Biology subjects

Sun, B.

Publications and source records attributed to Sun, B..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Molecular mechanisms of dynamics-mediated effects of pathogenic missense mutations on Menin protein function

Understanding how disease-causing missense mutations (DCMMs) affect protein function is fundamental. The traditional structure-function paradigm for proteins has evolved into a structure-dynamics-function model, as dynamics is increasingly recognized as a key regulator of protein function. Consequently, it is essential to incorporate dynamics into the once heavily emphasized structure-function framework to explain the effects of DCMMs. Although research in this area is emerging, evidence supporting a definitive role of dynamics in mediating DCMM effects on protein function remains limited. In this study, we used Menin--a mutation-prone scaffold protein involved in various pathologies--as a model system to explore how DCMMs affect Menins function. By performing molecular dynamics (MD) simulations on 24 clinically confirmed DCMMs, we showed that DCMMs do not necessarily destabilize protein stability. Instead, they induce similar dynamic changes in the protein. The consequences of DCMMs on Menins function were further assessed through umbrella sampling of the Menin-JunD protein protein interaction (PPI). We found that DCMMs attenuate this interaction and disrupt a highly conserved JunD dissociation pathway in wild-type (WT) Menin. The underlying mechanism was revealed through allosteric analysis, which showed that, despite being located far from the JunD binding site, DCMMs uniformly disturbed the coupling between residue E179 and the binding pocket. Additionally, forced maintenance of E197-pocket coupling restored the impaired Menin-JunD PPI in DCMMs. Together, these data demonstrate that DCMMs alter Menins function through dynamics, with allostery playing a crucial role. This study further supports the incorporation of dynamics into the traditional "structure-function" diagram to better explain the effects of DCMMs.

biophysics↗

bioRxiv2024

Mobilization of nuclear antiviral factors by Exportin XPO1 via the actin network inhibits RNA virus replication

The intricate interplay between +RNA viruses and their hosts involves the exploitation of host resources to build virus-induced membranous replication organelles (VROs) in cytosol of infected cells. Previous genome- and proteome-wide approaches have identified numerous nuclear proteins, including restriction factors that affect replication of tomato bushy stunt virus (TBSV). However, it is currently unknown how cells mobilize nuclear antiviral proteins and how tombusviruses manipulate nuclear-cytoplasmic communication. The authors discovered that XPO1/CRM1 exportin plays a central role in TBSV replication in plants. Based on knockdown, chemical inhibition, transient expression and in vitro experiments, we show that XPO1 acts as a cellular restriction factor against TBSV. XPO1 is recruited by TBSV p33 replication protein into the cytosolic VROs via direct interaction. Blocking nucleocytoplasmic transport function of XPO1 inhibits delivery of several nuclear antiviral proteins into VROs resulting in dampened antiviral effects. The co-opted actin network is critical for XPO1 to deliver nuclear proteins to VROs for antiviral activities. We show that XPO1 and XPO1-delivered restriction factors accumulate in vir-condensates associated with membranous VROs. Altogether, the emerging theme on the role of vir-condensates is complex: we propose that vir-condensate serves as a central battleground between virus and the host for supremacy in controlling virus infection. It seems that the balance between co-opted pro-viral and antiviral factors within vir-condensates associated with membranous VROs could be a major determining factor of virus replication and host susceptibility. We conclude that XPO1 and nuclear antiviral cargos are key players in nuclear-cytoplasmic communication during cytosolic +RNA virus replication. SignificanceTomato bushy stunt virus (TBSV), similar to other (+)RNA viruses, replicates in the cytosol and exploits organellar membrane surfaces to build viral replication organelles (VROs) that represent the sites of virus replication. The authors discovered that XPO1 exportin nuclear shuttle protein inhibited TBSV replication in plants. The conserved XPO1 is a central protein interaction nod, which propelled nucleocytoplasmic transport of several viral restriction factors into the cytosolic VROs that restricted tombusviruses replication. The delivered virus restriction factors provided inhibitory functions within virus-induced condensates associated with membranous VROs. The authors propose that the VRO-associated condensate serves as a central battleground between virus and the host for supremacy in controlling virus infection. Altogether, XPO1 is a critical protein interaction hub with major implications in viral replication. The authors conclude that XPO1 and its nuclear antiviral cargos are key players in nuclear-cytoplasmic communication during cytosolic (+)RNA virus replication.

microbiology↗

bioRxiv2024

Molecular mechanisms of GSK3β-driven modulation of ABLIM1 and titin interactions in cardiac muscle

1The heart adapts to cardiac demand through various mechanisms, including chemical modifications of myofilament proteins responsible for cell contraction. Many of these modifications, such as phosphorylation, occur in unstructured, or intrinsically disordered, regions (IDRs) of proteins. Although often challenging to study, these IDRs are increasingly recognized as dynamic, tunable regulators of protein function. Given that cardiac dysfunction can involve changes in the post-translational modification (PTM) status of myofilament proteins, it is critical to assess how alterations within these disordered regions impact intact protein and myofilament behavior. We hypothesized that the function of ABLIM1, a myofilament protein containing an important IDR, is regulated by altering its IDR conformational ensemble through PTMs, primarily phosphorylation. We proposed that this conformational change would modulate its ability to bind to other myofilament proteins. To evaluate this hypothesis, we employed a multiscale modeling approach including molecular dynamics simulations. This was used to predict the conformational ensembles of ABLIM1 before and after phosphorylation, at sites known to be altered in a canine model of heart failure with reduced GSK3{beta} activity. We then used a state-based model of contraction to rationalize the physiological consequences of the molecular-scale predictions. Based on our data, we observed that local physicochemical alterations induced by phosphorylation in ABLIM1s intrinsically disordered regions significantly affect its overall conformational ensemble properties. This ensemble change subsequently influences the ability of its LIM domains to interact with titin. Furthermore, using the contraction model, we show that a reduced ability to recruit myosin heads for cross-bridge formation, resulting from the modified LIM domain/titin interactions, provides a mechanism that elucidates previous findings of diminished length-dependent activation. These findings offer crucial molecular insights, reframing IDRs not merely as structural noise but as key, tunable elements that control protein interactions and ultimately impact mechanical behavior in the sarcomere. This work bridges molecular disorder and biomechanical function, providing a new lens to understand dynamic control and dysfunction in cardiomyocyte contraction.

biophysics↗

bioRxiv2024

STEP: Deciphering Spatial Atlas at Single-Cell Level with Whole-Transcriptome Coverage

Recent advances in spatial transcriptomics have revolutionized our understanding of tissue spatial architecture and biological processes. However, many of these technologies face significant challenges in achieving either single-cell resolution or comprehensive whole-transcriptome profiling, hindering their capacity to fully elucidate intercellular interactions and the tissue microenvironment. To address these limitations, we present STEP, a hybrid framework that synergistically integrates probabilistic models with deep learning techniques for spatial transcriptome analysis. Through innovations in model and algorithm design, STEP not only enhances sequencing-based spatial transcriptome data to single-cell resolution but accurately infers transcriptome-wide expression levels for image-based spatial transcriptomic. By leveraging the nuclear features extracted from histological images, STEP achieves precise predictions of cell type and gene expression and effectively diffuses the discriminative ability to serial sections for modeling solid tissue landscapes. The capability is particularly advantageous for analyzing cells with distinctive characteristics, such as cancer cells, enabling cross-sample inference. In addition, STEP simulates intercellular communication through a spatially resolved cell-cell interaction network, uncovering intrinsic biological processes. Overall, STEP equips researchers with a powerful tool for understanding biological functions and unveiling spatial gene expression patterns, paving the way for advancements in spatial transcriptomics research. Code is available at https://github.com/childishHU/STEP.

bioinformatics↗

bioRxiv2024

Defining the genetic determinants of CD8+ T cell receptor repertoire in the context of immune checkpoint blockade

CD8+ T cells play a central role in the cancer response to immune checkpoint blockade (ICB) treatment, with activity predicated upon antigen recognition by the associated T cell receptor (TCR) repertoire. The contribution of genetic variation to this in cancer treatment is under-explored. We have conducted a genome-wide and human leukocyte antigen (HLA)-focused analysis of CD8+ T cell TCR repertoire to identify genetic determinants of variable gene (V-gene) and CDR3 K-mer usage from samples taken prior to and after ICB treatment (n=250). We find 11 genome-wide significant cis associations and 10 trans associations, primarily to the HLA, with V-gene usage meeting permuted P-value thresholds. Notably, TCR clones containing V-genes associated with HLA were less likely to be persistent across treatment. In a single-cell experiment, we find cells with HLA-matched TCR clones have increased tumor reactivity expression profiles and patients with HLA-matched TCR clones have improved overall survival. Our work indicates a complex relationship between genotype and TCR repertoire in the context of treatment with ICB, which has novel implications for understanding determinants of treatment response and patient outcomes. One Sentence SummaryTCR repertoire is strongly associated with specific HLA alleles in cancer patients, but immune checkpoint blockade influences this association.

genetics↗

bioRxiv2024

3D Printing of Multiscale Scaffolds with Microtopography for Guiding Tissue Organization and Regeneration

Engineering biomaterial scaffolds with multiscale structures, integrating anatomically accurate macroscale architecture (millimeters to centimeters) with microtopographic features (sub-microns to tens of microns), is critical for guiding cellular organization and tissue regeneration. However, fabricating such multiscale scaffolds remains challenging due to the limitations of conventional manufacturing techniques and the trade-off between speed and resolution in current 3D printing methods. Here, we present a multiscale micro-continuous liquid interface production (M{micro}CLIP) technique that enables rapid, one-step 3D printing of centimeter-scale scaffolds with spatially tunable microtopography of various sizes and geometries in just a few minutes (up to 1 mm/min). To showcase the versatility of our technique, we printed a one-centimeter-long tubular scaffold with dual microtopographic patterns, i.e. 20 {micro}m axially aligned grooves on the internal surface and 15 {micro}m circumferentially aligned rings on the external surface. These scaffolds induced the simultaneous orientation of vascular endothelial cells along the axial grooves and vascular smooth muscle cells along the circumferential rings, mimicking the orthogonally aligned bilayer architecture of natural arteries. Moreover, the groove patterns significantly accelerated endothelial cell migration, potentially enhancing endothelialization in vascular implants. This approach provides a versatile tool for designing advanced scaffolds and medical devices that harness microtopography to guide tissue organization and enhance regeneration.

bioengineering↗

bioRxiv2024

Imputed DNA methylation outperforms measured loci associations with smoking and chronological age

Multi-locus signatures of blood-based DNA methylation are well-established biomarkers for lifestyle and health outcomes. Here, we focus on two CpGs that are strongly associated with age and smoking behaviour. Imputing these loci via epigenome-wide CpGs results in stronger associations with outcomes in external datasets compared to directly measured CpGs. If extended epigenome-wide, CpG imputation could augment historic arrays and recently-released, inexpensive but lower-content arrays, thereby yielding better-powered association studies.

genetics↗

bioRxiv2024

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining

The exponential growth of microbial genome data presents unprecedented opportunities for mining the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent advances in microbial pangenomic research have generated substantial data and literature, yielding valuable knowledge across diverse microbial species. PanKB (pankb.org), a knowledgebase designed for microbial pangenomics research and biotechnological applications, was built to capitalize on this wealth of information. PanKB currently includes 51 pangenomes on 8 industrially relevant microbial families, comprising 8, 402 genomes, over 500, 000 genes, and over 7M mutations. To describe this data, PanKB implements four main components: 1) Interactive pangenomic analytics to facilitate exploration, intuition, and potential discoveries; 2) Alleleomic analytics, a pangenomic- scale analysis of variants, providing insights into intra-species sequence variation and potential mutations for applications; 3) A global search function enabling broad and deep investigations across pangenomes to power research and bioengineering workflows; 4) A bibliome of 833 open- access pangenomic papers and an interface with an LLM that can answer in-depth questions using their knowledge. PanKB empowers researchers and bioengineers to harness the full potential of microbial pangenomics and serves as a valuable resource bridging the gap between pangenomic data and practical applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/608241v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@4d3daaorg.highwire.dtl.DTLVardef@10b6d49org.highwire.dtl.DTLVardef@133da4forg.highwire.dtl.DTLVardef@141ae7e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multicompartmental alterations in gene expression and signaling cross-talk

Vulvar diseases are a critical yet often neglected area of womens health, profoundly affecting patients quality of life and frequently resulting in long-term physical and psychological challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disorder that predominantly affects the vulva, leading to severe itching, pain, scarring, and an increased risk of malignancy. Despite its profound impact on affected individuals, the molecular pathogenesis of vulvar LS (VLS) is not well understood, hindering the development of FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our findings demonstrate histologic, cellular, and molecular heterogeneities within VLS, yet highlight unifying molecular changes across keratinocytes, fibroblasts, immune cells, and melanocytes in lesional skin. They reveal cellular stress and damage in fibroblasts and keratinocytes, enhanced T cell activation and cytotoxicity, aberrant cell-cell signaling, and increased activation of the IFN, JAK/STAT, and p53 pathways in specific cell types. Using both monolayer and organotypic culture models, we also demonstrate that knockdown of select genes, which are downregulated in VLS lesional keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.

genomics↗

bioRxiv2024

Transocular detection of premotor Parkinson's disease via retinal neurovascular coupling through functional OCT angiography

Early detection of Parkinsons disease (PD) is essential for timely initiating neuroprotective interventions before significant loss of dopaminergic (DAergic) neurons, but faces challenges in accurately and noninvasively detecting subtle neuronal changes in the midbrain. Here, we propose a transocular functional imaging method termed fOCTA-rNVC, which detects premotor PD by measuring alterations in retinal neurovascular coupling (rNVC) at the capillary level using specialized functional OCT angiography (fOCTA). Our findings demonstrate that capillary rNVC is significantly attenuated and delayed due to concurrent retinal dopaminergic degeneration in premotor PD mice. Notably, this PD-related rNVC attenuation can be temporarily reversed in acute levodopa challenge. Utilizing the functional characteristics of capillary rNVC in PD, we achieved an impressive accuracy of [~]100% in detecting premotor PD mice even with only [~]14.1% loss of midbrain DAergic neurons, at which stage prompt treatment offered superior outcomes. In contrast, no significant changes were observed in retinal thickness or vasculature in the premotor PD mice. These findings suggest that fOCTA-rNVC is a promising noninvasive solution for accurately detecting premotor PD and guiding early interventions.

bioengineering↗

bioRxiv2024

PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis

BackgroundBeta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities. ResultsHere, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof-of-concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFuncs performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pydigger.com/pypi/PhyloFunc), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset. ConclusionsUnlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study.

bioinformatics↗

bioRxiv2024

Pi-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing

Peptide sequencing via tandem mass spectrometry (MS/MS) is fundamental in proteomics data analysis, playing a pivotal role in unraveling the complex world of proteins within biological systems. In contrast to conventional database searching methods, deep learning models excel in de novo sequencing peptides absent from existing databases, thereby facilitating the identification and analysis of novel peptide sequences. Current deep learning models for peptide sequencing predominantly use an autoregressive generation approach, where early errors can cascade, largely affecting overall sequence accuracy. And the usage of sequential decoding algorithms such as beam search suffers from the low inference speed. To address this, we introduce{pi} -PrimeNovo, a non-autoregressive Transformer-based deep learning model designed to perform accurate and efficient de novo peptide sequencing. With the proposed novel architecture,{pi} -PrimeNovo achieves significantly higher accuracy and up to 69x faster sequencing compared to the state-of-the-art methods. This remarkable speed makes it highly suitable for computation-extensive peptide sequencing tasks such as metaproteomic research, where{pi} -PrimeNovo efficiently identifies the microbial species-specific peptides. Moreover,{pi} -PrimeNovo has been demonstrated to have a powerful capability in accurately mining phosphopeptides in a non-enriched phosphoproteomic dataset, showing an alternative solution to detect low-abundance post-translational modifications (PTMs). We suggest that this work not only advances the development of peptide sequencing techniques but also introduces a transformative computational model with wide-range implications for biological research.

bioinformatics↗

bioRxiv2024

Generators of the frequency-following response in the subthalamic nucleus: implications for non-invasive deep brain stimulation

While Deep Brain Stimulation (DBS) is effective treatment for several movement disorders, non-invasive stimulation modes have major clinical relevance. We report on a novel method holding potential for non-invasive subthalamic nucleus (STN) stimulation. We used an auditory frequency-following response task (FFR), a popular tool for studying the auditory brainstem as the neural response in the cortical and midbrain generator, as it precisely reflects the ongoing dynamics of a speech or non-speech sound. We recorded EEG and DBS electrodes from 5 patients, in 4 from the STN, and one from the anterior thalamus and a number of cortical and subcortical areas located in the hippocampus and frontal regions, during an FFR at a frequency higher than the upper limit of phase-locking in the cortex (333Hz). Our results revealed a neural response local to the STN, but not other structures. This finding is novel. Auditory perception in the basal ganglia is rather unexplored, and the STN generator of the FFR has likely gone unseen due to the limitations of our tools and research focus. The potential clinical implications are far-reaching. Future research should investigate whether auditory stimuli at common electrical stimulation frequencies and waveforms of electrical DBS stimulation can induce clinical improvement.

neuroscience↗

bioRxiv2024

SKP2-mediated FBXO2 proteasomal degradation drives hepatocellular carcinoma progression via stabilizing Hsp47

Accumulating studies highlight that dysregulated E3 ubiquitin ligases are associated with the onset and advancement of cancers. Nevertheless, the impact and mechanism of most E3 ubiquitin ligases on tumorigenesis and tumor metastasis remain poorly understood. Here, we show that loss of FBXO2, an E3 ubiquitin ligase, accelerates hepatocellular carcinoma (HCC) tumor growth and metastasis to the lung through stabilizing heat shock protein 47 (Hsp47). Downregulation of FBXO2, caused by DNA-PKcs-medicated phosphorylation at serine 17 and E3 ligase SKP2-mediated ubiquitination at lysine 79 and subsequent proteasomal degradation, is observed in tumor tissues compared to their parallel non-tumor tissues resected from patients with HCC. Patients whose tumors are enriched for SKP2 or Hsp47 or express low levels of FBXO2 have poor median survival compared to those whose tumors have reversed levels of SKP2, FBXO2 and Hsp47. Together, FBXO2 acts as a tumor suppressor in HCC development. The components of the SKP2-FBXO2-Hsp47 axis provide newly prognostic and therapeutic factors for anti-HCC.

cancer biology↗

bioRxiv2024

Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay

Amyloid-beta (A{beta}42) aggregates are characteristic signatures of Alzheimers disease, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to A{beta}42 fibrils. We quantify correlations between fibril architectures, measured by SMOLM, and their growth and decay visualized by single-molecule localization microscopy (SMLM). We discover that stable A{beta}42 fibrils tend to be well-ordered, signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying A{beta}42 fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve {beta}-sheet organization. SMOLM reveals that increased heterogeneity in fibril architectures is correlated with more dynamic remodeling and that large-scale fibril remodeling tends to originate from local regions that exhibit strong heterogeneity.

biophysics↗

bioRxiv2024

Granzyme B-based CAR T cells block metastasis by eliminating circulating tumor cells

Chimeric antigen receptor (CAR) T cells have limited efficacy against solid tumors due to the hostile microenvironment. Circulating tumor cells (CTCs) are essential to metastasis, which is the cause of most of cancer-related death. Here, we generated GrB-CAR T cells targeting membrane-bound HSP70 (mHSP70), a highly tumor-specific antigen detected in numerous cancers. GrB-CAR T cells exhibited potent cytotoxicity against a broad spectrum of cancer cell lines and stem-like cancer cells in vitro and effectively inhibited xenograft tumor growth in vivo. Importantly, GrB-CAR T cells markedly decreased the number of CTCs and, therefore, hindered cancer metastasis in spontaneous metastasis models with uncontrollable primary tumor growth, a scenario commonly encountered in clinical trials of CAR T therapies for solid tumors. Furthermore, despite the 100% homology between human and macaque HSP70 protein, the autotransplantation of macaque T cells expressing human GrB-CAR did not cause any obvious toxic effects. These results not only demonstrate GrB-CAR T cells as a safe and effective tactic with broad-spectrum anticancer activity, but also offer strong experimental evidence and proof-of-concept validation for CAR T cell-mediated metastasis inhibition by targeting CTCs.

immunology↗

bioRxiv2024

Enhancing Gastrodin Production in Yarrowia lipolytica by Metabolic Engineering

Gastrodin, 4-hydroxybenzyl alcohol-4-O-{beta}-D-glucopyranoside, has been widely used in the treatment of neurogenic and cardiovascular diseases. Currently, gastrodin biosynthesis has been achieved in model microorganisms. However, the production levels are insufficient for industrial applications. In this study, we successfully engineered a Yarrowia lipolytica strain to overproduce gastrodin through metabolic engineering. Initially, the engineered strain expressing the heterologous gastrodin biosynthetic pathway, which comprises chorismate lyase, carboxylic acid reductase, phosphopantetheinyl transferase, endogenous alcohol dehydrogenases, and a UDP-glucose dependent glucosyltransferase, produced 1.05 g/L of gastrodin from glucose in a shaking flask. Then, the production was further enhanced to 6.68 g/L with a productivity of 2.23 g/L/day by over-expressing the key node DAHP synthases of the shikimate pathway and alleviating the native tryptophan and phenylalanine biosynthetic pathways. Finally, the best strain, Gd07, produced 13.22 g/L of gastrodin in a 5-L fermenter. This represents the highest reported production of gastrodin in an engineered microorganism to date, marking the first successful de novo production of gastrodin using Y. lipolytica. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/584284v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1eddb6corg.highwire.dtl.DTLVardef@e0bd94org.highwire.dtl.DTLVardef@be472dorg.highwire.dtl.DTLVardef@32fe9d_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

EGF/STAT1 signals to maintain ECM1 expression in hepatic homeostasis are disrupted by IFNγ/NRF2 in chronic liver disease

In healthy livers, extracellular matrix protein 1 (ECM1) is essential for liver homeostasis by keeping latent transforming growth factor-{beta} (LTGF-{beta}) quiescent. Upon hepatocyte damage, ECM1 is downregulated, facilitating LTGF-{beta} activation and fibrogenesis. However, little is known about how hepatic ECM1 is regulated. Here we found in healthy hepatocytes, EGF/EGFR signaling sustains ECM1 expression through phosphorylating STAT1 at S727, enhancing its binding to the ECM1 promoter and boosting gene transcription. During liver inflammation, accumulating IFN{gamma} disrupts this process by downregulating EGFR and inhibiting EGF/EGFR/STAT1-mediated ECM1 promoter binding. Mechanistically, IFN{gamma}-induced STAT1 phosphorylation at Y701 impairs the binding of p-STAT1 S727 to the ECM1 promoter. Additionally, IFN{gamma} induces NRF2 nuclear translocation, which repressively binds to the ECM1 promoter, further reducing its expression. These findings were confirmed in several chronic liver disease (CLD) mouse models. Moreover, AAV8-ECM1 significantly attenuates liver fibrosis and injuries in Western diet (WD)-fed mice. Notably, in patients with CLD, ECM1 levels align with EGFR expression, while NRF2 and LTGF-{beta} activation show a negative correlation with both.

cell biology↗