Biology subjects

Chang, W.

Publications and source records attributed to Chang, W..

At least 19 recordsLinked to original sources

bioRxiv2026

A SUN1-ApoD feedback loop promotes cellular aging via microtubule-nuclear mechanotransduction

Alterations in nuclear envelope proteins such as SUN1 and prelamin A are known hallmarks of cellular aging, but how they cause aging phenotypes beyond the expressing cells is unknown. With a tissue culture version of parabiosis, we found that aged fibroblasts secrete an activity that induces aging-related polarity defects in young fibroblasts. Secretomics identified the factor as apolipoprotein D (ApoD), a circulating protein whose levels are known to rise with age. ApoD increased SUN1 levels and disrupted polarity in fibroblasts via SUN1-promoted coupling of microtubules to the nucleus. In turn, elevated SUN1 enhanced ApoD expression and secretion, forming a feedback loop that promotes acquisition of aged phenotypes. In mice, ApoD induced aging-related phenotypes in muscle. Elevated ApoD expression required coupling between SUN1, its outer nuclear membrane binding partner nesprin-2, and microtubules. Broader analysis revealed that this pathway regulates hundreds of genes. These findings define microtubule-nuclear coupling as a direct mechanotransduction pathway controlling gene expression and promoting aging-associated phenotypes.

cell biology↗

bioRxiv2026

VC1 and the production of vicine and convicine in the genus Vicia

Many Vicia species contain vicine and convicine (VC), which limit the use of faba bean and some vetches in food and feed. The first step in VC biosynthesis in V. faba is shared with the riboflavin pathway and attributed to VC1, a member of the ribAB family. Since riboflavin is ubiquitous to life, we examined the distribution of VC production in genus Vicia. Three accessions of each of 33 Vicia species were grown in glasshouse conditions to provide fresh seeds for VC analysis and leaves for DNA analysis. PCR was used to amplify fragments of the VC1/ribAB gene for sequencing, and these sequences were used to create a phylogenetic tree. COX1 and ITS2 sequences were used for examining the nucleotide diversity in the subgenera. VC and DNA sequences consistent with VC1 were found only in members of subgenus Vicia. In V. lathyroides, VC1 was present but no VC was detected. There was less sequence diversity in VC1/ribAB sequences of subgenus Cracca than in those of subgenus Vicia, suggesting that ribAB remained under stricter purifying selection than VC1. VC1 is confirmed as a prerequisite for the presence of VC, and the gene and its products are restricted to subgenus Vicia. HighlightThe favism-causing factors of vetches and faba bean, vicine and convicine, depend on the presence of the VC1 variant of the ribAB gene, which is found in only one subgenus.

plant biology↗

bioRxiv2026

A Metabolic Enzyme, Pyruvate Carboxylase, Functions as a Sequence-Selective Small RNA Sensor for Antiviral Immunity

Interleukin-27 (IL-27) is an anti-HIV cytokine that induces 14 novel microRNAs (miRNAs) in primary CD4(+) T cells. We previously reported that transfection of two of these miRNA mimics, miRTC10 and miRTC14 into human primary macrophages, differentially induced interferon (IFN)-2, -8, -13, and -{lambda}1 expression. However, the mechanism underlying this activation remains unclear. Here, we demonstrate that miRTC14 does not directly target canonical IFN-regulatory genes but instead engages with pyruvate carboxylase (PC) and laboratory of genetics and physiology-2 (LGP2/DHX58) as direct binding partner proteins. Functional analysis revealed that miRTC14 transfection induces IFN expression by more than 100-fold (p<0.001), whereas PC or LGP2 depletion by siRNAs markedly attenuated this response (50-100-fold reduction, p<0.01). Reconstitution of PC and LGP2 in deficient HEK293 cells restored miRTC14-driven IFN induction. Notably, IFN activation depended on sequence features at the duplex termini. However, PC-miRTC14-LGP2 axis activates TBK1-dependent phosphorylation of IRF3/7, similarly to canonical RNA sensors (RIG-I/MDA5), but this process induced differential IFN subtype. These findings establish PC as a miRNA-binding protein and define a previously unrecognized RNA-sensing mechanism, linking metabolic enzymes to RNA sequence-dependent innate immunity. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/735367v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ea70d3org.highwire.dtl.DTLVardef@1953a73org.highwire.dtl.DTLVardef@305f16org.highwire.dtl.DTLVardef@1b2daff_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO microRNA sequence-dependent activation of innate immunity by pyruvate carboxylase (PC). PC-miRTC14-LGP2 axis induces TBK1 phosphorylation via an as-yet-unidentified adapter(s). The activated TBK1 (p-TBK1) subsequently phosphorylates IRF3 and/or IRF7 leading to selective IFN subtypes (IFN-2, IFN-8, IFN-13, and IFN-{lambda}1). (Created in BioRender. Kariyawasam, U. (2027) https://BioRender.com/u82s04p) C_FIG

immunology↗

bioRxiv2026

Systemic interindividual epigenetic variants link periconceptional environment to human fetal development

At rare human genomic regions, DNA methylation states are established in the early embryo and maintained during cellular differentiation, yielding systemic (i.e. not tissue-specific) interindividual epigenetic variation. Previous screens for such correlated regions of systemic interindividual variation (CoRSIVs) were limited to White Americans. Here, we describe the first human CoRSIV screen including self-identified Black and White Americans. We integrate deep whole-genome bisulfite sequencing data for three tissues from each of ten Black and ten White donors in the NIH Genotype-Tissue Expression program. This approach identifies twice as many CoRSIVs among Black than White Americans. Establishment of CoRSIV methylation is sensitive to periconceptional environmental exposures including assisted reproduction, seasonal variation, and famine. CoRSIV-associated genes are enriched for GWAS variants linked to cancer and neurodevelopment. Although only 15% of Black CoRSIVs overlap with those among White individuals, both sets are associated with the same subfamilies of transposable elements. Within multiple cell lines, ranked enrichments of transcription factor binding to Black and White CoRSIVs are exquisitely coordinated and related to genome organization, indicating that CoRSIV methylation states established in the early embryo play an important role in guiding subsequent cellular differentiation.

Molecular Biology↗

bioRxiv2026

β-Catenin Drives Apical-Basal Polarization to facilitate TE lineage commitment In Vitro and In Vivo

Embryo polarization is critical for the first cell fate segregation. While mechanisms underlying its initiation have been described, the intrinsic signaling pathways that regulate this process remain poorly understood. Here, we show that mouse embryonic stem cells, when aggregated under defined conditions, recapitulate the first lineage segregation to generate trophectoderm (TE)-like cell populations and undergo self-organized morphogenesis into blastocyst-like structures. In the blastoid-forming medium, we identify CHIR99021 is essential for the generation of blastoids from both ESCs and totipotent-like cells. CHIR99021 promotes cell polarization and TE differentiation by activating the WNT/{beta}-catenin pathway and upregulating associated genes. Consistent with this, genetic ablation of {beta}-catenin abolished the cell polarization and disrupted blastoid formation from ESCs, a defect that was restored by {beta}-catenin overexpression. Moreover, {beta}-catenin depletion compromised cell polarization in natural embryos. Collectively, this study establishes the Wnt/{beta}-catenin as a critical regulator initiating polarization in vitro and in mouse early embryo development.

developmental biology↗

bioRxiv2026

Structure and functional analyses of vaccinia virus J5 protein reveal distinct determinants for entry-fusion complex assembly and activation

Vaccinia virus enters host cells through a multi-component entry fusion complex (EFC) that is structurally distinct from canonical viral fusion systems. Understanding how vaccinia virus EFC mediates membrane fusion is crucial for elucidating poxvirus entry and identifying potential antiviral targets. Here, we report the solution NMR structure of a truncated ectodomain of vaccinia J5 protein, residues 2-68. Using recombinant vaccinia viruses expressing J5 mutants, we analyzed substitutions in conserved and surface-exposed residues, as well as chimeric constructs between vaccinia J5 and its entomopoxvirus ortholog AMV232. Functional analyses revealed that the conserved P38YYCWY43 motif is dispensable for EFC assembly but required for membrane fusion activity whereas the flexible region spanning residues 90-110 mediates interactions required for stable incorporation of J5 into the EFC. ImportanceVaccinia virus enters host cells through membrane fusion mediated by a unique multi-component entry fusion complex (EFC) that is distinct from classical viral fusion proteins. Although J5 has been identified as a central component of the pre-fusion EFC, the structural regions of J5 required for membrane fusion remain unclear. Here, we determined the solution NMR structure of the J5 ectodomain and identified two regions, the conserved P38YYCWY43 motif and residues 90-110, as key determinants of EFC function during vaccinia virus entry.

microbiology↗

bioRxiv2025

Type 2 diabetes Reprograms Bone Marrow Hematopoiesis and Dysregulates Immune Signaling in Response to Stroke

Type 2 diabetes mellitus (T2DM) worsens stroke outcomes, but the underlying mechanisms linking T2DM to systemic immune dysfunction remain unclear. We investigated whether T2DM alters bone marrow (BM) hematopoiesis and dysregulate immune signaling following ischemic stroke in mice. Single-cell RNA sequencing, GeoMx digital spatial profiling (DSP), nCounter, and flow cytometry were used to analyze BM cells from control (db/+, Ctrl) and diabetic (db/db, T2DM) mice underwent experimental stroke or sham surgery. Diabetes caused marked structural remodeling of BM, with reduced cellularity and imbalance of hematopoietic lineages. Pseudotime trajectory analysis revealed impaired differentiation and maturation signatures of hematopoietic progenitor cells (HPC1) and granulocytes, and overactivation toward monocytes in diabetes after stroke. CellChat analysis demonstrated reorganization of intercellular communication, with hematopoietic progenitor cells (HPC1) and monocytes emerging as dominant signaling hubs through upregulated MIF, SIRP, and THBS pathways. AUCell enrichment indicated increased glycolysis and oxidative phosphorylation but reduced interferon-{gamma} (IFN-{gamma}) signaling, reflecting metabolic activation coupled with immune dysregulation. DSP and nCounter further confirmed upregulation of genes in the MIF, SIRP and THBS pathways in CD115 monocytes and Ly6G neutrophils, indicating proinflammatory and migratory activation in diabetic bone marrow. Our data suggest that T2DM reprograms hematopoiesis and signaling networks, leading to maladaptive myeloid responses and impaired immune regulation after stroke. This maladaptive BM environment amplifies inflammation and limits repair, linking diabetic metabolic stress to worsened ischemic outcomes. Targeting bone marrow immune dysfunction may offer a therapeutic strategy to improve stroke recovery in diabetic patients.

neuroscience↗

bioRxiv2025

Structure and functional analyses of Vaccinia virus entry- fusion complex component J5 protein

Vaccinia virus enters host cells through an 11-protein entry fusion complex (EFC) that operates by a mechanism distinct from those of canonical viral fusion systems. Understanding how this multiprotein complex mediates membrane fusion is crucial for elucidating poxvirus entry and identifying potential antiviral targets. Here, we determined the NMR structure of a truncated J5 protein, (J5 2-68). To further dissect the functional determinants of J5, we generated recombinant vaccinia viruses expressing various J5 mutants, including substitutions in conserved residues, alterations of exposed charged residues, and chimeric constructs between vaccinia J5 and its orthologous AMV232 gene from an entomopoxvirus. Functional analyses revealed that residues 90-110 and the conserved P38YYCWY43 motif are indispensable for maintaining EFC integrity and promoting membrane fusion. Together, we define the structural and functional elements of J5 that are essential for poxvirus entry and advance our understanding of the unique membrane fusion mechanism employed by poxviruses. ImportanceVaccinia virus enters host cells through an eleven-protein entry fusion complex (EFC) that is mechanistically distinct from canonical viral fusion systems. Understanding how this multiprotein machinery mediates membrane fusion is essential for elucidating poxvirus entry mechanisms and for developing antiviral strategies. Here, we determined the NMR structure of the J5 ectodomain and generated a series of recombinant vaccinia viruses carrying J5 mutations. Functional analyses identified two regions, residues 90-110 and the conserved P38YYCWY43 motif, as essential for EFC stability and membrane fusion. These findings provide the first structure-function framework for J5, a core component of the EFC, and reveal key determinants required for complex integrity and viral entry.

microbiology↗

bioRxiv2025

Generation of apical-out nasal organoids to facilitate viral infection and drug screening

Advanced culture systems such as organoids can serve as powerful platforms to study epithelial physiology, as they recapitulate the organisation and many key functions of the tissue of origin. The nasal epithelium is the first respiratory epithelium that is exposed to inhaled airborne pathogens. As a result, it is crucial to model host-pathogen interactions occurring in this tissue. To facilitate the efficient modelling of these interactions, we have developed a method to generate de novo apical-out nasal organoids from nasal epithelial cell aggregates. Optimisation of this method revealed a stark tissue-specific effect of the culture temperature, as apical-out nasal organoids were generated in much higher efficiency at 32.5 {degrees}C, compared to more widely used temperatures of 37{degrees}C. These organoids are composed of ciliated, basal and goblet cells and are produced in a completely standardised and scalable manner, devoid of any extracellular matrix hydrogel. Moreover, they displayed high homogeneity in size and cellular composition, as well as susceptibility to viral infections and capability to model antiviral drug responses. Here, we describe a method for the efficient and reproducible generation of apical-out nasal organoids with high potential to be utilised in host-pathogen interaction studies and personalised medicine from easy-to-access nasal swabs.

cell biology↗

bioRxiv2025

Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability

Polysaccharides are known to be synthesized by enzymes in the endoplasmic reticulum and Golgi apparatus and transported through the secretory pathway to the cell surface or extracellular space1, where they mediate essential biological processes2-6. While classical localization and functions of polysaccharides are well established, their presence and potential roles in the nucleus remain unclear. Here, we demonstrate that N-glycans, a type of polysaccharides, are present in the cell nucleus and modify inner nuclear membrane (INM) proteins across diverse cell types--a modification referred to as N-linked glycosylation (N-glycosylation). N-glycosylation is enriched in chromatin regions marked by H3K9me3 and long interspersed nuclear element-1 (LINE-1) retrotransposons. N-glycosylation inhibition and INM protein N-glycosylation site mutation both downregulate H3K9me3 within lamina-associated domains (LADs) and lead to genomic instability. Mechanistically, N-glycosylation regulates the interaction between the histone H3K9 methyltransferase SETDB1 and INM proteins, promotes the association of SETDB1 with the INM, and maintains H3K9me3. Moreover, we reveal that canonical N-glycan biosynthetic machinery in ER contributes to the N-glycosylation of INM proteins. These findings uncover a previously unrecognized nuclear role for polysaccharides, broadening our understanding beyond their traditional subcellular distributions and functional profiles.

molecular biology↗

bioRxiv2025

Anthrax toxin receptor 2 is the Receptor for Clostridium perfringens NetF: Structural Insights into Toxin Binding and Pore Formation

Hemolysin {beta}-pore-forming toxins ({beta}PFTs) are key virulence factors of Clostridium perfringens, associated with severe diseases in humans and animals. Yet, the mechanisms by which Clostridium {beta}PFTs recognize and engage specific target cells remain poorly understood. Here, we identify the cellular receptor for C. perfringens necrotizing enteritis toxin F (NetF), a recently discovered toxin implicated in severe enteritis in dogs and foals. We show that NetF binds to the same receptor as anthrax toxin, namely ANTXR2. Using cryo-electron microscopy, we determined the structure of the oligomeric NetF pre-pore as well as the transmembrane pore, both alone and in complex with the extracellular domain of ANTXR2. Unlike anthrax toxin, which binds to the apical MIDAS motif of ANTXR2 - as does the natural ANTXR2 ligand collagen type VI - NetF engages the receptor laterally, spanning both the von Willebrand A and the Ig-like domains. This interaction positions the toxin near the membrane, facilitating contact with membrane lipids and promoting transmembrane pore formation. Our findings uncover key principles of hemolysin {beta}PFT-receptor recognition and advance our understanding of how pathogenic bacteria use these toxins to breach host defenses.

microbiology↗

bioRxiv2025

HSF4: A Prognostic Predictor and Potential Therapeutic Target in Colorectal Cancer with Implications for Patient Immune Status

Colorectal cancer (CRC) is among the most prevalent malignancies globally, characterized by high morbidity and mortality rates. The Heat Shock Factor (HSF) family of genes plays a critical role in the cellular response to environmental stress, particularly heat stress. These genes encode transcription factors that regulate the expression of heat shock proteins, which are essential for maintaining cellular homeostasis under stressful conditions. Recently, there has been a growing interest in the role of HSF family genes in the development and progression of CRC. In this study, we conducted a comprehensive analysis of CRC samples from The Cancer Genome Atlas (TCGA) database to identify potential therapeutic targets. A total of 533 gene expression matrices, were downloaded and processed, including 42 normal and 491 tumor samples. Differential expression analysis of the HSF family genes, revealed HSF4 as the most significantly differentially expressed gene between normal and tumor samples. Consequently an HSF4-related signature was constructed, stratifying all CRC patients in the TCGA dataset into low-risk or high-risk groups based on HSF4 expression. Survival analysis demonstrated a significant association between HSF4 expression and clinical outcomes indicating that the signature possesses substantial. Correlation analysis further revealed significant relationships between HSF4 expression and clinical features including Stage, T stage, M stage, and N stage. Univariate and multivariate Cox regression analyses confirmed the prognostic significance of HSF4. Functional analysis of differentially expressed genes based on HSF4 expression levels demonstrated enrichment in critical biological processes and pathways. Furthermore, HSF4 exhibited unique properties within the tumor microenvironment (TME). Additional analysis indicated that different risk groups exhibit varying levels of immune cell infiltration and cell proliferation capacity. Notably, the low-risk group showed increased sensitivity to multiple chemotherapeutic agents due to its lower IC50 values. In conclusion, this study presents the first signature for predicting the prognosis and immunological status of CRC patients based on HSF family genes. Our findings suggest that HSF4 may serve as a potential therapeutic target in CRC.

cancer biology↗

bioRxiv2025

Transcriptional and functional profiles of muscarinic receptor-expressing neurons in primate lateral prefrontal and anterior cingulate cortices

Acetylcholine modulates anterior cingulate (ACC) and lateral prefrontal (LPFC) cortices for cognitive-motivational integration, via specific m1-m4 muscarinic receptors (mAChR) encoded by CHRM1-4 genes. Single-nucleus RNA sequencing and mRNA-protein histology in macaques revealed CHRM3 to be the most enriched mAChR gene in neurons, while m1 predominates at the protein level, likely due to nuclear retention of CHRM3 and cytoplasmic trafficking of CHRM1. CHRM3 and CHRM1 showed strong co-expression and functional overlap, and were transcriptomically-distinct from CHRM2, which was uniquely enriched in deep layer excitatory and PVALB+ inhibitory neurons. Although CHRM+ cell distributions were similar between areas, CHRM1-3+ excitatory neurons in ACC exhibited upregulation of synaptic plasticity genes relative to LPFC. Functional in vitro experiments confirm a more robust cholinergic-mediated decrease in excitatory:inhibitory synaptic ratio in ACC than in LPFC neurons, accompanied by compensatory changes in spine morphology. These findings highlight region-specific acetylcholine signaling essential for flexible processing, learning and memory.

neuroscience↗

bioRxiv2025

Delayed forebrain excitatory and inhibitory neurogenesis inSTRADA-related megalencephaly via mTOR hyperactivity

Biallelic pathogenic variants in STRADA, an upstream regulator of the mechanistic target of rapamycin (mTOR) pathway, result in megalencephaly, drug-resistant epilepsy, and severe intellectual disability. This study explores how mTOR pathway hyperactivity alters cell fate specification in dorsal and ventral forebrain development using STRADA knock-out human stem cell derived brain organoids. In both dorsal and ventral forebrain STRADA knock-out organoids, neurogenesis is delayed, with a predilection for progenitor renewal and proliferation and an increase in outer radial glia. Ventrally, interneuron subtypes shift to an increase in neuropeptide-Y expressing cells. Inhibition of the mTOR pathway with rapamycin results in rescue for most phenotypes. When mTOR pathway variants are present in all cells of the developing brain, overproduction of interneurons and altered interneuron cell fate may underlie mechanisms of megalencephaly, epilepsy, and cognitive impairment. Our findings suggest mTOR inhibition during fetal brain development as a potential therapeutic strategy in STRADA deficiency.

neuroscience↗

bioRxiv2025

Structural Dissection of Vaccinia G9 Identifies Residues Essential for Membrane Fusion and Complex Assembly

Vaccinia virus, a prototypical poxvirus, utilizes a unique multi-protein Entry Fusion Complex (EFC), comprising 11 components, to mediate membrane fusion during host cell entry. Although the crystal structure of a truncated form of the G9 protein has been determined, the functional relevance of its structural features remains poorly understood. In this study, we systematically analyzed 47 G9 mutants to identify critical functional residues. Using trans-complementation assays, co-immunoprecipitation, membrane fusion assays, and structural analysis, we identified nine key mutants, which were categorized into three functional groups. Group 1 mutants failed to interact with A16 and other EFC components, highlighting their essential roles in G9-A16 subcomplex formation. Group 2 and Group 3 mutants retained A16 binding but disrupted interactions with other EFC proteins, suggesting their roles in broader complex assembly. Notably, Group 3 mutants targeted a conserved P(R/Y)XCW motif and a loop structure shared among vaccinia G9, A16, and J5 proteins. A similar motif was also identified in G9 homologs from Nucleocytoviricota, suggesting an evolutionarily conserved fusion mechanism. Collectively, our findings demonstrated that G9 function requires multiple domains, including A16-binding interfaces and conserved motifs not resolved in previous protein structure. These results establish G9 as a central EFC component and underscore its potential as a target for antiviral development. ImportanceUnderstanding how viruses enter host cells is critical for developing antiviral strategies. Vaccinia virus, a model poxvirus, uses a unique 11-protein entry fusion complex (EFC) to mediate membrane fusion--unlike other viruses that rely on a single fusion protein. In this study we identified specific residues in the G9 protein that are critical for maintaining EFC function. Notably, we discovered a conserved P(R/Y)XCW motif within G9 that is also present in orthologs from both poxviruses and members of the Nucleocytoviricota phylum, suggesting an evolutionarily conserved mechanism of membrane fusion. These conserved structural elements can serve as potential targets for antiviral intervention against pathogenic poxvirus infections in humans.

microbiology↗

bioRxiv2025

Transcriptional and neuroprotective effects of hexokinase-2 inhibitors administered afterstroke

The inflammatory response induced by stroke can exacerbate injury to peri-infarct tissue. Microglia and other immune cells that mediate this response require increased glycolytic flux during pro-inflammatory activation. These cells, unlike neurons and most other cell types, utilize hexokinase-2 (HK2) rather than hexokinase-1 for glycolysis, such that HK2 inhibitors may selectively target them to suppress post-ischemic inflammation. Here we compared the effects of the non-selective hexokinase inhibitor 2-deoxyglucose to the HK2-selective inhibitors lonidamine and 3-bromopyruvate on secondary injury after stroke. A spatial transcriptomic assessment was performed in parallel to compare effects of the inhibitors on microglial gene expression and microglia - neuron interactions and to screen for off-target effects. Each of the inhibitors suppressed pro-inflammatory gene upregulation in peri-infarct microglia and attenuated the upregulation of cell stress functional pathways in the neighboring neurons, but had minimal effect on neuronal gene expression in uninjured cortex. The HK2-selective inhibitors were more effective than 2-deoxyglucose in suppressing morphological microglial changes, neuronal oxidative stress, and neurite loss. 3-bromopyruvate administered after stroke produced long-term improvements in functional outcome. Selective HK2 inhibitors may thus provide a clinically applicable means to suppress microglial activation and thereby improve outcomes after stroke without endangering neuronal energy metabolism.

neuroscience↗

bioRxiv2025

Elevated SUN1 promotes aging-related polarity defects through mechanical coupling microtubules to the nuclear lamina

In migratory fibroblasts, the front-rear polarity required for cell migration is defined by an anterior centrosome relative to the nucleus. To achieve this polarity, actin cables drive the nucleus backward by coupling to nuclear membrane proteins nesprin-2G and SUN2. Aging disrupts this cell polarity by increasing the protein levels of SUN1, a SUN2 homolog. Here, we investigated the molecular mechanisms behind this disruption and found that the dominant negative effect of SUN1 and progerin, an aging-related lamin A variant, required direct SUN1-lamin A interaction. Microtubule interaction and force transmission through a nesprin, identified as nesprin-2, are crucial for SUN1s effect. We further discovered that stable microtubules are both necessary and sufficient to inhibit cell polarity. Using SUN1-SUN2 chimeric proteins, we demonstrated that the SUN domains determine their roles in cell polarization. Our findings reveal how elevated SUN1 disrupts cell polarity through coupling microtubule and nuclear lamina, emphasizing the impact of altered microtubule stability and nuclear mechanotransduction in aging.

cell biology↗

bioRxiv2024

spaDesign: A Statistical Framework to Improve the Design of Sequencing-based Spatial Transcriptomics Experiments

MotivationRigorous experimental design is essential for obtaining biologically meaningful findings and high-throughput spatial transcriptomics studies are not an exception. While some efforts have been made to improve the design of these studies, it is still significantly understudied yet how to optimize key experimental factors of these experiments. In the case of sequencing-based spatial transcriptomics studies, determining the minimum sequencing depth is an important experimental factor to decide. ResultsTo address this critical limitation, here we propose spaDesign, a statistical framework to improve the design of sequencing-based spatial transcriptomics experiments. spaDesign is a statistically rigorously designed framework that employs Poisson Gaussian process and Fisher-Gaussian kernel mixture. It can easily simulate a range of spatial transcriptomics data with various sequencing depths, effect sizes, and spatial patterns, which allows rigorous estimation of needed total sequencing depths to detect spatial domains based on spatial transcriptomics experiments. We demonstrated the utility and power of spaDesign using 10X Visium data of the human brain and the chicken heart. AvailabilityThe R package and associated tutorial are freely available at https://github.com/JuanXie19/spaDesign.

bioinformatics↗