Biology subjects

Yu, M.

Publications and source records attributed to Yu, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Host Phosphatase PPM1G Governs Influenza vRNP Homeostasis by Orchestrating NP Phosphorylation Dynamics and Autophagy

The influenza viral ribonucleoprotein (vRNP) serves as the machinery for viral RNA replication. It self - assembles from the RNA - dependent RNA polymerase (RdRp), viral RNA, and nucleoprotein (NP). During vRNP replication, NP proteins must rapidly switch between monomeric and polymeric states to sustain dynamic equilibrium, which relies on NP phosphorylation-dephosphorylation cycling and is crucial for viral nucleic acid replication. However, the regulatory mechanisms controlling this process remain poorly understood. In this study, we employed an RdRp/vRNP-targeted affinity mass spectrometry-based differential analysis method, discovered that the cellular protein phosphatase Mg2+/Mn2+-dependent 1G (PPM1G) is a phosphatase of NP and required for maintaining viral polymerase activity. Overexpression of PPM1G decreased viral replication. In ppm1g flox/flox-Sftpc Cre mice, lethal influenza infection led to survival and mild disease, as well as reduced lung viral loads and inflammation. These results suggest that PPM1G is a key host molecule for maintaining steady state of viral replication. PPM1G expression is upregulated upon influenza virus infection. This heightened expression occurs in response to increased viral protein production, simultaneously leading to elevated dephosphorylation of NP, which accelerates NP polymerization to promote viral replication. Meanwhile, surplus NP can be degraded through the ATG7 autophagylysosome pathway. Our research elucidates a mechanism that PPM1G maintains viral replication homeostasis by regulating NP status and fate.

microbiology↗

bioRxiv2025

Remodeling of the immune-metabolic landscape triggered by long-term high-altitude exposure

Growing evidence indicates that immunological and metabolic outcomes are key mediators of long-term high-altitude exposure (LTHAE) adaption, but the underlying mechanisms remain poorly understood. This study employs plasma metabolomics and peripheral blood single-cell transcriptomic sequencing to analyze the metabolic and immune dynamic regulation in 46 young male lowlanders following a 90-day adaptation period at high altitude. Single-cell analysis shows a pattern of "innate immune activation and adaptive immune suppression" under LTHAE, characterized by facilitated maturation of neutrophils, enhanced cytotoxicity of CD56dim NK cells, and increased immune responsiveness of cDC2 and pDC, while inhibited maturation of plasmablasts and suppressed immune responsiveness of CD8{square}TEM and CD4+ T cells. Plasma metabolic analysis reveals significant alterations, involving enhanced steroid hormone synthesis, unsaturated fatty acid and amino acid metabolism under LTHAE, which in turn are associated with immune remodeling. Moreover, transcriptomic-metabolic integration analysis indicates the molecular mechanisms of enhanced aerobic oxidation efficiency under LTHAE. Collectively, these findings provide integrated insights into immune-metabolic landscape remodeling and suggest potential mutual regulatory relationship between immune and metabolic state following LTHAE, offering a molecular foundation for high-altitude adaptation research.

genomics↗

bioRxiv2025

Biomechanical Phenotyping Reveals Unique Mechanobiological Signatures of Early-Onset Colorectal Cancer

While both incidence and mortality of sporadic average-onset colorectal cancer (AO CRC, above 50 years of age) are in constant decline, sporadic early-onset colorectal cancer (EO CRC, under 50 years of age) is rising rapidly. Yet, the causes behind this rise remain poorly understood. Epidemiological studies indicate that lifestyle and environmental exposures may result in chronic inflammation, which is known to trigger tissue fibrosis. This study tests the hypothesis that fibrotic remodeling and biomechanical stiffening of colorectal tissues represent measurable hallmarks and potential drivers of EO CRC. Using primary human tissues, this work shows that EO CRC is associated with changes in collagen microstructure, increased stiffness and elevated viscosity of primary tumors. Spatial transcriptional profiling and immunostaining reveal pro-fibrotic signatures in stromal cells, alongside enhanced Yes-associated protein (YAP) mechanotransduction and proliferation in epithelial cells of EO CRC tissues. Mechanistically, increasing matrix stiffness in vitro promotes proliferation of epithelial cells in 2D and 3D colorectal cancer models. Together, these findings establish EO CRC as a disease marked by early and widespread biomechanical remodeling, suggesting that a fibrotic and stiffened tissue microenvironment may orchestrate EO CRC tumor initiation.

bioengineering↗

bioRxiv2025

Scar-associated endothelial-stellate cellular crosstalk drives fibrosis resolution in MASH

Fibrosis, or scarring, can affect many organs including liver, lung, heart, kidney, intestines etc. and is responsible for [~]40% of mortality in the industrialized world. Compared to other organs, fibrosis in the liver typically resolves when the source of injury is extinguished. Elucidating the molecular mechanisms that underlie spontaneous fibrosis resolution in the liver may lead to novel antifibrotic strategies for all organs. In this study we established a robust mouse model of fibrosis regression in MASH (Metabolic dysfunction-Associated Steatohepatitis), a highly prevalent chronic liver diseases worldwide, and performed single cell and in situ molecular profiling of the liver to define novel drivers of fibrosis regression. As fibrosis regressed, we detected a reduction of inflammatory cells and an expansion of endothelial cells. Prediction of cell-cell communication using the Calligraphy pipeline identified a Wnt9b-Sfrp2 crosstalk that emerges as fibrosis resolved in our model. To establish the Wnt9b-Sfrp2 crosstalk as a driver of fibrosis resolution we treated mice with recombinant Sfrp2, which slowed spontaneous fibrosis regression compared to vehicle treated mice. From our single cell datasets we identified a subset of endothelial cells, termed "Endo4", as the source of Wnt9b. Immunostaining of the Endo4 marker VWF using tissue clearing and 3D imaging revealed VWF+ vasculature enveloped by activated hepatic stellate cells (HSCs) that penetrated deep into the fibrotic septa, establishing Endo4 as de facto scar-associated endothelial cells and providing a structural basis of their cellular crosstalk with HSCs. Finally, using a recently developed in situ protease activity screen, prominent serine protease activity co-localized with both scar-associated Endo4 cells and HSCs. In summary, we uncovered an WNT-dependent endo-stellate crosstalk within the fibrotic niche as a novel regulatory node underlying murine MASH fibrosis regression, and a promising therapeutic target.

molecular biology↗

bioRxiv2025

Mechanical Responses of the Giant Nesprin-2

The nesprin protein family serves as a critical physical bridge between the cytoskeleton-a fundamental structural scaffold and mechanotransduction hub of the cell, and the nucleus-an intriguing and emerging mechano-responsive element. Due to the external mechanical cues and the nucleo-cytoskeletal dynamics, the nesprins are physiologically under forces. However, the dynamics of nesprins within physiological forces and loading rates remain largely unexplored. In this study, we employ magnetic tweezers based single-molecule manipulation alongside molecular dynamic simulations and AlphaFold structural predictions to comprehensively investigate the dynamics of force-bearing spectrin repeat (SR) domains of the giant nesprin-2 protein. Through direct quantification, we unveil that the numerous SRs undergo mechanical unfolding and refolding dynamics with distinct transition rates within several pN scale. Furthermore, we show that the giant nesprin-2 could act as an effective molecular absorber adeptly maintaining forces on the nucleoskeleton and cytoskeleton linkage within a few pN across displacement spans exceeding {micro}m. Notably, our findings imply that subtle pN-level mechanical forces intricately modulate nesprin-protein interactions via the dynamics of domain folding and unfolding. Collectively, our study offers a comprehensive understanding of the mechanical characteristics of giant nesprin-2, shedding light on its pivotal role in nucleoskeleton-cytoskeleton mechanotransduction.

biophysics↗

bioRxiv2025

HDL Nanodiscs Loaded with Liver X Receptor Agonist Decreases Tumor Burden and Mediates Long-term Survival in Mouse Glioma Model

Glioblastoma multiforme (GBM) is highly aggressive primary brain tumor with a 5-year survival rate of 7%. Previous studies have shown that GBM tumors have a reduced capacity to produce cholesterol and instead depend on the uptake of cholesterol produced by astrocytes. To target cholesterol metabolism to induce cancer cell death, synthetic high-density lipoprotein (sHDL) nanodiscs delivering Liver-X-Receptor (LXR) agonists and CpG oligonucleotides for targeting GBM were investigated. LXR agonists synergize with sHDL nanodiscs by increasing the expression of the ABCA1 cholesterol CpG oligonucleotides are established adjuvants used in cancer immunotherapy that work through the toll-like receptor 9 pathway. In the present study, treatment with GW-CpG-sHDL nanodiscs increased the expression of cholesterol efflux transporters on murine GL261 cells leading to enhanced cholesterol removal. Experiments in GL261-tumor-bearing mice revealed combining GW-CpG-sHDL nanodiscs with radiation (IR) therapy significantly increases median survival compared to GW-CpG-sHDL or IR alone. Furthermore, 66% of long-term survivors from the GW-CpG-sHDL +IR treatment group showed no tumor tissue when rechallenged.

cancer biology↗

bioRxiv2025

Effect of Shufeng Xingbi Therapy on Th1/Th2 immune balance and intestinal flora in rats with allergic rhinitis

ObjectiveTo study the effect of Shufeng Xingbi Therapy (SFXBT) on Th1/Th2 immune balance and intestinal flora in allergic rhinitis (AR) rats. Methods32 SD rats were randomly divided into control group, OVA group, antibiotic + SFXBT group and acetic acid + SFXBT group. Evaluate the AR behavioral score, observe the pathological changes of nasal mucosa with H&E, detect the composition and content of colonic contents with 16S rDNA, the levels of serum IgE, IL-4 and short-chain fatty acid (SCFAs) with ELISA, the mRNA expressions of STAT5, STAT6 and GATA3 in nasal mucosa with RT-qPCR, and the protein expressions of IL-4, STAT5, STAT6 and GATA3 in nasal mucosa with Western Blot. ResultsCompared with the OVA group, the AR behavioral score in the antibiotic + SFXBT group and acetic acid + SFXBT group decreased (P < 0.01), and the pathological changes of nasal mucosa were alleviated. At the door level, the relative abundance of Firmicutes in feces increased significantly, while the relative abundance of Bacteroidetes decreased significantly. At the genus level, The relative abundance of fecal Lactobacillus, Romboutsia, Allobaculum and Dubosiella increased significantly, the levels of serum IgE and IL-4 decreased (P < 0.05), the content of SCFAs increased significantly (P < 0.05), and the expression levels of STAT5, STAT6 and GATA3 mRNA and protein in nasal mucosa decreased significantly (P < 0.05). ConclusionShufeng Xingbi Therapy can significantly improve the inflammatory symptoms of nasal mucosa in AR rats, and its mechanism may be closely related to regulating Th1/Th2 immune balance and intestinal flora.

immunology↗

bioRxiv2025

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

The rabbit owns commercial importance in meat and fur production, and also has long served as a valuable animal model in biomedical research. Yet, the complete assembly of a high-quality rabbit reference genome has not been established. Here, we present a telomere-to-telomere (T2T) genome assembly of the New Zealand White (NZW) rabbit, the most complete and accurate rabbit genome to date. Using a haploid embryonic stem cells (haESCs) to overcame the challenges of homologous sequence interference and structural variation, we generate a genome with a contig N50 of 137.71 Mb, anchoring all chromosomes with only three gaps, through integrating long-read sequencing (PacBio HiFi, Oxford Nanopore), Hi-C, and Illumina data. Quality assessments reveal near-complete coverage of the BUSCO mammalian gene set, with 99.61% completeness. Notably, this complete assembly allowed for the first comprehensive annotation of the rabbit immunoglobulin loci and major histocompatibility complex region, which were previously unresolved in earlier genome versions. The NZW-T2T assembly based on haESCs not only provides a critical resource for advancing rabbit-based research, but also set a new benchmark for de novo genome assembly for other animals with complex genome.

genomics↗

bioRxiv2025

Functional redundancy in chicken ANP32A mediates species-specific support of avian influenza virus polymerase

Host restriction of avian influenza virus (AIV) polymerase in human cells is driven by species-specific differences in ANP32A/B proteins. While AIV polymerase relies on ANP32A/B containing a 33-amino-acid insert unique to avian species, the structural and/or mechanistic basis for this requirement remains poorly characterized. Here, we demonstrate that chicken ANP32A (chANP32A) displays three functional determinants enabling its species-specific support of AIV polymerase: (1) a SUMO-interacting motif (SIM), (2) SUMOylation at residues K68/K153, and (3) a 28-amino-acid segment within the avian-specific insertion. These determinants function synergistically and redundantly, requiring at least two for optimal activity, to enhance interactions between AIV viral ribonucleoprotein (vRNP) and chANP32A, thereby promoting AIV vRNP assembly. In contrast, human ANP32A/B--which lack the other two determinants and rely solely on SUMOylation--exhibit a limited capacity to support AIV polymerase activity. Our findings unveil a cooperative mechanism where SUMO-dependent processes and structural motifs in chANP32A enforce species-specific adaptation of AIV polymerase, shedding light on how ANP32A/B governs host restriction of AIV polymerase.

microbiology↗

bioRxiv2025

GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

Functional genomic sequences occupy an infinitesimal fraction of the astronomically large DNA sequence space, implying that evolution explores a low-dimensional manifold shaped by universal biochemical and evolutionary constraints. To investigate this underexplored Genomic Manifold Hypothesis using scalable, data-driven evidence, we developed GenomeOcean, a 4-billion-parameter generative model trained on 219 TB of diverse, co-assembled global environmental metagenomic data using an optimized transformer. The model captures both universal phylogenetic syntax and protein-coding fidelity. Furthermore, we validate the embeddings intrinsic low dimensionality. Crucially, comparisons with the independently trained Evo 2 model demonstrate a strong linear correspondence between their embedding spaces and convergent generative behaviors. These results suggest that the genomic manifold represents a fundamental biological principle, offering a unified framework for understanding evolutionary constraints and guiding synthetic biology.

bioinformatics↗

bioRxiv2025

Single-cell transcriptomics-guided development of flow cytometric tests predicting chronic myeloid leukemia blast crisis transformation at chronic phase diagnosis

Clinical risk scores in chronic myeloid leukemia (CML) are inadequate for identifying chronic phase (CP) patients at high-risk of blast crisis (BC) progression. The lack of accurate predictive tests hamper timely interventions, including stem cell transplants, that are more effective in early disease. By interrogating a single cell atlas of primary imatinib resistance for a BC-like gene expression signature, we identify aberrant CD42A+ megakaryocytic and CD10+CD19+ lymphoid progenitor expansion, as well as STAT1- and IFN{gamma}-related inflammatory programs, as consistent features in the bone marrow and peripheral blood of CP patients at high-risk of BC transformation. We develop multi-color flow cytometry-based tests (MFC) to detect these features in CP patients at the time of diagnosis. Validating our MFC panels on a combined Australia-Singapore cohort comprising 28 CP patients, including 14 who underwent transformation, we demonstrate their ability to detect 100% of CP patients who transform with no false positives. Our findings highlight small populations of inflamed hematopoietic stem and progenitor cells, present at CP diagnosis, as powerful harbingers of future BC transformation. The ability of MFC panels to detect these cells at diagnosis support their inclusion as accurate risk-assessment tools to improve management of high-risk patients.

cancer biology↗

bioRxiv2025

Localized delivery of corticosteroids via in situ modification of gut commensals using a synthetic stem peptide prodrug

Oral colonic drug delivery systems (CDDSs) are oftentimes associated with a short duration of action and poor tissue specificity. To address these challenges, we engineered an oral prodrug that leverages the engraftment and semi-permanence of gut commensals to create a long-acting colonic drug depot. We show that two synthetic stem peptide probes can be stereoselectively incorporated onto the surface of gut bacteria in C57BL/6 mice following oral administration. We then show that a prodrug consisting of budesonide, a corticosteroid with otherwise limiting side effects used to treat ulcerative colitis (UC), conjugated to one of these probes via a hydrolyzable ester is significantly less bioactive and is cleaved over a period of days to weeks in simulated physiological fluids. This prodrug can be integrated into the bacterial peptidoglycan in vitro and be cleaved into free budesonide over time, thereby improving drug localization and potentially rendering it safer for longer-term use. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/632432v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@2fa797org.highwire.dtl.DTLVardef@a3b5e2org.highwire.dtl.DTLVardef@1fa11fdorg.highwire.dtl.DTLVardef@b316c7_HPS_FORMAT_FIGEXP M_FIG C_FIG SIGNIFICANCECorticosteroids are highly effective anti-inflammatory drugs used in the treatment of a variety of conditions. Unfortunately, long-term corticosteroid ingestion can lead to a host of dangerous and undesirable side effects including osteoporosis, glaucoma, and a higher risk of infection, among others. Topical corticosteroids delivered via inhalation (chiefly, budesonide and fluticasone) are the primary long-term treatment modality for chronic asthma symptoms. In contrast to oral corticosteroids, they are considered safer for long-term use when given in moderation because they are directly applied to the airways and exhibit low systemic bioavailability. We sought to apply this successful paradigm to another autoimmune-related disease, ulcerative colitis (UC). We developed a drug delivery system that combines the weakly targeting method of ingestion with a highly specific parameter, microbe prevalence along the gastrointestinal tract, to help improve the specificity and colonic retention of the corticosteroid budesonide, which is currently limited to being used as a short-term treatment for moderate-to-severe UC. Our approach utilizes a largely inert prodrug that can be incorporated into the peptidoglycan of commensal bacteria found at high densities in the colon. After tethering to the bacterial surface via a synthetic stem peptide, the prodrug passively hydrolyzes (cleaves) to release the active, unadulterated form of the drug into the local area, whereas prodrug that traffics elsewhere has a higher chance of being cleared from the body before cleavage. In this manner, we can achieve targeted immunosuppression and sustained release, rendering corticosteroids, and potentially other small molecules, safer for longer term use in treating patients with UC.

bioengineering↗

bioRxiv2024

TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues

The spatial organization of cells plays a pivotal role in shaping tissue functions and phenotypes in various biological systems and diseased microenvironments. However, the topological principles governing interactions among cell types within spatial patterns remain poorly understood. Here, we present the Triangulation Cellular Community Motif Neural Network (TrimNN), a graph-based deep learning framework designed to identify conserved spatial cell organization patterns, termed Cellular Community (CC) motifs, from spatial transcriptomics and proteomics data. TrimNN employs a semi-divide-and-conquer approach to efficiently detect over-represented topological motifs of varying sizes in a triangulated space. By uncovering CC motifs, TrimNN reveals key associations between spatially distributed cell-type patterns and diverse phenotypes. These insights provide a foundation for understanding biological and disease mechanisms and offer potential biomarkers for diagnosis and therapeutic interventions.

bioinformatics↗

bioRxiv2024

PRMT1-Mediated Metabolic Reprogramming Promotes Leukemogenesis

Copious expression of protein arginine methyltransferase 1 (PRMT1) is associated with poor survival in many types of cancers, including acute myeloid leukemia. We observed that a specific acute megakaryocytic leukemia (AMKL) cell line (6133) derived from RBM15-MKL1 knock-in mice exhibited heterogeneity in Prmt1 expression levels. Interestingly, only a subpopulation of 6133 cells expressing high levels of Prmt1 caused leukemia when transplanted into congenic mice. The PRMT1 inhibitor, MS023, effectively cured this PRMT1-driven leukemia. Seahorse analysis revealed that PRMT1 increased the extracellular acidification rate (ECAR) and decreased the oxygen consumption rate (OCR). Consistently, PRMT1 accelerated glucose consumption and led to the accumulation of lactic acid in the leukemia cells. The metabolomic analysis supported that PRMT1 stimulated the intracellular accumulation of lipids, which was further validated by FACS analysis with BODIPY 493/503. In line with fatty acid accumulation, PRMT1 downregulated the protein level of CPT1A, which is involved in the rate-limiting step of fatty acid oxidation. Furthermore, administering the glucose analogue 2-deoxy-glucose (2-DG) delayed AMKL progression and promoted cell differentiation. Ectopic expression of Cpt1a rescued the proliferation of 6133 cells ectopically expressing PRMT1 in the glucose-minus medium. In conclusion, PRMT1 upregulates glycolysis and downregulates fatty acid oxidation to enhance the proliferation capability of AMKL cells. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/628174v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1ae96borg.highwire.dtl.DTLVardef@d27916org.highwire.dtl.DTLVardef@ba63corg.highwire.dtl.DTLVardef@cee9af_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Cell Type Differentiation Using Network Clustering Algorithms

Single cell RNA-seq (scRNA-seq) technologies provide unprecedented resolution representing transcriptomics at the level of single cell. One of the biggest challenges in scRNA-seq data analysis is the cell type annotation, which is usually inferred by cell separation approaches. In-silico algorithms that accurately identify individual cell types in ongoing single-cell sequencing studies are crucial for unlocking cellular heterogeneity and understanding the biological basis of diseases. In this study, we focus on robustly identifying cell types in single-cell RNA sequencing data; we conduct a comparative analysis using methods established in biology, like Seurat, Leiden, and WGCNA, as well as Infomap, statistical inference via Stochastic Block Models (SBM), and single-cell Graph Neural Networks (scGNN). We also analyze preprocessing pipelines to identify and optimize key components in the process. Leveraging two independent datasets, PBMC and ROSMAP, we employ clustering algorithms on cell-cell networks derived from gene expression data. Our findings reveal that while clusters detected by WGCNA exhibit limited correspondence with cell types, those identified by multiresolution Infomap and Leiden, and SBM show a closer alignment, with Infomap standing out as a particularly effective approach. Infomap notably offers valuable insights for the precise characterization of cellular landscapes related to neurodegenration and immunology in scRNA-seq.

bioinformatics↗

bioRxiv2024

Omega-3 fatty acid normalizes postsynaptic density proteins via miRNAs regulation in hippocampus and prevents DEHP-induced impairment of learning and memory in mice

AbstractsDEHP is the most widely used plasticizer in many products. However, growing evidence has indicated that DEHP may induce neurotoxicity. DEHP exposure affects mircoRNAs (miRNAs) expression in brain. A growing body of evidence suggests that nutrients and other bioactive food components prevent neurotoxicity through regulation of miRNA expression. Due to the increasing concern about the risks of DEHP to human health, we explored the neuroprotective effect of Omega-3 fatty acid (Omega-3FA) on subchronic DEHP-induced neurotoxicity in mice, and the potential involved miRNAs and their targets in the protective action of Omega-3FA against DEHP-induced neurotoxicity. Omega-3FA protected against the DEHP-induced impairment of learning and memory and alleviated the thinning of postsynaptic density (PSD) thickness in hippocampal synapses. We observed that there are fourteen up or down regulated miRNAs associated PSD in DEHP exposure which were normalized by Omega-3FA treatment. Protein targets in PSD of these differentially expressed miRNAs were predicted. Furthermore, the expression levels of protein mGluR5, Homer1, and NMDAR2B were carried out via Western blot, for further verifying PSD associated miRNAs targets are involved in neuroprotection of Omega-3FA against DEHP. These findings suggested that Omega-3FA protected DEHP-induced impairment of learning and memory as well as synaptic structure alteration in the hippocampus by regulating the expression of PSD associated miRNAs and their targets. Thus, Omega-3FA should be included in diet to prevent or suppress neurotoxicity caused by continuous exposure to DEHP.

neuroscience↗

bioRxiv2024

Neuronal loss of Galnt2 Impairs O-glycosylation and Leads to Neurobehavioral Deficits Mimicking GALNT2-CDG

GALNT2-CDG is a multi-system genetic disorder due to biallelic pathogenic mutations in GALNT2, which encodes a ubiquitously expressed Golgi-localized glycosyltransferase that initiates mucin-type O-glycosylation. Affected individuals exhibit dysmorphic facial features, short stature, decreased HDL-C, and notable impairments in brain function. GALNT2-CDG patients show global developmental delay without speech development, childhood epilepsy, autistic-like features, and white-matter brain abnormalities. The extent of O-glycosylation in brain development and function remains poorly understood. To address this question, we selectively ablated Galnt2 from pan-neuronal cells in the brain and found that conditional knockout mice exhibit deficits across numerous behavioral domains, including locomotion, motor coordination, sociability, learning, and memory, as well as experience spontaneous seizures, recapitulating characteristic neurological manifestations of GALNT2-CDG. Given the catalytic activity of GALNT2 to initiate mucin-type O-glycosylation, we used glycoproteomics to identify disrupted O-glycosylation in synaptosomes purified from cortical tissues. We ascertained a non-redundant, isoform-specific contribution of GALNT2 to the cortical synaptosomal O-glycoproteome, identifying candidate glycoproteins and disrupted O-glycosites that accompany behavioral abnormalities in knockout mice. These findings demonstrate functional impact of O-glycosylation in neurons, implicating roles of O-glycosylation in diverse molecular and cellular pathways related to neuronal function and provide new opportunities to gain insights into the neurological pathophysiology of GALNT2-CDG.

neuroscience↗

bioRxiv2024

An integrated view of the structure and function of the human 4D nucleome

The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.

genomics↗