Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 523 records · Page 29Linked to original sources

bioRxiv2025

Protease mimicry: dissecting the ester bond crosslinking mechanics in bacterial adhesin proteins

The ester bond crosslink discovered within bacterial adhesin proteins offers a captivating insight into the convergent evolution of enzyme-like machinery. Crystal structures reveal a putative catalytic triad comprising an acid-base-nucleophile combination and an oxyanion-like site that suggest a serine protease-like mechanism drives the crosslinking process. We now provide confirmation of the mechanism, revealing functional catalytic dyads or triads, and the recapitulation of protease machinery from a Pseudomonas bacterium and a human cytomegalovirus related only by convergent evolution. Molecular dynamics simulations show how a conservative threonine-to-serine mutation of the nucleophile induces hydrolysis and eliminates the ester bond crosslink. Collectively, our structural, functional, and computational efforts detail the molecular intricacies of intramolecular ester bond formation and underscore the convergent evolutionary adaptations of bacteria in exploiting enzyme-like machinery to protect essential adhesin proteins from the mechanical, biological, and chemical hostilities of the bacterias replicative niche.

biochemistry↗

bioRxiv2025

Spermatogonia derived RpS13 non-autonomously regulates the cyst cell differentiation via Rho1-mediated adhesion junctions in Drosophila testis

ObjectiveIn the testis of Drosophila, spermatogonia transit-amplification (TA) divisions are necessary for germline proliferation and differentiation. Both the germline and the surrounding somatic cyst cells (SCCs) have a significant influence on these processes. However, the underlying mechanism is largely unknown. MethodsFlies were used to generate tissue-specific gene knockdown. Immunofluorescence was used to determine protein localization and expression pattern. Small interfering RNAs were used to knockdown genes in S2 cells. qRT-PCR was used to examine the relative mRNA expression level. ResultsOur findings indicate that spermatogonial RpS13 regulates cyst cell growth through a non-autonomous manner. In terms of mechanism, RpS13 may regulate the adhesion junctions of the soma-germline via the DE-cad and Arm proteins in addition to dpERK, which is found in SCCs. Interestingly, Rho1 and RpS13 mutually inhibit each other in Drosophila S2 cells. Additionally, Rho1 controlled cell adhesions that rely on DE-cad, Arm, and dpERK and imitated the actions of RpS13 in Drosophila testis. ConclusionAll of these findings implied that during spermatogonia TA-divisions in the testis of Drosophila, RpS13 regulates the development of cyst cells via Rho1-mediated adhesion junctions.

developmental biology↗

bioRxiv2025

Rational design of a foldon-derived heterotrimer guided by quantitative native mass spectrometry

Designing stable hetero-oligomeric protein complexes with defined inter-subunit stoichiometries remains a significant challenge. In this study, we report the design of a highly selective heterotrimeric assembly derived from the well-known foldon homotrimer. We generated an aab heterotrimer by introducing the Q11E modification to destabilize the homotrimer and a compensatory modification, either V14A or V14L, to stabilize the hydrophobic core of the heterotrimer. Native mass spectrometry (MS) was essential for guiding the design process, enabling precise characterization of oligomeric states and their equilibrium distributions. The heterotrimer structure was validated by x-ray crystallography. Our findings highlight the effectiveness of combining rational design with native MS to develop specific hetero-oligomeric assemblies.

biochemistry↗

bioRxiv2025

Deciphering the Pathogenic Landscape of Amyloid Light-Chain Cardiomyopathy

Amyloid light-chain cardiomyopathy (ALCA) is an infiltrative disorder marked by misfolded immunoglobulin light-chain deposition in the myocardium, ultimately leading to cardiac dysfunction. Despite its clinical severity, the underlying mechanisms remain poorly understood. Here, we integrated multi-omics analyses of human cardiac samples to construct a comprehensive cellular and spatial atlas of the ALCA heart. We observed a marked expansion of PTX3+ fibroblasts (FB), which undergo a distinct phenotypic transition into pro-fibrotic POSTN+ FB regulated by EGR1.Concurrently, SPP1+ macrophages (Mac) emerged as major drivers of fibrosis, interacting robustly with PTX3+ FB via APP-CD74, GAS6-MERTK, and TGF-{beta}1-TGF-{beta}1/2 pathways. Endothelial cell (EC) profiling revealed substantial vascular remodeling characterized by the emergence of specialized capillary-like immune endothelial cells expressing chemokines CXCL1, CXCL3, and CCL2, alongside depletion of functional capillary EC. Immunologically, elevated cytotoxic CD8+ T cells and reduced NK cells contributed to an imbalanced inflammatory milieu, with NF{kappa}B2 orchestrating both fibrotic and immune pathways across multiple cell types. These findings highlight the pivotal role of fibroblast-immune crosstalk, particularly the SPP1+ Mac-PTX3+ FB axis, in driving ALCA pathogenesis. Targeting these pathological cellular interactions may offer a promising therapeutic avenue to mitigate fibrosis, restore immune homeostasis, and improve cardiac function in ALCA.

bioinformatics↗

bioRxiv2025

High-resolution NMR spectroscopy of proteins in intact mitochondria

Understanding protein structure and function within mitochondria is essential for unraveling the molecular mechanisms underlying cellular energy production, stress response, and disease. Here, we present a novel approach for NMR observation of proteins within intact mitochondria by delivering proteins directly into isolated mitochondria via electroporation. Using this method, we investigate the interaction of -synuclein (-syn) with the mitochondria membrane and examine how post-translational modifications regulate this interaction. Additionally, we assessed the stability of GB1 and the dimerization of its variant within mitochondria, achieving quantitative insights into mitochondrial environmental impact on protein function. This approach offers a valuable framework for exploring mitochondrial related biomolecular events at atomic-resolution within intact mitochondria, paving the way for a more comprehensive understanding of the molecular events governing mitochondrial health and dysfunction.

biochemistry↗

bioRxiv2025

Structural variants contribute to the gut microbiome, blood metabolic traits and their causal relationships

Research on genetic variants affecting the gut microbiome and blood metabolites has mainly focused on single nucleotide variants (SNPs), with structural variants (SVs) remaining largely unexamined. In this study, we utilized an advanced structural variant detection pipeline on whole-genome sequencing data from 2,002 individuals with an average sequencing depth of 42 folds, identifying 138,859 high-confidence SVs, 49.57% of which were previously unreported. We performed genome-wide association studies on 22,519 common SVs with 616 gut microbial features and 121 blood metabolic traits, uncovering 30 significant links between SVs and microbial taxa/pathways and 48 connections between SVs and blood metabolites. Notable results include 19 associations reaching study-wide significance, such as an Asian-specific 6.5k deletion at the TENT2 gene, which is strongly associated with the abundance of Coprobacillus sp. 29_1 ({beta}=0.158, p=2.5x10-9), and a deletion covering HBA1/HBA2/HBM/HBQ118 linked to nine blood metabolic traits, most significantly with mean corpuscular volume (MCV; {beta}=-0.570, p=1.22x10-91). Most SVs showed a greater impact than nearby SNPs in their associations with the microbiome/metabolites. Analysis of rare SVs also identified multiple genes associated with the microbiome/metabolites. Additionally, Mendelian randomization using SVs demonstrated causal relationships, including effects from the microbiome to metabolites, such as Clostridium ramosums impact on serum uric acid and hyperuricemia, and from metabolites to the microbiome, like the influence of mean corpuscular hemoglobin concentration on MF0064: triacylglycerol degradation. This study provides a detailed SV catalog for the Chinese population and highlights the significant role of SVs in the gut microbiome, blood metabolites, and their causal relationships. HighlightsO_LIProvides a catalog of 138,859 high-confidence SVs and 49.57% of which were novel C_LIO_LIIdentify 30 genome-wide significant "SVs--microbial taxa/pathways" and 48 "SVs--blood metabolites" associations, respectively C_LIO_LIAn Asian-specific 6.5k deletion at TENT2 gene associated with the species Coprobacillus sp. 29_1 C_LIO_LIA deletion spanning HBA1/HBA2/HBM/HBQ118 associated with 9 blood metabolic traits C_LIO_LIThe majority of SVs demonstrated a more pronounced impact than neighboring SNPs in the associations with microbiome/metabolites C_LIO_LISVs help to reveal the host-microbe causal relationships such as Clostridium ramosums causal effects on serum uric acid and hyperuricemia C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/643427v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@e660d0org.highwire.dtl.DTLVardef@ddfe4dorg.highwire.dtl.DTLVardef@62a704org.highwire.dtl.DTLVardef@c31bb5_HPS_FORMAT_FIGEXP M_FIG Graphic abstract Based on a multi-omics cohort of 2,002 individuals comprising high-depth whole genome and metagenomic sequencing data, blood metabolites, and detailed questionnaires, we identified 138,859 high-confidence SVs, uncovering 36 significant associations between SVs and microbial taxa/pathways, as well as 48 associations between SVs and blood metabolites. Mendelian randomization using SVs demonstrated causal relationships, such as Clostridium ramosums causal effect on serum uric acid and hyperuricemia. This study provides a detailed SV catalog for the Chinese population and highlights the significant role of SVs in the gut microbiome, blood metabolites, and their causal relationships. C_FIG

genomics↗

bioRxiv2025

A transcriptional atlas of the pubertal human growth plate reveals direct stimulation of cartilage stem cells by growth hormone.

The cartilaginous growth plate is a critical organ responsible for longitudinal bone growth. It remains open throughout life in mice but closes in humans after puberty. Growth hormone (GH) is a widely used therapy for children with growth retardation and open growth plates. However, it remains unclear whether GH directly targets human growth plates. Furthermore, while cartilage stem cells have recently been identified in mouse growth plates, their presence and GH responsiveness in human growth plates are unknown. To address these gaps, we characterized the cellular and molecular organization of early pubertal human growth plates using unique tissue samples obtained during growth-restricting surgeries. Our analysis identified two distinct populations of stem cells differing in cycling activity, molecular profiles, and regulatory factors. Quiescent stem cells were localized within a niche characterized by low Wnt and TGF{beta} signaling. To investigate the direct effects of GH, we developed a human growth plate explant culture system. GH directly stimulated explant growth and promoted stem cell proliferation by activating the JAK/STAT, TGF{beta}, and ERK pathways while inhibiting the AKT pathway. Notably, activation of the TGF{beta} pathway occurred in an autocrine manner. These findings provide critical new insights into human longitudinal growth and the mechanisms of GH action, with potential implications for optimizing treatments for growth disorders. One Sentence SummaryThis study reveals that growth hormone (GH) directly promotes proliferation within the human growth plate and activates TGF{beta} and ERK signaling pathways in cartilage stem cells, providing critical insights into human longitudinal growth and potential improvements in treatments for growth disorders.

cell biology↗

bioRxiv2025

Chimeric Collagen-like Proteins with Tunable Structural Heterogeneity for Precise Control and Targeted Doxorubicin Delivery

Protein-based drug delivery systems offer advantages such as genetic tunability, structural homogeneity, and high biocompatibility. However, precisely controlling the assembly of protein nanoparticles and establishing correlations between their macroscopic properties and molecular architecture remain significant challenges. Here, inspired by chimeric collagen-like proteins, we rationally designed a series of de novo chimeric proteins comprising an N-terminal globular domain fused to a linear collagen-like domain. These structurally heterogeneous proteins were conjugated with doxorubicin (DOX) and homogenized to form chimeric collagen-like protein-DOX nanocomplexes (CDCNs). By fine-tuning the protein structure and domain organization, we achieved precise control over CDCN architecture and drug release kinetics. Furthermore, to enhance tumor specificity, triple-negative breast cancer (TNBC)- and glioblastoma (GBM)-targeting peptides were genetically fused to the chimeric proteins, respectively. In both in vitro and in vivo models of TNBC and GBM, CDCNs facilitated selective tumor accumulation, enhanced cellular uptake, and promoted apoptosis while minimizing off-target toxicity. This work establishes a strategy for designing protein-based nanoplatforms with programmable structures and tunable functionalities, offering promising potential for precisely controlling of protein-based delivery system.

bioengineering↗

bioRxiv2025

Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomics

The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the hearts structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq (PIP-seq), a high-throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

developmental biology↗

bioRxiv2025

Harnessing Generative Pre-trained Transformer for Antimicrobial Peptide Generation and MIC Prediction with Contrastive Learning

Antimicrobial peptides (AMPs) have garnered considerable attention due to their reduced likelihood of inducing resistance in pathogens compared to traditional antibiotics, which has spurred the interest in de novo design of AMPs. Despite the availability of various methods, accurately generating AMPs and predicting their inhibitory effects remains a challenging task. In this work, we introduce AMPCLGPT, a novel approach that leverages contrastive learning and generative pre-training for AMP design and minimum inhibitory concentration (MIC) prediction. First, AMPCLGPT is pre-trained on a large-scale unlabeled peptide dataset to learn peptide sequence patterns and enhance its ability to extract powerful representations. Second, the pre-trained AMPCLGPT is fine-tuned on AMP data with contrastive learning to increase the distance between antimicrobial and non-antimicrobial peptides in the latent space, improving its ability to accurately generate AMPs. Additionally, the pre-trained AMPCLGPT is fine-tuned to predict MIC values based on the learned peptide features. Empirical results demonstrate that our model can effectively generate AMPs and accurately predict their MIC values. By integrating these two capabilities, AMPCLGPT enables fully automated design of AMPs with low MIC values. AMPCLGPT represents a significant advancement in the field of AMP research, potentially accelerating the development of potent AMP-based therapeutics.

bioinformatics↗

bioRxiv2025

A rapidly prototyped, simple yet versatile dynamic breathing Exposure-on-a-Chip for investigating nanoparticle deposition in the alveoli

We developed and characterized a three-layer microfluidic Exposure-on-a-Chip (EOC) model to replicate the alveolar microenvironment and simulate breathing motions, offering a physiologically relevant platform for studying inhaled nanomedicines. The EOC chip, fabricated from biocompatible polydimethylsiloxane (PDMS), features a fluidic chamber for cell culture, a pneumatic chamber for pressure application, and a thin PDMS membrane (150 {micro}m) separating the chambers to support cell growth and enable mechanical stretching. Xurography and 3D printing were validated as efficient and reproducible fabrication methods. Mechanical characterization, using fluorescent bead tracing, confirmed that the PDMS membrane accurately mimics alveolar breathing motions under physiological conditions (1-8% strain). Biological validation showed that alveolar epithelial and endothelial cells cultured on the EOC formed functional monolayers, maintaining barrier integrity under cyclic and static stretching, separately. To study nanoparticle behavior, we examined the deposition of nanoparticles under dynamic stretching versus static conditions. Significantly fewer nanoparticles accumulated in cells under continuous dynamic exposure with stretching compared to static culture, highlighting the critical role of mechanical forces in nanoparticle-cell interactions. The EOC platform provides a robust and scalable tool for evaluating nanomedicine efficacy in dynamic environments, representing a significant advancement in alveolus-on-chip technology.

bioengineering↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

A central, shared role for disulfide bonds in Bacteroidota protein transport and gliding motility

Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using the Type 9 Secretion System (T9SS). Here we discover that gliding motility and the T9SS share a novel mechanism of energisation in which outer membrane proteins are covalently attached by disulfide bonds to a moving internal track structure which propels them through the membrane. We determined the structure of a representative Bacteriodota mobile track by obtaining the cryoEM structure of a 3 MDa circular mini-track from Porphyromonas gingivalis. Our discoveries identify a novel mechanistic and evolutionary link between gliding motility and T9SS-dependent protein transport.

microbiology↗

bioRxiv2025

Intratumoral Resident Microbes Directly Participate in Resistance to EGFR-TKI Targeted Drug Therapy through Metabolism in NSCLC

EGFR-TKIs targeted therapy represents a cornerstone in the treatment of non-small cell lung cancer (NSCLC). Nonetheless, a subset of patients inevitably develops acquired resistance to EGFR-TKIs, posing a significant clinical challenge. An increasing number of evidence has documented the presence of microbial communities within tumor microenvironments, but the potential interplay between tumor-resident microbiota and resistance to EGFR-TKIs remains poorly understood. Here, we report that prolonged EGFR-TKIs treatment markedly alters the diversity of tumor-resident microbiota, characterized by a notable enrichment of Bacillus mycoides and Pseudomonas veronii. In vitro experiments revealed that co-culture of gefitinib with either B. mycoides or P. veronii significantly attenuated its tumor-suppressive efficacy, both in vitro and in vivo. Mechanistically, gefitinib underwent extensive biotransformation in the presence of these bacteria, yielding redox derivatives and conjugation products, which collectively diminished its antitumor activity. Specifically, B. mycoides metabolized gefitinib into B.mPM9-C33 H45 Cl F N3 O4, while P. veronii generated P.vPM2-C24 H29 Cl N4 O3, both of which were consistently detected in in vivo and in vitro models. Furthermore, heterologous expression of maltose acetyltransferase from B. mycoides in E. coli BL21 conferred the capacity to metabolize gefitinib, underscoring the enzymatic basis of this metabolic conversion. Collectively, these findings demonstrate that B. mycoides and P. veronii drive tumor resistance to EGFR-TKIs through metabolic inactivation of the drug, unveiling a previously unrecognized role of tumor-resident microbiota in modulating therapeutic responses and providing novel insights into the mechanisms underlying EGFR-TKIs resistance in NSCLC.

microbiology↗

bioRxiv2025

Redefining the Role of the EryM Acetyltransferase in Natural Product Biosynthetic Pathways

The GNAT (GCN5-related N-acetyltransferase) superfamily comprises enzymes with a conserved fold and diverse catalytic activities, including primarily acyl transfer, with a few examples of decarboxylation. EryM, a GNAT enzyme from Saccharopolyspora erythraea, has been implicated in both erythromycin and erythrochelin biosynthesis, with dual functionality as an acetyltransferase and a decarboxylase. Despite an historical association with malonyl-coenzyme A decarboxylation activity, the structural basis for this dual activity has remained unknown as its close homologs were identified with only acyl transfer activity. Here, crystal structures of EryM in its free form (2.5 [A]) and in complex with acetyl-CoA (2.9 [A]) reveal insights into the active site architecture and substrate interactions. Functional assays demonstrate that EryM catalyzes acyl transfer but lacks decarboxylation activity, challenging long-standing assumptions about its biosynthetic role. Comparative analysis of EryM and homologs in siderophore biosynthetic pathways highlights a conserved catalytic pocket with an essential His and identically positioned side chains common to GNAT enzymes for N-acyl transfer from CoA to primary hydroxylamine substrates. Bioinformatic analysis defines a large GNAT subfamily that is broadly distributed in the microbial world. These findings redefine EryM as an acetyltransferase and provide a foundation for understanding GNAT functional diversity in natural product biosynthesis.

biochemistry↗

bioRxiv2025

Inhibiting B-cell-mediated Immunosuppression to Enhance the Immunotherapy Efficacy in Hepatocellular Carcinoma

BackgroundImmunotherapy is efficacious in hepatocellular carcinoma (HCC), but the benefits are limited to a minority of patients. Most HCC patients show resistance to immune checkpoint blockade (ICB). Agonists of the stimulator of interferon genes (STING), potent immune stimulators, showed limited effectiveness. Using preclinical models, we studied the mechanisms of resistance to ICB and STING agonism. MethodsMurine HCA-1 and RIL-175 HCCs were orthotopically grown in mice with underlying liver fibrosis, to mimic the presentation of human HCC. Established tumors were treated with a STING agonist (BMS-986301) or anti-PD1 ICB, and mice were followed to evaluate safety and efficacy, as well as the mechanisms of treatment resistance by RNA sequencing, flow cytometry, and immunofluorescence, B-cell depletion and T-cell immunoglobulin and mucin domain 1 (TIM-1) ICB. ResultsUnbiased analyses of transcriptomic data from murine HCC tissues from ICB-treated mice showed an increased abundance of intratumoral CD8+ T cells and B cells. STING agonism alone showed efficacy in the ICB-responsive RIL-175 HCC model but more limited efficacy in the ICB-resistant HCA-1 model. STING agonism increased circulating IL-10 and intratumoral infiltration by B-cells, including TIM-1+ B cells, and promoted the formation of tertiary lymphoid structure (TLS)-like structures, especially in the peritumoral areas. Strikingly, adding B cell depletion to ICB or STING agonism treatment significantly increased survival. Interestingly, unlike ICB, STING agonism also had a pronounced anti-metastatic activity. In addition, the combination of STING agonism and TIM-1 blockade augmented B cell differentiation and antigen presentation in vitro and improved the anti-tumor effects in murine HCC in vivo. This approach decreased the number of TIM-1+ B cells in the tumor and shifted B cells to higher expression of CD86 and MHC class II, enhancing the antigen presentation capability and further boosting the antitumor efficacy of CD8+ cytotoxic T cells. ConclusionOur findings demonstrate that B cells are associated with ICB- and STING-mediated therapy resistance, and that depleting B-cells or targeting TIM-1 enhances both innate and acquired therapeutic efficacy in HCC.

cancer biology↗

bioRxiv2025

Murine Leukemia Virus GlycoGag Antagonizes SERINC5 via ER-phagy Receptor RETREG1

Serine incorporator 5 (SERINC5) is a host restriction factor that targets certain enveloped viruses, including human immunodeficiency virus type 1 (HIV-1) and murine leukemia virus (MLV). It integrates into the viral envelope from the cell surface, inhibiting viral entry. SERINC5 is transported to the cell surface via polyubiquitination, while a single K130R mutation retains it in the cytoplasm. Both HIV-1 Nef and MLV glycoGag proteins antagonize SERINC5 by reducing its expression in producer cells. Here, we report that MLV glycoGag employs selective autophagy to downregulate SERINC5, demonstrating a more potent mechanism for decreasing its cell surface expression. Although glycoGag is a type II integral membrane protein, it primarily localizes to the cytoplasm and undergoes rapid proteasomal degradation. Employing the K130R mutant, we show that Nef, primarily associated with the plasma membrane, downregulates SERINC5 only after it has trafficked to the cell surface, whereas glycoGag can reduce its expression before reaching the plasma membrane while still in the cytoplasm. Nonetheless, an interaction with SERINC5 stabilizes and recruits glycoGag to the plasma membrane, enabling it to downregulate SERINC5 from the cell surface. Through affinity-purified mass spectrometry analysis combined with CRISPR/Cas9 knockouts, we find that glycoGags activity depends on reticulophagy regulator 1 (RETREG1), an ER-phagy receptor. Further knockout experiments of critical autophagy genes demonstrate that glycoGag downregulates cytoplasmic SERINC5 via micro-ER-phagy. These findings provide crucial new insights into the ongoing arms race between retroviruses and SERINC5 during infection. AUTHOR SUMMARYHIV-1 Nef and MLV glycoGag are unrelated viral proteins, yet both counteract the same host restriction factor, SERINC5, to facilitate productive infection. In this study, we report a novel pathway through which glycoGag downregulates SERINC5. We demonstrate that while Nef downregulates SERINC5 only after it has trafficked to the cell surface, glycoGag can directly downregulate SERINC5 in the cytoplasm before it reaches the plasma membrane. Furthermore, we show that this pathway is mediated by the ER-phagy receptor RETREG1, which targets SERINC5 for degradation via micro-ER-phagy. This mechanism provides a more effective means of blocking SERINC5 antiviral activity. These findings reveal that retroviruses have evolved different strategies to antagonize SERINC5, highlighting the critical role of SERINC5 in restricting retroviral infections.

microbiology↗

bioRxiv2025

Cross-family Signaling: PDGF Mediates VEGFR Activation and Endothelial Function

Cross-family signaling between platelet-derived growth factors (PDGFs) and vascular endothelial growth factor receptors (VEGFRs) is a newly discovered yet unexplored mechanism of angiogenesis regulation. This study elucidates the role of PDGFs in endothelial cell (EC) signaling and functions, focusing on VEGFR1 and VEGFR2 activation. Using human dermal microvascular ECs (HDMECs) with double knockout of PDGFR/{beta} and human brain microvascular ECs (HBMECs), we show three key findings: (1) PDGF-AA and -BB induced VEGFR1 phosphorylation, peaking at 2-fold increases at low concentrations (0.5 ng/mL), while PDGF-AB stimulated a 2-fold rise in VEGFR2 phosphorylation. (2) Downstream effectors PLC{gamma}1, Akt, and FAK were activated by all three PDGFs at levels comparable to VEGF-A. (3) PDGF-BB significantly enhanced EC proliferation (up to 240%) and migration (up to 170%), with lower PDGF concentrations (0.5-5 ng/mL) eliciting stronger effects than higher concentrations (50-100 ng/mL). Overall, PDGF subtypes differentially induce VEGFR phosphorylation, downstream effector activation, and angiogenic hallmarks such as proliferation and migration, revealing novel mechanisms for regulating endothelial function.

bioengineering↗