Biology subjects

Song, Y.

Publications and source records attributed to Song, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Open neuroinformatics infrastructure ecosystem for federated multisite studies

Despite growing understanding of the benefits of having Findable, Accessible, Interoperable, and Reusable (FAIR) data, many datasets still cannot be shared. Federated analysis methods can enable multisite studies that do not require the sharing of participant-level information. However, there are many practical hurdles that prevent the large-scale adoption of federated methods. We discuss challenges related to cross-site data preparation for federated learning, present solutions offered by recent neuroinformatics projects, and showcase an example of tool integration applied to neurodegenerative disease data.

neuroscience↗

bioRxiv2026

Isolation of folate-producing probiotics and its regulatory effects on homocysteine metabolism and gut microbiota composition

BackgroundFolate deficiency is a global nutritional problem associated with multiple adverse health outcomes, including impaired one-carbon metabolism and elevated homocysteine levels (hyperhomocysteinemia). Gut microbiota-mediated folate biosynthesis has emerged as a promising strategy for improving host folate status. This study aimed to isolate folate-producing probiotic strains, clarify their folate synthesis mechanisms, and evaluate their regulatory effects on folate metabolism and gut microbiota in folate-deficient mice. MethodsHigh-throughput cultivation and screening were performed to isolate folate-producing probiotics. Whole-genome sequencing, pathway reconstruction, and metabolite profiling in fermented milk were used to explore folate biosynthesis pathways and potential microbial cross-feeding interactions. A folate-deficient mouse model was established to evaluate the effects of a probiotic cocktail on serum folate, homocysteine (Hcy) levels, and gut microbiota composition using microbiological assays, biochemical analyses, qPCR, 16S rRNA gene sequencing, alpha diversity analysis, principal coordinates analysis (PCoA), and Linear discriminant analysis Effect Size (LEfSe) analysis. ResultsOver 1,000 bacterial isolates were obtained, and over 10 strains, mainly belonging to Lactobacillus, Bifidobacterium, and Bacillus, showed folate production levels above 100 ng/mL. Genomic analysis revealed that most selected probiotic strains lacked genes involved in para-aminobenzoic acid (pABA) biosynthesis but retained downstream folate synthesis modules, suggesting a potential dependence on pABA-producing gut commensals for precursor supply through microbial cross-feeding. In fermented milk, probiotic strains mainly produced bioactive folates (5-MeTHF and THF), with strain-specific production capacities; L. plantarum, W. coagulans, and B. animalis subsp. lactis significantly increased 5-MeTHF levels in fermented milk. In vivo, high-dose probiotic intervention significantly elevated serum folate (p<0.01) and reduced Hcy (p<0.05) in folate-deficient mice, while medium-dose intervention showed no significant effects. The probiotic strains colonized the mouse gut in a dose-dependent manner: high-dose group exhibited >4,000-fold increase in relative abundance (Bifidobacteriaceae and Bacillaceae enriched), medium-dose group only enriched Bacillaceae, and low-dose group showed no effective colonization. High dose probiotic treatment enhanced gut microbial species diversity (increased Shannon index) and restored folate deficiency-induced gut microbiota dysbiosis (PCoA clustering closer to normal group). ConclusionThis study screened high folate-producing probiotic strains and demonstrated their ability to synthesize active 5-MeTHF, which may rely on microbial cross-feeding in gut microbiota. Furthermore, we demonstrated that folate-producing probiotic intervention significantly improves folate status and Hcy metabolism and restores gut microbiota homeostasis in folate-deficient mice. These findings suggensted that such probiotics could serve as a safer, more physiological intervention for folate deficiency and hyperhomocysteinemia, especially in populations with MTHFR polymorphisms.

microbiology↗

bioRxiv2026

Targeting ALA3 with propiconazole regulates plant growth and enables discovery of promising inhibitor leads

Propiconazole (PCZ) is widely misused growth regulator in leafy Brassica vegetables. Developing green strategies for managing plant architecture has become an urgent agricultural priority. Here, we identified from a membrane-protein-defective yeast library a P4-ATP phospholipid flippase, aminophospholipid ATPase 3 (ALA3), as a target sensitive to PCZ. ALA3 exhibits high binding affinity for PCZ, which inhibits its ATPase activity. Knockdown of ALA3 rendered yeast, Arabidopsis, and Brassica rapa less sensitive to PCZ and conferred a growth-inhibited phenotype. This dwarfing phenotype is mediated through the interaction between ALA3 and CYP51G1 that jointly acts within the brassinosteroid regulatory pathway. Furthermore, we identified lead compounds A01 and A15 as ALA3-targeting agents, and compared to PCZ, they display superior binding affinity and reduced toxicity. Our work establishes ALA3 as a key mediator of PCZ-induced dwarfism and provides dual strategies--creating promising varieties through gene editing and developing targeted green pesticides--to reduce PCZ use. TeaserTargeting ALA3 reduces PCZ use through gene-edited varieties and green pesticides.

plant biology↗

bioRxiv2026

Direct Assessment of Short-Latency Intracortical Inhibition via Immediate TMS-Evoked Potentials

Short-interval intracortical inhibition (SICI) is the most widely used neurophysiological index of GABAergic inhibition in the human cortex. However, it is an indirect measure, inferring synaptic inhibition from suppression of peripherally recorded motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS). In the standard protocol, a subthreshold conditioning pulse suppresses the MEP evoked by a suprathreshold test pulse delivered 1-5 ms later. Interpretation is further complicated by temporal overlap with short-interval intracortical facilitation (SICF), reflecting excitatory interactions at interstimulus intervals of [~]1.5 and 2.7 ms. To overcome these limitations, we recorded immediate TMS-evoked EEG potentials (iTEPs; 1-10 ms post-stimulus) as a more direct measure of motor cortical activity in 16 healthy volunteers (20-35 years; 7 male). The conventional SICI protocol suppressed only later components of the iTEP, likely corresponding to late corticospinal volleys previously identified in epidural spinal recordings after suprathreshold TMS, while the earliest iTEP component was unaffected. Importantly, later iTEPs were suppressed to a similar extent whether conditioning-test intervals coincided with SICF peaks or troughs, and the magnitude of iTEP suppression correlated with concurrently recorded paired-pulse MEP suppression. SICI also reduced an early TEP component (N15; 10-20 ms), but paired-pulse N15 suppression showed a different dependence on stimulus intensity and did not correlate with MEP suppression. These findings demonstrate that SICI measured via MEPs does not reflect a global index of cortical GABAergic motor cortical inhibition but instead reflects inhibition within specific cortical circuits that can be investigated directly with iTEPs.

neuroscience↗

bioRxiv2026

The BraALA3 Homologs Mediate Propiconazole-Modulated Plant Growth in flowering Chinese cabbage

In agriculture, propiconazole (PCZ) controls excessive growth in flowering Chinese cabbage but poses dietary safety risks due to residue accumulation. Therefore, identifying novel PCZ targets and breeding PCZ-free cultivars is critical for the safe production of flowering Chinese cabbage. Here, we identified three P4-ATPase flippase homologs aminophospholipid ATPase 3 (BraALA3a/b/c) in flowering Chinese cabbage that function as sensitive targets for PCZ. These proteins exhibit high binding affinity for PCZ, which directly inhibits their ATPase activity. Overexpression of the BraALA3 homologs enhanced plant growth and increased sensitivity to PCZ, whereas knockdown led to dwarfism and reduced sensitivity. Based on these findings, we identified editable active sites via protoplast-based screening. Genetic transformation of one such site yielded BraALA3a/braala3aK200T mutant lines, which displayed a dwarf and compact architecture. These findings provide a precise molecular target for developing PCZ-free germplasm in flowering Chinese cabbage through gene editing.

plant biology↗

bioRxiv2026

Immune Checkpoint Therapy Drives Maturation of a Cellular Neighborhood Nucleated by T Cell-APC Triads Enabling Spatially Compartmentalized Tumor Immunity

Spatially organized immune hubs of T cells and antigen-presenting cells (APCs) have been linked to immune checkpoint therapy (ICT) efficacy, yet the mechanisms underlying their function remain unclear. Using CODEX multiplex imaging, we longitudinally characterized the dynamic evolution of intratumoral cellular neighborhoods (CN) defined by "triad" interactions of CD4 and CD8 T cells with two distinct myeloid APC populations: cDC1s and IFN{gamma}-activated macrophages. We termed this CN the immunity-promoting CN (IP-CN) and tracked its progressive development during tumor rejection induced by -CTLA-4/-PD-1 therapy. A coordinated IFN{gamma} and TNF signaling signature accompanied the IP-CN assembly. Over time, the IP-CN underwent functional maturation, forming specialized sub-neighborhoods that compartmentalized proliferating T cells at the tumor periphery versus cytotoxic T effector cells interacting with tumor cell targets. Our findings reveal a spatiotemporal mechanism by which the IP-CN sustains and amplifies cytotoxic T cell responses, demonstrating how T cell-APC neighborhoods orchestrate tumor immunity.

immunology↗

bioRxiv2026

The ENL-USP7 Complex Regulates HIV Latency Through BRD4 Stabilization

HIV-1 persists in CD4 T cells and brain microglia through host factors that enforce viral latency, yet the mechanisms that stabilize key transcriptional regulators remain incompletely understood. Here, we identify the YEATS domain-containing protein ENL and its associated deubiquitinase USP7 as a host complex that maintains HIV-1 latency. USP7 stabilizes BRD4 by deubiquitination, suppressing HIV transcription and sustaining viral quiescence. Disruption of the ENL-USP7 complex using selective PROTACs reactivates latent HIV in cell line models, as well as in resting CD4 T cells and microglia isolated from people with HIV on antiretroviral therapy. These findings uncover a critical ENL-USP7-BRD4 axis that enforces HIV-1 latency and highlight USP7 as a potential target for latency-reversing strategies. HighlightsO_LIENL, a YEATS domain-containing crotonylation reader, acts as a suppressor rather than an activator of HIV-1 transcription. C_LIO_LIENL recruits USP7 to stabilize BRD4 and enforce viral latency. C_LIO_LIDisruption of the ENL-USP7-BRD4 axis reactivates latent HIV in T cells and microglia. C_LIO_LITargeting USP7 or ENL reveals a therapeutic vulnerability in HIV reservoirs. C_LI

microbiology↗

bioRxiv2026

AI-Guided Structure-Aware Modeling and Thermal Proteomics Reveal Direct Demethylzeylasteral-ACLY Interaction

Target deconvolution of bioactive natural products (NPs) is frequently hampered by the inability of traditional thermal shift assays to distinguish direct ligand binding from indirect proteomic stabilization. Here, we developed an integrated target discovery framework combining MAPS-iTSA thermal proteomics with a structure-aware graph neural network (HoloGNN). This strategy identified ATP-citrate lyase (ACLY) as a high-confidence target of Demethylzeylasteral, a bioactive triterpenoid from Tripterygium wilfordii. Crucially, orthogonal biochemical assays, including surface plasmon resonance and limited proteolysis, validated its direct binding (KD = 9.86 M) and profound enzymatic inhibition (IC50 = 3.84 M). To establish the relevance of this interaction in the context of the source herb, thermal profiling of Tripterygium wilfordii extract together with ACLY-based affinity-ultrafiltration mass spectrometry supported ACLY engagement and identified Demethylzeylasteral as an ACLY-binding constituent. Given the established role of ACLY-mediated lipid metabolic reprogramming in psoriasis, we further evaluated the pharmacological significance of this interaction. Demethylzeylasteral suppressed keratinocyte proliferation, alleviated imiquimod-induced psoriasiform dermatitis, and reduced inflammatory cytokine expression in vivo. Single-cell RNA sequencing further revealed reversal of ACLY-SREBP-associated lipogenic reprogramming in keratinocytes. Collectively, these findings establish ACLY as a functionally relevant target of DEM and provide a robust AI-chemoproteomic paradigm for mechanism-guided NP drug discovery.

biochemistry↗

bioRxiv2026

Comprehensive characterization of V(D)J recombination from long-read transcriptomic data with VDJcraft

V(D)J recombination generates antigen receptor diversity in developing B and T cells. Long-read transcriptome technologies (e.g., PacBio Iso-Seq, Nanopore RNA/cDNA) capture full-length transcripts and thus resolve V(D)J events more accurately than short-read platforms. However, existing short-read tools are not applicable to or optimized for long-read data. We developed VDJcraft, the first integrated pipeline designed for V(D)J recombination analysis using long-read transcriptome sequencing data. The workflow uses a two-pass alignment strategy: global alignment to the GENCODE reference with minimap2, followed by local realignment and annotation using the international ImMunoGeneTics information system (IMGT). A customized module enhances D-gene detection sensitivity and positional precision. Sequencing errors are reduced through consensus-based correction toward the predominant subclass. Antigen-binding regions are annotated using IMGT-defined motifs to characterize CDRs and binding site composition. VDJcraft was validated on simulated and Human Genome Structural Variation Consortium (HGSVC) datasets and applied to disease datasets. It accurately recovered full-length V(D)J-C sequences and outperformed existing methods in gene detection and recombination accuracy. Long-read calls also showed significantly higher concordance with high-confidence short-read calls (Mann-Whitney U test, p = 1.55 x 10-4). Additionally, we identified 31 putative novel gene subclasses absent from the IMGT database from HGSVC datasets. Analyses of longitudinal blood samples from a COVID-19 patient revealed distinct V(D)J recombination patterns and segment enrichment, characterized by increased IGHV1-2 usage, enrichment of the IGHV3-7/IGHD6-9/IGHJ5_02 rearranged clonotype, and a transient peak in IgG2 levels at day 4 followed by a gradual return to baseline. In conclusion, VDJcraft provides a robust framework for long-read V(D)J characterization and enables the discovery of disease-associated immune signatures.

bioinformatics↗

bioRxiv2026

Cognition emerges from phase dynamics of intrinsic coordination

The brain generates diverse cognitive states while maintaining a stable functional architecture, a duality that remains difficult to reconcile. Prevailing views assume that flexible cognition necessitates correspondingly flexible architecture with different tasks demanding distinct reconfigurations, leaving the coexistence of stability and flexibility unexplained. Here we introduce the intrinsic network flow (INF) framework as a complementary view. This framework is built on temporally coordinated signal flows across brain networks that constitute a universal scaffold, stable across diverse cognitive states and common across individuals. We show that a wide range of task-evoked activation patterns can be reconstructed by modulating only the temporal phase alignment of these flows, whose fixed structure determines functional connectivity topology, gradients, and large-scale networks, thereby preserving these properties across task states and reconciling flexibility with stability. This situates resting-state and task-state dynamics within a unified framework and suggests a generative relationship from flow-like dynamics to the full landscape of resting-state and task-state phenomena. Crucially, phase information achieved 89.9% accuracy in classifying 23 cognitive tasks, outperforming amplitude- or activation-based markers. These findings reframe task-evoked activation and deactivation as interference among concurrent flows. Together, our work indicates that a key variable for cognition is when intrinsic dynamics align in time, not where or how much the brain activates.

neuroscience↗

bioRxiv2026

Seeded aggregation of ANXA11 induces prion-like propagation, TDP-43 co-pathology and nucleocytoplasmic transport defects

Mutations in ANXA11 cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet the mechanisms linking ANXA11 dysfunction to neurodegeneration remain poorly defined. Recent cryo-EM studies revealed heteromeric ANXA11-TDP-43 filaments in patient brains, suggesting a direct pathological connection between these two ALS-associated proteins. However, whether ANXA11 possesses intrinsic amyloidogenic properties and how its aggregation relates to TDP-43 proteinopathy remain unknown. Here, we demonstrate that ANXA11 undergoes liquid-liquid phase separation and subsequently matures into amyloid fibrils through a liquid-to-solid phase transition. ANXA11 fibrils exhibit prion-like properties, including self-templating seeding activity and intercellular propagation in human iPSC-derived neurons. Strikingly, ANXA11 fibrils induces pathological conversion of TDP-43, including hyperphosphorylation, accumulation in detergent-insoluble fractions, and formation of cytoplasmic aggregates. TurboID proximity-labeling proteomics further revealed aggregation-dependent enrichment of nuclear pore complex and nucleocytoplasmic transport factors in the ANXA11 aggregate-proximal proteome. Consistently, ANXA11 aggregation was associated with nuclear envelope abnormalities, altered nucleoporin distribution, impaired mRNA export, and progressive neuronal toxicity in iPSC-derived neurons. Together, these findings establish ANXA11 as an intrinsically amyloidogenic, phase-transition-competent protein whose seeded assemblies propagate between cells, induce TDP-43 co-pathology, and are linked to nucleocytoplasmic transport defects and neuronal injury, thereby providing a mechanistic framework for ANXA11-associated ALS/FTD pathogenesis. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/713853v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1aaad3org.highwire.dtl.DTLVardef@c51d5eorg.highwire.dtl.DTLVardef@10b2891org.highwire.dtl.DTLVardef@1945575_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIANXA11 undergoes liquid-liquid phase separation and matures into amyloid fibrils through a liquid-to-solid phase transition. C_LIO_LIANXA11 fibrils supports homotypic seeding and propagate within SH-SY5Y cells and iPSC-derived neurons. C_LIO_LIANXA11 fibrils induce TDP-43 pathological conversion, including phosphorylation and accumulation in insoluble aggregates. C_LIO_LIANXA11 aggregation is associated with nuclear pore complex remodeling, impaired mRNA export, and neuronal toxicity. C_LI In BriefANXA11 undergoes phase separation and matures into prion-like amyloid fibrils through a liquid-to-solid transition. These seeded assemblies propagate between cells and human neurons, induce TDP-43 pathological conversion, and are associated with remodeling of nuclear pore complexes, impaired mRNA export, and progressive neuronal toxicity. ANXA11 forms seeded amyloid assemblies that spread between cells, induce TDP-43 pathology, and disrupt nucleocytoplasmic transport.

neuroscience↗

bioRxiv2026

A Dynamic Oligomerization Network Coordinates Hemagglutinin-Mediated Membrane Fusion on Influenza Virions

Influenza A virus (IAV) entry is mediated by the trimeric glycoprotein hemagglutinin (HA), which undergoes low-pH-triggered conformational rearrangements to drive membrane fusion. Although biochemical and biophysical studies have long suggested that HA trimers function cooperatively, the structural basis for this cooperativity on intact virions has remained unclear. Here, using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), we determine the in situ structure of prefusion HA on native virions at 3.58 [A] resolution, enabling atomic modeling of membrane-anchored HA. We show that neighbouring HA trimers engage in lateral interactions mediated by HA1 subunits, assembling into flexible dimeric, pentameric, and hexameric organizations that form locally ordered lattices on the viral surface. A 6.0 [A] reconstruction of the HA-dimer reveals the molecular interfaces underlying these assemblies. Disruption of the dominant HA1-HA1 interaction markedly impairs viral entry and slows membrane fusion kinetics. Together, these findings define a virion-level mechanism for coordinated HA activation and establish a structural framework for understanding cooperative membrane fusion by class-I viral fusion proteins.

biophysics↗

bioRxiv2026

Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas

Gliomas comprise a heterogeneous group of central nervous system tumors in which gene fusions (GFs) are significant oncogenic drivers and emerging diagnostic and therapeutic biomarkers. In cancer diagnosis, GF detection largely relies on targeted short-read sequencing fusion panels, such as the Childrens Hospital of Philadelphia (CHOP) Fusion Panel (FUSIP). While these panels are effective for detecting recurrent, well-characterized GFs, they are limited to predefined gene sets and cannot identify full-length transcripts. Here, we analyzed 49 high-and low-grade gliomas previously classified as fusion-negative by FUSIP using an untargeted whole-transcriptome RNA sequencing approach with Oxford Nanopore Technologies (ONT) long-read sequencing. This enabled transcriptome-wide fusion discovery of additional known and potentially novel oncogenic GFs beyond panel constraints. Long-read sequencing further allowed direct resolution of full-length fusion transcripts and their associated isoform structures. By integrating GF detection with isoform-level transcript analysis, we identified fusion-associated transcript isoforms with alternative splicing patterns that aligned near reported GF breakpoints, including ZNF254::GNAS and PTPRK::NOX3, which have not been reported in literature or existing fusion databases. To assess functional relevance, candidate GFs were evaluated using the Drosophila melanogaster model, with ventral nerve cord (VNC) morphology serving as a quantitative in vivo readout of fusion-induced disruption of glial regulation. VNC enlargement or elongation reflects abnormal glial growth or defects in brain tissue organization. Of the 15 candidate GFs subjected to experimental functional testing, 8 induced significant VNC abnormalities relative to wild-type controls, indicating fusion-specific disruption and oncogenic potential. Notably, CLDND1::WRN and DUSP22::APOE produced the most pronounced VNC phenotypes. Together, these findings demonstrate that untargeted transcriptome-wide GF discovery, coupled with long-read isoform-level analysis and in vivo functional validation, enables the identification and prioritization of potentially novel and clinically relevant GFs that are missed by standard targeted short-read fusion panels in glioma.

cancer biology↗

bioRxiv2026

Global O-GlcNAcome Identifies O-GlcNAcylated Proteins Regulating Oligodendrocyte Precursor Cells Differentiation

Oligodendrocyte precursor cells (OPCs) differentiate into myelinating oligodendrocytes to form the myelin sheaths essential for neural function, a process frequently compromised during aging and in diseases like multiple sclerosis. However, the regulatory landscape of myelination remains incompletely understood. Here, we perform a comprehensive proteomic analysis of the O-GlcNAcome in postnatal day 0 mouse OPCs, identifying 165 O-GlcNAcylation sites across 118 proteins. These proteins are mostly nuclear and characterized by single-site modifications. Comparative analysis identifies 74 novel sites and 22 proteins uniquely O-GlcNAcylated in OPCs. Molecular docking suggestes that O-GlcNAcylation might act as a dynamic regulator of OPC differentiation. Notably, global O-GlcNAcylation levels increase during the OPC-to-oligodendrocyte transition. By integrating our findings with multiple sclerosis-related transcriptomic and proteomic datasets, we identify candidate proteins linking O-GlcNAc dysregulation to demyelination. Among these, Vimentin (Vim) exhibits a pronounced age-dependent discrepancy between decreased protein levels and elevated mRNA expression during differentiation. We validate Threonine 35 and 63 as key O-GlcNAcylation sites on Vimentin. Functional assays confirm that blocking Vimentin O-GlcNAcylation enhance the OPC differentiation. Collectively, our study establishes the first O-GlcNAc landscape for OPCs and suggests O-GlcNAcylation as a pivotal regulator for OPC differentiation.

neuroscience↗

bioRxiv2026

Mitotic bookmarking by Prox1 preserves mammalian neuronal lineage identity memory via promoting timely H3K27me3 restoration

Mitosis poses a daunting challenge to transgenerational inheritance of cell identity memory. How neuronal lineage identity is faithfully transmitted across mitosis remains largely unexplored. Here we report that, in mouse hippocampus, the transcription factor Prox1 acts as a mitotic bookmark for safeguarding neuronal lineage identity across cell divisions. Prox1 exhibits mitotic retention in dentate gyrus (DG) neural stem cells and defines DG lineage identity by suppressing the alternative cornu ammonis (CA) identity. Mitotic bookmarking by Prox1 at key bivalent CA identity genes promotes timely and precise restoration of Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition to avoid ectopic expression of CA identity genes and lineage identity crisis. Remarkably, specific mitotic retention-deficient Prox1 conditional knock-in mice produce severe DG developmental defects. Thus, mitotic bookmarking imprints neuronal lineage identity in mouse hippocampus, which is likely to represent a fundamental principle underlying the preservation of lineage identity memory in mammalian brain development.

developmental biology↗

bioRxiv2026

Unleashed condensation by recurrent mutations of an epigenetic regulator promotes cancer

The pathological mechanisms and significance for the prevalent hotspot mutations in disordered protein regions are poorly understood. ASXL1 is an obligate co-factor for BAP1 in H2AK119 deubiquitination. ASXL1 mutations are very frequent in myeloid malignancies, and are mostly C-terminal truncating mutations concentrated in a specific disordered region of ASXL1. ASXL1 truncations are gain-of-function mutations that promote myeloid malignancies, but the underlying mechanisms remain poorly understood. Here we show that the frequently truncated mutants of ASXL1 possess an intrinsic property of forming phase-separated biomolecular condensates, and this property is normally suppressed by the frequently deleted regions. A disease-mutant of the endogenous ASXL1 in leukemia cells forms dynamic nuclear co-condensates with other endogenous factors important for gene activation. The ASXL1 disease-mutants can greatly enhance H2A deubiquitination activity of BAP1 in cells and in vitro reconstituted system, enhance myeloid leukemia cell growth, and promote leukemogenesis in a mouse transplant model by turning on myeloid leukemogenic transcriptional programs. However, substitution of residues important for condensation disrupted or impaired all these abilities, suggesting that the condensation property is crucially important for the ASXL1 mutants in promoting cancer. Moreover, we discover that the conserved negative charges in the highly disordered and frequently deleted region on ASXL1 suppress the condensation of the wild type ASXL1. Charge-neutralizing mutations in this region restores condensation of the full-length ASXL1, and are sufficient to turn ASXL1 into a leukemogenic protein. Biochemical, biophysical, and simulation analyses suggest the intramolecular interactions normally mask the N-terminal region in engaging intermolecular interactions required for phase separation, and disease truncations escape from the regulatory interactions and unleash the phase separation property to form nuclear hubs to promote expression of tumorigenic gene programs. Finally, by showing a striking correlation of the mutation frequencies with the condensation properties and leukemogenesis activity for a series of human patient mutations, we suggest that dysregulation of condensation is a central mechanism for ASXL1 mutations in promoting myeloid malignancies. This suggests that dysregulation of condensation may be a key mechanism for some of the prevalent hotspot disease mutations in the disordered proteomes.

biochemistry↗

bioRxiv2026

Elimination of intramuscular immunoglobulin accumulation alleviates Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is a devastating neuromuscular disorder due to loss of dystrophin, a cytoskeletal protein critical for muscle integrity and functionality. Despite recent therapeutic advances, there remains a significant unmet need for more effective and accessible therapeutics. Here, we discovered an early accumulation of immunoglobulin G (IgG) in the sarcolemma, which exacerbates tissue inflammation and disease progression. The IgG accumulation primarily resulted from ectopic localization of Fc{gamma}R1, a high-affinity IgG Fc receptor, on dystrophin-deficient myofibers. In two independent murine models, eliminating IgG accumulation via B cell depletion provided sustained benefit to alleviate DMD progression. Our findings uncover a novel disease accelerator in DMD and demonstrate the potential to target this mechanism as therapeutics for broader population of patients with DMD.

immunology↗

bioRxiv2026

A lightweight, ultrafast and general embedding framework for large-scale spatial omics data

Deciphering ultra-large-scale omics data with minimal resources while maintaining high computational efficiency is a longstanding challenge in biology. Here, we present Local Pooling (LP), a lightweight, ultrafast and general framework that leverage neighbor-indexing strategy and local pooling module to generate omics embedding and compatible with variety of downstream analyses. We developed its adaptation for spatial omics, SpaLP, and evaluated it on over 20 large-scale datasets spanning 9 technology platforms. SpaLP consistently outperformed baseline methods across multiple benchmarks, including niche identification, expression reconstruction, multiple slices integration, 3D organ construction, multi-omics integration and cross-platform generalization. Notably, SpaLP processed a 1.35-million-cell mouse embryo slice in just 47 seconds, achieving up to 300-fold increase in computational efficiency compared to Graph Neural Network (GNN)-based methods. Meanwhile, SpaLP increased the average adjusted rand index (ARI) by over 30% for niche identification in simulated and realistic settings. Furthermore, we applied SpaLP to integrate 8.4 million mouse brain cells within 4 minutes on a single GPU and constructed a 3D spatial atlas. Finally, we explored SpaLPs ability of cross-platform generalization and potential for developing an omics foundation model. As a novel and general framework, we believe that LP could help more researchers develop new model on large-scale data and overcome the research barriers caused by computing resources in more fields.

bioinformatics↗