisciplinary, i.e., drawing on knowledge and methods from multiple scholarship domains. However, these hypothesized trends have not yet been characterized quantitatively at the level of individual discipline. The widespread availability of scholarly metadata on scientific publications makes it possible to examine how science has evolved over time. Here, we use OpenAlex metadata to examine potential trends in two groups of peer-reviewed research journals: disciplinary journals in biology, chemistry, economics, medicine, physics, and political science, and multidisciplinary journals that publish articles from multiple fields. Supporting existing perceptions, we find an almost universal trend towards increasing internationalization of both sets of journals. Nevertheless, we find disparities: journals in medicine are less international than journals in other disciplines and are not increasing their levels of internationalization, whereas journals in physics appear to be segregating between those that are international and those that are not. We also find that multidisciplinary journals have undergone significant shifts in their disciplinary focuses over the past century, whereas disciplinary journals appear to have largely maintained their degree of interdisciplinarity.

scientific communication and education↗

bioRxiv2025

Perturbation of epithelial and limbal stem cell identity in a mouse model of pathologic corneal neovascularization

The epithelial layer of the cornea is a critical physical and ocular immune barrier for maintaining tissue integrity, homeostasis, and transparency for proper vision. Corneal injury can trigger inflammation, impair wound healing and compromise immune privilege and avascularity, leading to vision loss. Moreover, injury to the cornea can disrupt the engine of epithelial repair and restoration, the limbal stem cell (LSC) niche. Here we used a corneal suture model to induce epithelial damage, sustained inflammation and neovascularization, to examine the impact on LSCs. Using single-cell transcriptomics, we analyzed corneal cell state changes and additionally evaluated the potential of duloxetine, an FDA-approved medicine, to promote wound healing and corneal homeostasis. Single-cell RNA-seq analysis revealed loss of homeostatic limbal stem cells, basal and differentiated epithelial cells and an increase in distinct limbal-like, conjunctival, inflammatory, and vascular cell states, suggesting a coordinated wound healing response in different tissue layers. Importantly, duloxetine treatment promoted epithelial homeostasis, enhanced stem cell-like and stromal repair processes, and suppressed immune and vascular responses. Examination of corneal cell perturbation and transformations at the single-cell level thorough marker profile annotations can improve the understanding of LSC plasticity and function while yielding potential biomarkers of corneal repair processes.

molecular biology↗

bioRxiv2025

An aphid-resistant plant metabolite as a candidate aphicide: Insight into the bioactivity and action mode of betulin against aphids

Pest-resistant plants usually utilize secondary metabolites to cope with insect infestation. Betulin, a key bioactive compound in aphid-resistant wild peach, possesses promising applications in crop protection. Here, betulin, in both greenhouse and field experiments, displayed excellent control efficacy against Myzus persicae. RNA-seq, qRT-PCR, and western blotting revealed that betulin significantly inhibited the expression of MpGABR (encoding a GABAA receptor). Besides, RNAi-mediated silencing of MpGABR markedly increased aphid sensitivity to betulin. Furthermore, MST (microscale thermophoresis) and voltage-clamp assays indicated that betulin bound to MpGABR (Kd = 2.24 {micro}M) and acted as an inhibitor of MpGABR. Molecular docking, mutagenesis and genome editing suggested that THR228 is a critical and highly conserved site in MpGABR that betulin binds to specifically, causing aphid death. Overall, the activity of betulin depends on specific targeting and inhibition of MpGABR. Elucidating the mechanism of action of this peach-derived insecticide may offer a sustainable green strategy for aphid control.

molecular biology↗

bioRxiv2025

Lactate metabolism antagonizes antiviral innate immunity bypromoting VDAC1-lactylation-mediated mtDNA release

Foot-and-mouth disease (FMD) is an acute, highly contagious disease caused by the foot-and-mouth disease virus (FMDV). Due to its zoonotic nature, this disease not only significantly impacts livestock productivity but also poses a serious threat to human health. FMDV exhibits distinct host specificity, mainly infecting cloven-hoofed animals such as cattle, sheep, pigs, and deer, while perissodactyl animals like horses and donkeys show natural resistance. Elucidating the interspecies differences in response to FMDV infection is essential for understanding the pathogenesis of the virus. In this study, we report that FMDV infection in horse epithelial cells induces the production of lactate, which modulates the function of VDAC1 protein through lactylation, facilitating the release of mtDNA from mitochondria into the cytoplasm. This process activates the cGAS-STING signaling pathway, which stimulates interferon-{beta} expression and suppresses FMDV replication. Our findings provide new insights into the mechanism behind horse resistance to FMDV and lay a theoretical foundation for further research concerning the differential pathogenesis of FMDV infection across species.

cell biology↗

bioRxiv2025

Metabolic reprogramming by endothelial ANGPTL4 depletion protects against diabetic kidney disease

The role of cell-specific ANGPTL4 is not well known in the context of ECs, specifically in pathological angiogenesis and its relation to diabetic kidney disease. Here, we demonstrate that endothelial ANGPTL4 is required to induce a metabolic phenotype that favors mesenchymal activation in ECs and tubules in diabetic conditions. Diabetes accelerates mesenchymal activation and fibrogenesis in control mice however, the same effects were not observed in endothelial-cell specific knock out mice. This mesenchymal activation in diabetes is directly linked with pathological neovascularization, endothelial leakage, lipid and glycolysis metabolite load, de novo lipogenesis (DNL) and related mitochondrial damage, activation of the immune system, c-GAS-STING activation and transcription of pro-inflammatory cytokines. However, endothelial ANGPTL4-depleted mice had stable vessels, improved levels of lipid and glucose metabolism, suppressed levels of DNL, restored mitochondrial function, and mitigated levels of c-GAS-STING-mediated inflammation. Moreover, Inhibition of DNL, and STING via small molecule inhibitors suppressed pathological neovascularization and endothelial leakage, normalized fatty acid oxidation and reduced pathological glycolysis and de novo lipogenesis (DNL). These data demonstrate the crucial roles of endothelial ANGPTL4 in regulating pathogenic angiogenesis in the renal vasculature during diabetes.

molecular biology↗

bioRxiv2025

BMDD: A Probabilistic Framework for Accurate Imputation of Zero-inflated Microbiome Sequencing Data

Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies. BMDD is available at: https://github.com/zhouhj1994/BMDD. Author SummaryUnderstanding the microbes living in and on our bodies--the microbiome--relies on analyzing complex sequencing data. However, these data often contain many zeros, either because a microbe is truly absent or simply missed due to insufficient sampling. These missing values make it hard to accurately analyze microbial patterns and identify important differences between groups, especially for methods that work on a log scale. To address this, we developed a new method called BMDD that uses a more realistic model to impute the zeros. Unlike existing tools that assume each microbe follows an unimodal abundance distribution, BMDD allows for microbes to follow a bimodal distribution, so they could behave differently in different conditions. It provides not just a single guess, but a range of possible values to better reflect the uncertainty. Our testing shows that BMDD more accurately recovers the true microbial profiles and improves the ability to detect meaningful differences between groups. This method can help researchers gain clearer insights into how the microbiome affects health and disease.

genomics↗

bioRxiv2025

Macrophage Migration Inhibitory Factor Suppresses Natural Killer Cell Response and Promotes Hypoimmunogenic Stem Cell Engraftment Following Spinal Cord Injury

Human induced pluripotent stem cells (iPSCs) offer immense potential as a source for cell therapy in spinal cord injury (SCI) and other diseases. The development of hypoimmunogenic, universal cells that could be transplanted to any recipient without requiring a matching donor, could significantly enhance their therapeutic potential and accelerate clinical translation. To create off-the-shelf hypoimmunogenic cells, we used CRISPR-Cas9 to delete B2M (HLA class I) and CIITA (master regulator of HLA class II). Double-knockout (DKO) iPSC-derived neural progenitor cells (NPCs) evaded T cell-mediated immune rejection in vitro and after grafting into the injured spinal cord of athymic rats and humanized mice. However, loss of HLA class I heightened susceptibility to host natural killer (NK) cell attack, limiting graft survival. To counter this negative effect, we engineered DKO NPCs to overexpress macrophage migration inhibitory factor (MIF), an NK cell checkpoint ligand. MIF expression markedly reduced NK cell-mediated cytotoxicity and improved long-term engraftment and integration of NPCs in the animal models for spinal cord injury. These findings demonstrate that MIF overexpression, combined with concurrent B2M and CIITA deletion, generates hiPSC neural derivatives that escape both T- and NK-cell surveillance. This strategy provides a scalable route to universal donor cells for regenerative therapies in SCI and potentially other disorders.

cell biology↗