Biology subjects

Lin, W.

Publications and source records attributed to Lin, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

f-BGM enables fungi-specific genome mining in high accuracy and interpretability

Emerging artificial intelligence (AI)-based genome mining methods have revolutionized the paradigm of bacterial secondary metabolite (SM) discovery. Fortunately, recent data accumulation of fungal biosynthetic gene clusters (BGC) fairly offers opportunities for systematic development and evaluation of fungi-specific pipelines. In this work, we proposed a deep learning framework termed as f-BGM specifically for fungal genome mining. By designing a novel self-attention-based architecture to augment inter-domain associations in local genomic contexts, f-BGM exhibits superior performance over existing AI-based methods in both in-distribution and out-of-distribution benchmark tests for BGC detection. Further analyses demonstrate that f-BGM is of decent interpretability on deciphering single-domain and -protein importance, as well as inter-domain partnership. By establishing additional binary classification models, f-BGM also achieves high-quality identification of core enzymes within given BGCs. Finally, case studies of f-BGM-driven genome mining in marine fungi uncovers biosynthetic potential underestimated by the rule-based method antiSMASH, as supported by experimental and computational validation.

bioinformatics↗

bioRxiv2025

Progressive Remodeling of Global Protein Interaction Networks in a Mouse Model of Tauopathy

Neurodegenerative disease is marked not just by loss of proteins or cells, but by dynamic rewiring of macromolecular interaction networks that precede and drive pathology. Here, we present the first temporally resolved, systems-scale map of multi-protein complex remodeling in a tauopathy model, integrating co-fractionation mass spectrometry, quantitative phosphoproteomics, and machine learning to decode phosphorylation-dependent shifts in protein interactomes across disease progression. This interactomic atlas identifies functionally validated assemblies--including MAPT-Dpysl2 and Cyfip1-actin complexes--that modulate early disease phenotypes in vivo. By revealing how phosphorylation tunes macromolecular complex architecture and function, this work reframes tauopathy as a disease of dynamic network instability, and establishes a generalizable framework for early detection and mechanistic dissection of neurodegeneration.

neuroscience↗

bioRxiv2025

Autophagy activators normalize aberrant Tau proteostasis and rescue synapses in human familial Alzheimer's disease iPSC-derived cortical organoids

Alzheimers disease (AD) is the most common form of dementia worldwide. Despite extensive progress, the cellular and molecular mechanisms of AD remain incompletely understood, partially due to inadequate disease models. To illuminate the earliest changes in hereditary (familial) Alzheimers disease, we developed an isogenic AD cerebrocortical organoid (CO) model. Our refined methodology produces COs containing excitatory and inhibitory neurons alongside glial cells, utilizing established isogenic wild-type and diseased human induced pluripotent stem cells (hiPSCs) carrying heterozygous familial AD mutations, namely PSEN1{Delta}E9/WT, PSEN1M146V/WT, or APPswe/WT. Our CO model reveals time-progressive accumulation of amyloid beta (A{beta}) species, loss of monomeric Tau, and accumulation of aggregated high-molecular-weight (HMW) phospho(p)-Tau species. This is accompanied by neuronal hyperexcitability, as observed in early human AD cases on electroencephalography (EEG), and synapse loss. Single-cell RNA-sequencing analyses reveal significant differences in molecular abnormalities in excitatory vs. inhibitory neurons, helping explain AD clinical phenotypes. Finally, we show that chronic dosing with autophagy activators, including a novel CNS-penetrant mTOR inhibitor-independent drug candidate, normalizes pathologic accumulation of A{beta} and HMW p-Tau, normalizes hyperexcitability, and rescues synaptic loss in COs. Collectively, our results demonstrate these COs are a useful human AD model suitable for assessing early features of familial AD etiology and for testing drug candidates that ameliorate or prevent molecular AD phenotypes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/661453v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@12ac9c6org.highwire.dtl.DTLVardef@24eceaorg.highwire.dtl.DTLVardef@3e3238org.highwire.dtl.DTLVardef@1530d1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Integrative cross-sample alignment and spatially differential gene analysis for spatial transcriptomics

Spatial transcriptomics (ST) technologies offer rich spatial context for gene expression, with varying spatial resolutions and gene coverages. However, aligning and comparing multiple ST slices, whether derived from the same or different platforms, remains challenging due to nonlinear distortions and limited spatial overlap caused by tissue processing. We present CODA, an integrative framework for CrOss-sample alignment and spatially Differential gene Analysis. CODA first learns a shared low-dimensional latent feature space across samples. Within the latent space, CODA performs global rigid alignment, applies transformer-based feature matching to identify common spatial domains, and utilizes local nonlinear refinements via large deformation diffeomorphic metric mapping, enabling a robust cross-sample comparison and extraction of spatial gene expression patterns. Benchmarking across various ST platforms demonstrates that CODA outperforms the existing methods in alignment accuracy, computational efficiency, and memory usage. Applications to vascular and brain datasets shows CODAs ability to uncover spatially informative genes associated with disease and sleep regulation. These results highlight CODAs broad applicability and effectiveness in ST analysis.

bioinformatics↗

bioRxiv2025

Distinct age- and pathology-dependent epitranscriptome and translational dysfunction in a tauopathy mouse model

Chronic neurodegenerative diseases, such as tauopathies, cause major metabolic changes in the brain affecting gene expression at both the transcriptional and translational levels. Our understanding of how regulation of translation changes with disease has focused on mRNA and its translational regulatory factors, RNA binding proteins, and microRNAs, despite clear evidence for translational and post-translational dysfunction in ADRD and tauopathies. The neurobiology of tRNA has only recently begun to be studied, but the impact of chronic neurodegenerative diseases on tRNA biology and translational dysfunction is largely unknown. We have previously shown that the tRNA pool and tRNA modifications behave as a system to regulate the cellular stress response by undergoing stress-specific reprogramming and causing selective translation of mRNAs from codon-biased stress response genes. Here we tested this stress-induced tRNA reprogramming and codon-biased translation system in the response to mutant tau expression by performing mass spectrometric quantification of [~]8500 proteins and 49 tRNA modifications, AQRNA-seq analysis of 222 cytosolic and mitochondrial tRNAs and other small RNAs, and informatic analysis of codon usage patterns in >23,000 protein-coding genes. Analysis of these datasets revealed that aging and tauopathy elicit major adaptation of the tRNA transcriptome and epitranscriptome as well as corresponding evidence of a program of translation of families of codon-biased genes for aging and disease responsive proteins. The mitochondrial tRNA transcriptome showed a strong response to aging and disease with 21 of the 22 mt-tRNAs showing age and disease-linked increases in expression, accompanied by mitochondria-specific modifications such as ms2i6A and f5C. Surprisingly, there were few significant changes in the 203 cytosolic tRNA isodecoders. However, a 10-fold increase tRNA isodecoder tRNA-Arg-TCT-5-1 was accompanied by increased translation of proteins encoded by genes highly enriched in its AGA cognate codon. These changes in tRNA biology are mirrored by strongly biased use of synonymous codons among the most highly upregulated and downregulated proteins in the P301S MAPT mice. Taken together these findings suggest the aging and disease brain produces an integrated response for translational control that is highly integrated with changes in tRNA biology.

neuroscience↗

bioRxiv2025

Elevated mitochondrial metabolism in Down syndrome iPSCs reduces commitment to neuroectoderm

A key feature of Down syndrome (DS) is reduced neurogenesis. Here, we provide evidence that increased mitochondrial metabolism in DS stem cells reduces their ability to commit to neuroectoderm (NE), one of the earliest steps in the development of the nervous system. We show that mitochondria in induced pluripotent stem cells derived from individuals with DS (3S-iPSCs) have a higher membrane potential and increased capacity for calcium uptake via the mitochondrial calcium uniporter (MCU) compared to isogenic, euploid controls. Consequently, 3S-iPSCs proliferate faster and spend less time in G1 of the cell cycle. This reduces the opportunity for growth of a primary cilium, an important developmental signaling hub. Inhibiting MCU or slowing proliferation of 3S-iPSCs is sufficient to increase ciliation and improve commitment to NE. In summary, we provide evidence that a mitochondria-to-cilia signaling axis important during the earliest steps of neurogenesis is dysregulated in DS, yet remains amenable to small molecule intervention.

developmental biology↗

bioRxiv2025

Structural insight into the transcription activation mechanism of the phage Mor/C family activators

Bacteriophage Mu, a temperate phage that infects E. coli K-12 and other enteric bacteria, precisely controls its replication cycle through hijacking host RNA polymerase (RNAP) by the middle operon regulator Mor and the late gene transcription activator C. Though a dimeric arrangement and significant conformational changes are proposed for the distinct Mor/C family activators, the underlying transcription activation mechanism remains unclear. In this study, we present two cryo-EM structures of the transcription activation complex (Mor-TAC and C-TAC) with phage Mu middle and late gene promoters, respectively. Remarkably, the Mor/C activators bind to promoter DNA as a centrosymmetric tetramer rather than as the proposed dimer, concurrently stabilizing by the N-terminal dimerization domains and C-termini. The C-terminal DNA binding domains and two anti-{beta}-strands simultaneously interact with two adjacent DNA major grooves. The activators also engage a variety of interactions with the conserved domains (CTD, {sigma}70R4, and {beta} FTH) of RNAP, providing evidences for a recruitment mechanism. In addition, single-molecule FRET assays show that C significantly enhances RPitc formation, suggesting a different multi-step activation mechanism for C. Collectively, these findings reveal the unique transcription activation mechanism of tetrameric Mor/C family activators, unraveling a novel mode of phage hijacking and bacterial transcription regulation.

biochemistry↗

bioRxiv2025

Disease-associated loci share properties with response eQTLs under common environmental exposures

Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro. With single-cell RNA-sequencing data from 1.4 million cells across 51 individuals, we identified hundreds of response expression quantitative loci (eQTLs) that are associated with inter-individual differences in regulatory changes following treatment with nicotine, caffeine, or ethanol in diverse cell types. We also identified dynamic regulatory effects that vary across differentiation trajectories in response to exposure. In contrast to steady-state eQTLs, and similar to disease risk loci, response eQTLs are enriched in distal enhancers and are regulating genes that experienced strong selective constraint, contain complex regulatory landscapes, and display diverse biological functions. We identified response eQTLs that coincide with disease-associated loci not explained by steady-state eQTLs. Our results highlight the complexity of genetic regulatory effects and suggest that our ability to interpret disease-associated loci will benefit from the pursuit of studies of gene-by-environment interactions in diverse biological contexts.

genetics↗

bioRxiv2025

A SUMO-interacting motif in the guanine nucleotide exchange factor EPAC1 is required for subcellular targeting and function

Exchange protein directly activated by cAMP (EPAC1), a multifunctional intracellular cAMP receptor, dynamically localizes to various cellular loci, engaging with diverse molecular partners to maintain cellular homeostasis. The study investigates the role of the SUMO interacting motif (SIM) in the subcellular targeting and cellular functions of EPAC1. It reveals that the SIM is a critical structural element for EPAC1s association with RanBP2/Nup358, a nucleoporin of the cytoplasmic filament component of the nuclear pore complex (NPC). Mutational disruption of EPAC1 SIM interferes with EPAC1s ability to activate its canonical effectors, small GTPases, Rap1 and Rap2, and non-canonical functions, such as the formation of nuclear condensates and cellular SUMOylation. Because SIM is also directly involved in cAMP binding, RanBP2s association with EPAC1 with the SIM attenuates EPAC1s cAMP binding affinity to generate an EPAC1 signaling microdomain with reduced cAMP sensitivity around the NPC. The coupling between EPAC1s scaffold association and cAMP binding enables EPAC1 to tune its sensitivity to stress stimuli spatially depending on the cellular locations. These findings provide novel structural insights into EPAC1 signaling, highlighting the importance of SIM in EPAC1s cellular functions and potential novel strategies for therapeutically targeting EPAC1.

cell biology↗

bioRxiv2025

Predicting Three-Dimensional Atomic-Level Structures of Biomolecular Complexes

OpenComplex1 is an open-source platform for comprehending and developing biomolecular models. Based on the architectures of AlphaFold2 and AlphaFold-Multimer, the current version of OpenComplex realizes end-to-end predictions of the biomolecular three-dimensional (3D) structures including protein, RNA, and protein-RNA complexes. OpenComplex makes it able to infer and train models of biomolecular complexes in a unified framework and supports encoders that use both MSAs and protein language models (pLM). Through extensive training on both structure and sequence databases such as the Protein Data Bank (PDB) and RNA families (Rfam) database, OpenComplex is able to generate models with equivalent or better accuracy for a wide range of biomolecules including monomers or multimers of protein and RNA as well as protein-RNA complexes. In summary, OpenComplex is a powerful tool for predicting accurate biomolecular structures in diverse application scenarios.

molecular biology↗

bioRxiv2025

DeepSeMS: a large language model reveals hidden biosynthetic potential of the global ocean microbiome

Microbial biosynthetic diversity holds immense potential for discovering natural products with therapeutic applications, yet a substantial quantity of natural products derived from uncultivated microorganisms remains uncharacterized. The intricate nature of biosynthetic enzymes poses a major challenge in accurately predicting the chemical structures of secondary metabolites solely based on genome sequences using current rule-based methods. Here, we present DeepSeMS, a large language model designed to predict the chemical structures of secondary metabolites from various microbial biosynthetic gene clusters. Built on the Transformer architecture, DeepSeMS innovatively identifies sequence features using functional domains of biosynthetic enzymes, and incorporates feature-aligned chemical structure enumeration for training data augmentation. External evaluation results show that DeepSeMS predicts more accurate chemical structures of secondary metabolites with a Tanimoto coefficient up to 0.6 compared with the ground truth, significantly outperforming antiSMASH and PRISM with coefficients of only 0.14 and 0.45 respectively. Moreover, DeepSeMS successfully predicted secondary metabolites for 96.60% of cryptic biosynthetic gene clusters, surpassing existing methods with success rates less than 50%. Leveraging DeepSeMS, we characterized over 65,000 novel secondary metabolites from the global ocean microbiome with previously undocumented structural types, ecological distribution, and biomedical applications especially antibiotics. A login-free and user-friendly web server for DeepSeMS (https://biochemai.cstspace.cn/deepsems/) has been launched, featuring an integrated global ocean microbial secondary metabolites repository to expedite the discovery of novel natural products. Collectively, this study underscores the great capacity of a large language model-driven method in revealing hidden biosynthetic potential of the global ocean microbiome.

synthetic biology↗

bioRxiv2025

MsyB-HU Interaction Modulates a Two-Tiered Bacterial Stress Response by Regulating DNA Supercoiling

Bacteria respond to stressful conditions through multiple pathways, including changes in gene expression patterns and mutations for adaptation. DNA supercoiling is a fundamental regulatory principle of bacterial gene expression, controlled antagonistically by DNA gyrase and topoisomerase I. Nucleoid-associated proteins, such as HU, also regulate supercoiling through interactions with DNA. Here, we identify Escherichia coli protein MsyB as a HU inhibitor and a {beta}-clamp binder. MsyB is fine-tuned under various stressful conditions, where it modulates the population of DNA-bound HU by forming a HU-MsyB complex. Consequently, the balance between DNA-bound HU and MsyB-bound HU adjusts the DNA supercoiling state, thereby influencing transcription for adaptation. Additionally, under prolonged starvation during the stationary phase, sustained high level of MsyB increases DNA exposure to damaging factors, acting as a damage inducer. The HU/MsyB/{beta}-clamp interaction suggests a model in which MsyB coordinates with HU and the {beta}-clamp to facilitate damage acquisition and error-prone DNA repair. Thus, MsyB-dependent supercoiling regulation represents a novel two-tiered bacterial stress response mechanism in gene expression and adaptive mutation. Our findings reveal a previously unrecognized regulatory mechanism of bacterial supercoiling, positioning HU as a promising antibiotic target.

microbiology↗

bioRxiv2025

Surface Expansion Regionalization of the Hippocampus in Early Brain Development

The hippocampal formation is implicated in a myriad of crucial functions, particularly centered around memory and emotion, with distinct subdivisions fulfilling specific roles. However, there is no consensus on the spatial organization of these subdivisions, given that the functional connectivity and gene expression-based parcellation along its longitudinal axis differs from the histology-based parcellation along its medial-lateral axis. The dynamic nonuniform surface expansion of the hippocampus during early development reflects the underlying changes of microstructure and functional connectivity, providing important clues on hippocampal subdivisions. Moreover, the thin and convoluted properties bring out the hippocampal maturity largely in the form of expanding surface area. We thus unprecedentedly explore the development-based surface area regionalization and patterns of the hippocampus by leveraging 513 high-quality longitudinal MRI scans during the first two postnatal years. Our findings imply two discrete hippocampal developmental patterns, featuring one pattern of subdivisions along the anterior-posterior axis (head, regions 1 and 5; body, regions 2, 4, 6, and 7; tail, region 3) and the other one along the medial-lateral axis (subiculum, regions 4, 5, and 6; CA fields, regions 1, 2, and 7). Most of the resulting 7 subdivisions exhibit region-specific and nonlinear spatiotemporal surface area expansion patterns with an initial high growth, followed by a transition to low increase. Each subregion displays bilaterally symmetric pattern. The medial portion of the hippocampal head experiences the most rapid surface area expansion. These results provide important references for exploring the fine-grained organization and development of the hippocampus and its intricate cognitions.

neuroscience↗

bioRxiv2025

Phosphoproteomics Uncovers Tumor Heterogeneity and Therapeutic Opportunities in Early-Stage Hepatocellular Carcinoma

Mechanisms driving progression and metastasis in early-stage hepatocellular carcinoma (HCC) remain poorly clarified. Although phosphoproteomics has been applied to broader HCC cohorts, the heterogeneity of phosphorylation signaling in early-stage HCC remains unexplored. Here, we conducted integrated phosphoproteomic and proteomic analysis on early-stage HCC tumors and paired non-tumor tissues. By comparing tumor and non-tumor tissues, we identified markedly reduced phosphorylation of EGFR-mediated canonical ERK/MAPK signaling, alongside elevated atypical MAPK signaling in HCC. To further explore the signaling heterogeneity within tumors, we applied nonnegative matrix factorization (NMF) and consensus-clustering, and identified three distinct phosphoproteomic subtypes with unique phosphorylation signatures and clinical characteristics. Interrogating the most malignant subtype, we found markedly high abundance of phosphorylation of mRNA splicing regulators, and an enrichment of epithelial-mesenchymal transition (EMT) pathways in the proteome, with phosphorylation of the splicing factor SRSF3 emerging as a critical feature. Mechanistically, we show that SRSF3 hyperphosphorylation, driven by SRPK1/CLKs and potential PP1 phosphatase suppression, promotes metastasis and proliferation. Critically, SRPK1/CLKs inhibitors effectively suppressed SRSF3 hyperphosphorylation-mediated migration and invasion of HCC cells. Our study uncovers a new dimension of signaling-driven tumor heterogeneity in early-stage HCC and identifies the SRPK1/CLKs-SRSF3 hyperphosphorylation axis as a key metastatic driver, suggesting a potential therapeutic target for early intervention in HCC.

cancer biology↗

bioRxiv2025

Infectome Analysis of Small Mammals in Southern China Reveals Ecological Associations and Emerging Threats from Diverse Pathogens

Small mammals harbor a diverse array of zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viral diversity, with limited attention paid to bacteria and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome of 2,408 individual samples, representing lung, liver, and gut tissues from 858 animals collected throughout Guangdong province, China, with a study design that accounted for host species, tissue, season, and geographic location. We identified 76 pathogen species, including 29 RNA viruses, 12 DNA viruses, 5 bacteria, and 30 eukaryotic pathogens, 33 of which were newly discovered. Tissue distribution analysis revealed distinct organotropisms, suggesting varied transmission routes, while host distribution analysis showed that each animal carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Our characterization of the geographic and seasonal patterns revealed that pathogen richness was primarily influenced by region, host species, and season, while pathogen composition was largely shaped by host genetic distance. Collectively, these data provide the first comprehensive insight into the dynamics of the pathogen infectome in these key mammalian disease reservoirs, highlighting the major factors driving pathogen diversity and transmission.

microbiology↗

bioRxiv2025

Pleomorphic effects of three small-molecule inhibitors on transcription elongation by Mycobacterium tuberculosis RNA polymerase

The Mycobacterium tuberculosis RNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N()-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared to Escherichia coli RNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizes E. coli pause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.

biophysics↗

bioRxiv2025

APOE-ϵ4-induced Fibronectin at the blood-brain barrier is a conserved pathological mediator of disrupted astrocyte-endothelia interaction in Alzheimer's disease

Blood-brain barrier (BBB) dysfunction is a key feature of Alzheimers disease (AD), particularly in individuals carrying the APOE-{varepsilon}4 allele. This dysfunction worsens neuroinflammation and hinders the removal of toxic proteins, such as amyloid-beta (A{beta}42), from the brain. In post-mortem brain tissues and in animal models, we previously reported that fibronectin accumulates at the BBB predominantly in APOE-{varepsilon}4 carriers. Furthermore, we found a loss-of-function variant in the fibronectin 1 (FN1) gene significantly reduces aggregated fibronectin levels and decreases AD risk among APOE-{varepsilon}4 carriers. Yet, the molecular mechanisms downstream of fibronectin at the BBB remain unclear. The extracellular matrix (ECM) plays a crucial role in maintaining BBB homeostasis and orchestrating the interactions between BBB cell types, including endothelia and astrocytes. Understanding the mechanisms affecting the ECM and BBB cell types will be critical for developing effective therapies against AD, especially among APOE-{varepsilon}4 carriers. Here, we demonstrate that APOE-{varepsilon}4, A{beta}42, and inflammation drive the induction of FN1 expression in several models including zebrafish, mice, iPSC-derived human 3D astrocyte and 3D cerebrovascular cell cultures, and in human brains. Fibronectin accumulation disrupts astroglial-endothelial interactions and the signalling cascade between vascular endothelial growth factor (VEGF), heparin-binding epidermal growth factor (HBEGF) and Insulin-like growth factor 1 (IGF1). This accumulation of fibronectin in APOE-{varepsilon}4- associated AD potentiates BBB dysfunction, which strongly implicates reducing fibronectin deposition as a potential therapeutic target for AD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/634732v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@1efff03org.highwire.dtl.DTLVardef@14f40cdorg.highwire.dtl.DTLVardef@27743aorg.highwire.dtl.DTLVardef@3fa9a9_HPS_FORMAT_FIGEXP M_FIG C_FIG Accessibility textThis image illustrates the effects of different APOE isoforms (ApoE-{varepsilon}3 and ApoE-{varepsilon}4) on blood-brain barrier (BBB) integrity, focusing on the molecular interactions between astrocytes and endothelial cells. This figure emphasizes the detrimental effects of ApoE-{varepsilon}4 on BBB integrity via fibronectin accumulation and altered signaling pathways. The top section provides a schematic overview of the blood-brain barrier, highlighting astrocytes, endothelial cells, and their interface. The left panel represents the ApoE-{varepsilon}3 condition: Normal fibronectin (FN1) levels support healthy interactions between astrocytes and endothelial cells. Growth factors, including VEGFA, HBEGF, and IGF1, maintain BBB integrity through their respective receptors (VEGFR and EGFR). Green arrows indicate activation of these signaling pathways. The right panel depicts the ApoE-{varepsilon}4 condition: Elevated fibronectin (FN1) disrupts astrocyte-endothelium interactions. FN1 binds integrins and activates focal adhesion kinase (FAK), inhibiting VEGFA, which is required for endothelial HBEGF that in turn activates IGF1 signaling. Red symbols indicate inhibition of HBEGF, VEGFA, and IGF1 pathways, leading to BBB dysfunction. HighlightsAPOE-{varepsilon}4 drives fibronectin deposition in Alzheimers, disrupting astrocyte-endothelia interactions. APOE-{varepsilon}4 and fibronectin co-localize, forming aggregates at blood-brain barrier (BBB). Fibronectin alters the signaling between VEGF, IGF1, and HBEGF impairing BBB function. Reducing fibronectin restores BBB integrity and offsets APOE-{varepsilon}4 pathology.

cell biology↗

bioRxiv2025

5' UTR-mediated retention of eIF3 on 80S ribosomes promotes co-translational folding of ER membrane proteins

Co-translational folding of nascent polypeptides is essential for protein function and cellular homeostasis. Ribosome-associated chaperones assist in this process, but coordination between their recruitment and translation initiation remains poorly understood. We report here that specific binding sites for eukaryotic translation initiation factor eIF3 within the 5 untranslated regions (5UTRs) of mRNAs promote its retention on 80S ribosomes during the synthesis of select endoplasmic reticulum (ER) membrane proteins. Disruption of these eIF3 binding sites leads to misfolding and sequestration of newly synthesized membrane proteins into ER whorls. Sequestration into ER whorls is exacerbated by HSP70 inhibition but can be rescued by overexpressing HSPA8 and HSPA1. Cross-linking assays reveal that 5UTR binding sites stabilize eIF3-80S interactions during early elongation, facilitating recruitment of HSPA8 to ribosomes. These findings indicate that genetic instructions within 5UTRs direct eIF3-mediated chaperone recruitment, ensuring proper co-translational folding of ER membrane proteins.

cell biology↗