Biology subjects

Ye, M.

Publications and source records attributed to Ye, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Fatty acid synthesis restricts HIV-1 infection through regulation of the nuclear envelope in CD4+ T cells

HIV-1 must breach intracellular defenses to establish infection in CD4+ T cells, yet the metabolic activities that sustain these barriers remain poorly understood. Using a metabolically targeted small molecule screen, we identify de novo fatty acid synthesis as an unexpected determinant of resistance to HIV-1 infection in activated CD4+ T cells. Inhibition of acetyl-CoA carboxylase 1 (ACC1) or fatty acid synthase (FASN) increased cellular susceptibility to infection, while fatty acid supplementation restored baseline levels of anti-viral resistance. Saturated fatty acids conferred the strongest protection, revealing that susceptibility depends on both cellular metabolic state and the composition of the extracellular lipid environment. Blocking fatty acid synthesis remodeled the cellular lipid pool, particularly for the membrane lipid phosphatidylcholine, and was accompanied by structural disruption of the nuclear envelope that serves as a physical barrier limiting passage of the HIV-1 capsid into the nucleus. FASN inhibition also selectively altered sensitivity to antiretroviral drugs that target the interaction between capsid and the nuclear pore. Broadly, these findings uncover a previously unrecognized role for cellular fat synthesis in the maintenance of the nuclear envelope and reveal that anti-viral pathways can emerge at the interface between cellular state and exposure.

microbiology↗

bioRxiv2026

Light Guiding in Scattering Media Using Focused Laser-Induced Acoustic Waves with an Open Elliptical Reflector

Light scattering in biological tissue limits deep optical imaging. Acoustic waves can modulate optical properties and enhance photon delivery, but source-positioning requirements can complicate integration with other imaging modalities. Here, we present an open elliptical reflector that focuses laser-induced acoustic waves at a spatially separated target while maintaining open optical access. We characterized the spatiotemporal optical modulation induced by the localized acoustic focus. The system increased the local transmitted-light intensity by a factor of 2.57-fold through a 2-mm-thick 1% intralipid hydrogel and enhanced fluorescence signal under two-photon excitation through a 1.5-mm-thick scattering sample. These results demonstrate spatially separated, reflector-based acoustically assisted light guiding for enhanced light delivery and fluorescence excitation through scattering media.

bioengineering↗

bioRxiv2026

The MOS4-associated complex subunit MAC5A maintains meristem development by regulating transcription elongation in Arabidopsis

The precise coordination of co-transcriptional RNA processing with transcriptional elongation is essential for eukaryotic gene regulation, yet the machineries coupling these processes remain largely elusive. Here, we reveal a role for the spliceosome-associated MOS4-associated complex (MAC) in regulating plant development through the direct regulation of transcriptional elongation. We demonstrate that the MAC subunit MAC5A physically interacts with Elongator Protein 6 (ELP6), a core component of the transcriptional Elongator complex. Genetic analyses reveal that MAC5A and ELP6 function synergistically to regulate apical meristem activity. Importantly, the MAC5A-Elongator module is required for the efficient expression of the critical auxin efflux carrier PIN-FORMED1 (PIN1) by enhancing RNA Polymerase II (RNAPII) occupancy across the PIN1 locus. Furthermore, we show that this elongation-promoting function is not unique to MAC5A, as other core MAC components are similarly required for efficient transcription progression. Together, our findings uncover a splicing-elongation nexus where MAC5A likely acts as a molecular bridge between the spliceosome and the elongation polymerase. This functional coupling ensures the efficient transcription of key developmental regulators, providing a mechanistic framework for the coupling of RNA processing to transcription and suggesting a conserved principle of gene expression control across eukaryotes.

plant biology↗

bioRxiv2026

Bone Lymphatic Endothelial Cells Form a Distinct Skeletal Population and Drive Skeletal Repair

Bone regeneration relies on specialized vascular niches, yet the contribution of lymphatic vessels across distinct skeletal sites remains poorly understood. Here, we identify bone lymphatics as an essential component of the regenerative microenvironment in the mandible and long bones. We demonstrate that bone lymphatic endothelial cells (LECs) constitute a specialized endothelial population that is transcriptionally and spatially distinct from periosteal LECs. During skeletal repair, bone LECs reactivate a regenerative transcriptional programme, and promote mandibular and fracture healing. In osteonecrosis of the jaw and periodontitis, bone lymphatic-associated signalling is disrupted, identifying impaired lymphatic function as a shared feature of mandibular disease. Therapeutic activation of VEGFC-FLT4 signalling during injury or mandibular disease restores lymphangiogenesis, enhances osteogenesis, and markedly improves bone regeneration. Together, our findings advance the paradigm-shifting role of bone lymphatics positive regulators of bone regeneration and identify lymphatic activation as a promising therapeutic strategy to enhance bone regeneration in mandibular diseases.

cell biology↗

bioRxiv2026

Immunometabolic Reprogramming by Thyroid-Stimulating Antibodies Drives Orbital Adipogenesis via Histone Lactylation in Thyroid Eye Disease

Thyroid eye disease (TED) is conventionally viewed as an autoimmune inflammatory disorder. However, the metabolic determinants driving orbital tissue remodeling remain largely undefined. Here, we uncover a paradigm-shifting mechanism whereby thyroid-stimulating antibodies (TSAbs) instigate profound metabolic reprogramming in orbital fibroblasts (OFs), driving a switch toward glycolysis and markedly elevating lactate production via the CREB/LDHA axis. Critically, we demonstrate that this TSAbs-induced metabolic perturbation is not a mere byproduct but the principal driver of pathology. Mechanistically, lactate functions as a signaling metabolite that directly potentiates adipogenesis via histone lactylation-dependent transcriptional activation of the master adipogenic regulators PPAR{gamma} and C/EBP. Collectively, our findings underscore metabolic reprogramming as a central pathogenic mechanism in TED, whereby autoimmune cues drive disease progression through metabolic-epigenetic crosstalk. This work substantiates the paradigm of TED as an immune- metabolic disorder.

immunology↗

bioRxiv2026

High-resolution transcriptomic profiling of Arabidopsis thaliana across a 37°C-40°C thermal gradient

Thermal adaptation is critical for organismal viability, with acquired thermotolerance (AT) in Arabidopsis thaliana typically conferred by acclimation temperatures between 34{degrees}C and 37{degrees}C, while acclimation at 40{degrees}C fails to protect against lethal heat stress. To elucidate the transcriptional mechanisms underlying the loss of AT at higher temperatures we performed RNA-seq profiling of Arabidopsis seedlings across a single-degree thermal gradient from 37{degrees}C to 40{degrees}C. Our analysis reveals that all of these temperatures result in a robust heat shock response, characterized by the upregulation of genes involved in protein folding and stress responses. However, each temperature elicits a distinct transcriptional signature. These findings demonstrate that temperature-specific fine-tuning of the heat shock response occurs within this narrow range and that these differences may dictate the successful acquisition of thermotolerance. This dataset provides a valuable resource for understanding the molecular architecture of heat-stress adaptation and the distinct transcriptional states associated with different thermal regimes.

plant biology↗

bioRxiv2026

Benchmarking AI Protein Structure Predictors Reveals a Persistent Bias in Multi-State Proteins

Protein structure predictors achieve high single-state accuracy, but it remains unclear whether they can recover functionally relevant conformational ensembles or account for the presence of ligands and/or binding partners. Here, we benchmark AlphaFold3, Boltz-2, Chai-1, and BioEmu on four canonical multi-state proteins (Pf-MATE, LAO, SecA, and {beta}2AR), quantifying state bias and sampling breadth against experimental reference structures. Models frequently default to a dominant state represented in the PDB; small-molecule ligands have weak or inconsistent effects, while large protein partners drive clear conformational switching between states. Multiple sequence alignment (MSA)-based approaches (AF-Cluster and random subsampling) recapitulate similar biases, indicating that this behavior is not unique to newer architectures. These results underscore current limitations for multi-state protein structure prediction and structure-guided ligand discovery. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/737860v1_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@278cc1org.highwire.dtl.DTLVardef@8a0b66org.highwire.dtl.DTLVardef@f28a21org.highwire.dtl.DTLVardef@14ab675_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

CellTosg2Sequence: A Unified Text-Omics-Signaling-Graph Large Language Model for Single-Cell Analysis

In single-cell (sc)-based scientific discovery, text-formatted biomedical prior knowledge and signaling graphs are essential for annotating and interpreting numeric sc-omics data and for generating novel testable hypotheses. A major limitation of existing single-cell large language models (scLLMs) is that they rely on numeric expression data with gene names as the only textual signal, while comprehensive biomedical priors -- cellular localization, gene function, disease associations, and signaling interaction patterns -- remain absent from the model input. We introduce CellTosg2Sequence, a textual-prior- and signaling-graph-augmented cell-omics-sentence language model. A lightweight heterogeneous graph encoder maps a curated 62,507-node biomedical knowledge graph (KG) into compact virtual tokens that are prepended to each cell sentence, allowing the language model to condition on biological structure with minimal sequence-length overhead. We train CellTosg2Sequence with a three-stage objective: Stage I anchors the KG channel under autoregressive language-model pretraining, leveraging Qwen2.5-32Bs own language reasoning for rapid KG alignment; Stage II aligns labels via supervised fine-tuning with KG-anchored InfoNCE; Stage III applies Group Relative Policy Optimization (GRPO) with an ontology-hierarchy reward, enabling free-generation cell-type prediction that generalizes beyond the closed training vocabulary. Across multiple benchmarks and ablation experiments, CellTosg2Sequence outperforms strong baselines. All results are achieved with lightweight LoRA training and a single unified checkpoint. Data ethicsThis work uses publicly available single-cell datasets from the Human Cell Atlas (https://www.humancellatlas.org) and the Tahoe-100M consortium. All HCA constituent studies were collected under appropriate donor consent and institutional oversight as described in their original publications; we perform computational re-analysis only and introduce no new human subjects data. HCA data access follows the HCA Data Portal terms of use. No new patient data are collected in this study; no additional IRB approval is required for this secondary computational analysis.

bioinformatics↗

bioRxiv2026

MARBL: A Live-Cell Method for Profiling Bioenergetic Heterogeneity by Noncanonical Methionine Labeling of the Cell Surface Proteome

Heterogeneity is a hallmark of biological systems, where cell-to-cell variability supports adaptation to changing environments, but also enables maladaptive states such as drug resistance. Many sources of non-genetic variation, particularly bioenergetics and metabolism, remain difficult to measure in living cells and connect to functional outcomes. Here, we introduce MARBL (Methionine Analogues for Ratiometric Bioenergetics in Live cells), a method that encodes translationally-coupled energetic responses to metabolic stress as an internally normalized signal within the surface proteome of living cells. Applying MARBL to primary immune cells reveals that differences in baseline translational activity can underlie apparent metabolic vulnerabilities, underscoring the importance of ratiometric measurements. We demonstrate that MARBL can enrich pathogenic from non-pathogenic TH17 cells based on resilience to bioenergetic stress, which functionally distinguishes cells that produce IFN{gamma} upon restimulation. Overall, MARBL offers a versatile platform to profile metabolic resilience in living cells and link bioenergetic state to cellular function.

cell biology↗

bioRxiv2026

Neuromodulation of Foxp2+ hypothalamic neurons induces therapeutic hypothermia

The inability to selectively trigger therapeutic hypothermia independent of environmental cooling has hindered causal analysis of its broader physiological benefits. Here, we employed P57, a natural product that pharmacologically induces therapeutic hypothermia circumventing external cold stress, to identify the neuronal substrates underlying hypothermia-induced antitumor effects. Integrating functional ultrasound imaging, activity-dependent neuronal labeling, and single-nucleus RNA sequencing, we identify a previously unrecognized population of Foxp2 neurons in the medial preoptic area (MPA) that are selectively activated by P57. Inhibition of MPA Foxp2+ neurons abolishes P57-induced hypothermia, whereas the paraventricular hypothalamus (PVH) serves as a critical downstream node. Importantly, targeted activation of MPA Foxp2 neurons is sufficient to induce sustained hypothermia, suppress systemic metabolism, and inhibit tumor growth, providing causal evidence that neuronally driven reductions in core body temperature can exert antitumor effects. Together, these findings establish MPA Foxp2 neurons as a controllable node for therapeutic hypothermia induction and demonstrate that neuromodulation of defined neuronal populations can achieve therapeutic benefit by directly controlling physiological states.

neuroscience↗

bioRxiv2026

Detergent-Free Nuclear-Cytoplasmic Fractionation Enables Spatially Resolved PELSA for Enhanced Nuclear Drug Target Identification

Accurate identification of drug target proteins remain major challenges in proteomics-based target discovery, particularly for low-abundance nuclear proteins that are difficult to detect because of the complexity of whole-cell lysates. Here, we developed a detergent-free nuclear-cytoplasmic fractionation strategy compatible with peptide-centric local stability analysis (PELSA), which markedly improves detection of nuclear drug targets. Using K562 cells, we demonstrated that mild detergent-free fractionation enables high-fidelity nuclear-cytoplasmic separation with minimal cross-contamination. When coupled with PELSA, this workflow significantly increases the number of detected nuclear targets relative to whole-cell analysis. Benchmarking with well-characterized nuclear drugs, including the histone deacetylase inhibitor panobinostat and the RNA polymerase II inhibitor -amanitin, our results showed improved identification of canonical nuclear targets. Broad profiling of staurosporine target further revealed expanded kinase target coverage by combining the results of nuclear and cytoplasmic fraction, with the CLK family kinases detected exclusively in the nuclear fractions. Additionally, we showed that PELSA can also be performed on intact nucleus level. Collectively, these findings establish detergent-free nuclear-cytoplasmic fractionation-PELSA as a robust and scalable strategy for spatially resolved drug target identification, improving sensitivity for nuclear and low-abundance proteins.

biochemistry↗

bioRxiv2026

MLL3/4 methyltransferases regulate the differentiation of pluripotent stem cells via cellular respiration

Enhancer-regulating epigenetic modifiers play critical roles in normal physiological processes and human pathogenesis. The major enhancer regulator paralogs MLL3 and MLL4 (MLL3/4) belong to the lysine methyltransferase 2 (KMT2) family, which catalyzes the methylation of lysine 4 on histone H3 (H3K4me). MLL3/4 are required for enhancer activation and are essential for mammalian development and stem cell differentiation. Although recent studies have linked MLL3/4 with different metabolic pathways in the regulation of stem cell self-renewal and cancer cell growth, the mechanisms connecting enhancer function to metabolic control remain elusive. Here, using respiration flux assays, stable isotope tracing, transcriptomics, and stem cell biology techniques, we show that the loss of MLL3/4 impairs glycolysis and mitochondrial respiration in murine embryonic stem cells. Mechanistically, MLL3/4 deficiency suppresses the expression of the rate-limiting glycolytic enzyme hexokinase 2 (HK2) and compromises the function of the oxoglutarate dehydrogenase (OGDH) complex, thereby coordinately impairing central carbon metabolism. Remarkably, combined restoration of HK2 and OGDH rescues the metabolic defects caused by MLL3/4 loss and reinstates differentiation capacity. Taken together, our study identifies a direct link between enhancer-regulating epigenetic machineries and metabolic control of cell fate transition, providing a mechanistic framework for understanding how enhancer malfunction contributes to developmental abnormalities and human diseases.

developmental biology↗

bioRxiv2026

VDJdive and ECLIPSE enhance single-cell TCR sequencing analysis through the probabilistic resolution of ambiguous clonotypes

Single-cell T cell receptor sequencing (scTCR-seq) has transformed our ability to track individual T cell clones and has been instrumental in advancing our understanding of human T cell differentiation. However, current computational pipelines for analysis, which require precise matching of CDR3 sequences from exactly 2 heterodimeric TCR chains to define the clonotype for each cell, are inherently limited because of the substantial proportion of cells possessing "ambiguous" clonotypes driven by missing (undetected from the technical issue of chain "dropout") or extra chains (present from either true biological expression or due to technical artifacts such as cellular doublets and ambient TCR contamination). As a result, clone sizes are artificially reduced, impeding the tracking of clones across conditions and differentiation states. Here we introduce VDJdive and ECLIPSE (Enhanced CLonotypic Inference via Prediction of Single-cell Expression), two computational methods that, together, resolve this clonal ambiguity by utilizing the expectation-maximization algorithm for the clonal prediction of ambiguous cells. These methods consider chain pairings across the sample, allowing for high-fidelity prediction of chains lost due to dropout and the discernment of biological expression of extra chains from technical artifacts. Consequently, clone sizes are augmented and cells without clonotype assignments are minimized. Our approach facilitates enhanced clonal tracking through these elevated clone sizes and is easily implementable, compatible with standard single-cell transcriptomic workflows, and broadly applicable across biological contexts and T cell subsets.

immunology↗

bioRxiv2026

Interorganelle competition for linoleic acid underlies steatotic liver pathology

Lipid droplets (LDs) are traditionally viewed as protective organelles that sequester potentially cytotoxic lipids. However, whether and how LD biogenesis in pathological contexts actively rewires interorganelle lipid homeostasis to drive organelle dysfunction and disease progression remains unexplored. Here, we identify the adipocyte-enriched protein calsyntenin 3{beta} (CLSTN3B) as a critical promoter of metabolic dysfunction-associated steatotic liver disease (MASLD). CLSTN3B, an ER-LD contact protein previously shown to support LD maturation in adipocytes, is robustly induced in mouse hepatocytes by peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) in response to dietary caloric overload. CLSTN3B drives LD biogenesis and neutral lipid storage by stabilizing hemifusion-like ER-LD membrane bridges via its arginine-rich segment. These bridges preferentially recruit cone-shaped linoleoylated phosphatidic acid (PA), diverting linoleic acid (LA) into triacylglycerides (TAGs) rather than mitochondrial cardiolipin (CL), leading to disrupted cristae architecture, deficient ETC supercomplex assembly, elevated electron leak, and oxidative stress. Hepatocyte-specific CLSTN3B deletion impairs LD formation, reduces TAG accumulation, enhances fatty acid oxidation, restores CL maturation, and mitigates oxidative stress, collectively attenuating MASLD progression. Consistently, hepatic CLSTN3B expression correlates with fibrosis severity and progression in human MASLD. These findings position LDs as active regulators of interorganelle lipid partitioning and establish CLSTN3B as a key determinant of mitochondrial vulnerability, providing a general framework for how dysregulated organelle interfaces shape disease.

cell biology↗

bioRxiv2026

AutoPELSA: an automated sample preparation system for proteome-wide identification of target proteins of diverse ligands

Protein-ligand interactions are fundamental to cellular function and drug discovery, and ligand-modification-free strategies have emerged as powerful tools for proteome-wide interrogation of these interactions. Among these, the peptide-centric local stability assay (PELSA) stands out for its high sensitivity. It uses a single digestion step to detect ligand-induced local stability shifts, enabling precise binding region localization and affinity estimation. However, manual PELSA workflows suffer from multiple labor-intensive steps that introduce variability and constrain throughput, limiting large-scale applications. To address these limitations, we developed AutoPELSA, an automated platform that streamlines the PELSA workflow including the limited proteolysis step and the following peptide separation step. AutoPELSA completes 96 samples in [~]4 h, enabling high-throughput analysis under native conditions. AutoPELSA reliably detected targets of both strong-affinity ligands (e.g., staurosporine, identifying 114 kinase targets) and low-affinity ligands, including -ketoglutarate (30 known targets). Furthermore, a mixed-ligand dose-response strategy enabled simultaneous determination of binding affinities for multiple ligand-protein interaction regions in a single experiment. Overall, AutoPELSA provides a scalable and modification-free platform for proteome-wide identification and affinity profiling of ligand-protein interactions.

molecular biology↗

bioRxiv2025

Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors

Female genital tumors (FGTs), including ovarian, endometrial, and cervical cancers, pose a major global health challenge, yet their spatial and molecular determinants of progression and therapy resistance remain poorly understood. Here we present a large-scale integrative spatial and multi-omics atlas of FGTs, combining exome, transcriptome, methylome, and miRNA sequencing with high-resolution Visium HD spatial transcriptomics, profiling over 62 million cells from 100 tumors. We show that HPV-driven suppression of TGF{beta} signaling in cervical cancer disrupts myofibroblast (myCAF) formation and reshapes immune infiltration, while serous tumors exhibit extensive oncogene amplifications that activate MYC and PI3K pathways, linking chromosomal instability (CIN) to proliferative, immune-cold phenotypes. In high-grade serous ovarian cancer, we identify a previously unrecognized malignant domain, the Proliferating Core Desert (PCD) niche, defined by CIN-high epithelial enrichment, immune exclusion, stromal protection, and chemotherapy resistance, maintained through crosstalk with macrophages and fibroblasts. Finally, we develop POWER, a pathology foundation model that predicts PCD niche abundance from routine H&E slides, enabling robust stratification of prognosis and anti-angiogenic therapy response.

genomics↗

bioRxiv2025

Aberrant 5-Methylcytosine tRNA Modification Disrupts Proteostasis and Exacerbates Age-Related Osteoporosis

Age-related protein aggregation drives senile osteoporosis. Aberrant tRNA modifications exacerbate the progression, yet mechanisms linking these to bone loss remain unclear. In this study, we identify Nsun2 (m5C methyltransferase) as key regulator: age-dependent Nsun2 downregulation in BMSCs reduces mC levels of tRNAs, destabilizing tRNAs and impairing translation efficiency of specific transcripts. This directly disrupts the protein synthesis of molecular chaperone and pro-osteogenic factors, accelerating misfolded protein aggregates and activating unfolded protein response, inducing BMSCs senescence and impairing osteogenesis. Mice specifically depleted of Nsun2 exhibited reduced bone mass, whereas mice overexpressing Nsun2 alleviated age-associated bone loss. Notably, the exacerbated protein aggregation and bone mass loss in Nsun2-deficient mice were ameliorated following treatment with the molecular chaperone activator-ML346. Remarkably, ML346 administration proved sufficient to reverse age-related functional deficits in aged mice. Overall, our findings demonstrate that aberrant tRNA-m5C modification alters protein synthesis and induces proteostasis collapse, which constitute a novel contributor to the pathogenesis of senile osteoporosis. Additionally, reduction of protein aggregation through the activation of molecular chaperones presents a promising therapeutic strategy for this disease.

cell biology↗

bioRxiv2025

Integrative Analysis of Proteomics and Metabolomics Reveals Impacts of Sam2 Knockout on Autism Spectrum Disorders

Neurokine Sam2 deficiency is associated with behavioral abnormalities including heightened anxiety and fear responses across evolutionarily conserved model organisms. Here, we employed an integrated proteomics and metabolomics approach using liquid chromatography-mass spectrometry (LC-MS) to elucidate molecular signatures associated with autism spectrum disorder (ASD) in Sam2 knockout mice. Comparative analysis of blood plasma samples from Sam2 knockout and wild-type mice revealed substantial alterations in both proteomic and metabolomic profiles. Proteomic analysis identified 68 differentially expressed proteins (comprising 102 peptides), with notable upregulation of complement component C1qc and downregulation of apolipoprotein A1 (Apoa1), implicating dysregulation of complement cascade pathways. Metabolomic profiling uncovered 15 significantly altered metabolites: nine upregulated species including D-glucuronic acid and 5,10-Methylenetetrahydrofolate, and six downregulated metabolites including folinic acid and acetate. Integrative pathway analysis revealed perturbations in glycolysis/gluconeogenesis and glycerophospholipid metabolism, providing mechanistic insights into the molecular consequences of Sam2 deficiency. These findings identify potential biomarkers for anxiety-related disorders and ASD while advancing our understanding of the complex interplay between genetic alterations and proteomic-metabolomic networks in neurodevelopmental conditions. Our results establish a foundation for developing targeted therapeutic interventions and highlight the utility of multi-omics approaches in dissecting the molecular basis of behavioral disorders.

systems biology↗