Biology subjects

Yu, Q.

Publications and source records attributed to Yu, Q..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment

Lung-resident immune cells, spanning both innate and adaptive compartments, preserve the integrity of the respiratory barrier, but become pathogenic if dysregulated1. Current in vitro organoid models aim to replicate interactions between the alveolar epithelium and immune cells but have not yet incorporated lung-specific immune cells critical for tissue residency2. Here we address this shortcoming by describing human lung alveolar immuno-organoids (LIO) that contain an autologous tissue-resident lymphoid compartment, primarily composed of tissue-resident memory T cells (TRMs). Additionally, we introduce lung alveolar immuno-organoids with myeloid cells (LIOM), which include both TRMs and a macrophage-rich alveolar myeloid compartment. The resident immune cells formed a stable immune-epithelial system, frequently interacting with the epithelium and promoting a regenerative alveolar transcriptomic profile. To understand how dysregulated inflammation perturbed the respiratory barrier, we simulated T-cell-mediated inflammation in LIOs and LIOMs and used single-cell transcriptomic analyses to uncover the molecular mechanisms driving immune responses. The presence of innate cells induced a shift in T cell identity from cytotoxic to immunosuppressive, reducing epithelial cell killing and inflammation. Based on insights obtained with bulk RNA-seq data from the phase 3 IMpower150 trial, we tested whether LIOM cultures could model clinically-relevant but poorly understood pulmonary side effects caused by immunotherapies such as the checkpoint inhibitor atezolizumab3. We observed a decrease in immunosuppressive T cells and identified gene signatures that matched the transcriptomic profile of patients with drug-induced pneumonitis. Given its effectiveness in capturing outcomes and mechanisms associated with a prevalent pulmonary disease, this system unlocks opportunities for studying a wide range of immune-related pathologies in the lung.

cell biology↗

bioRxiv2025

Neurons exploit stochastic growth to rapidly and economically build dense radially oriented dendritic arbors

Dendrites grow by stochastic branching, elongation, and retraction. A key question is whether such a mechanism is sufficient to form highly branched dendritic morphologies. Alternatively, are signals from other cells or is the topological hierarchy of the growing network necessary for dendrite geometry? To answer these questions, we developed a mean-field model in which branch dynamics is isotropic and homogenous (i.e., no extrinsic instruction) and depends only on the average lengths and densities of branches. Branching is modeled as density-dependent nucleation so there are no tree structures and no network topology. Despite its simplicity, the model predicted several key morphological properties of class IV Drosophila sensory dendrites, including the exponential distribution of branch lengths, the parabolic scaling between dendrite number and length densities, the tight spacing of the dendritic meshwork (which required minimal total branch length), and the radial orientation of branches. Stochastic growth also accelerated the overall expansion rate of the arbor. Therefore, stochastic dynamics is an economical and rapid space-filling mechanism for building dendritic arbors without external guidance or hierarchical branching mechanisms. Our model provides a general theoretical framework for understanding how macroscopic branching patterns emerge from microscopic dynamics.

developmental biology↗

bioRxiv2025

APOE4 exacerbates glucocorticoid stress hormone-induced tau pathology via mitochondrial dysfunction

APOE4 is the leading genetic risk factor for Alzheimers disease, and chronic stress is a leading environmental risk factor. Studies suggest that APOE4 confers vulnerability to the behavioral and neuropathological effects of chronic stress, representing a potential mechanism by which this genetic variant accelerates Alzheimers onset and progression. Whether and how APOE4-mediated stress vulnerability manifests in neurons of the hippocampus, a brain region particularly susceptible to stress and Alzheimers pathology, remains unexplored. Using a combination of in vivo and in vitro experiments in humanized APOE4 and APOE3 knockin mice and primary hippocampal neurons from these animals, we investigate whether and how APOE4 confers sensitivity to glucocorticoids, the main stress hormones. We find that a major hallmark of stress/glucocorticoid-induced brain damage, tau pathology (i.e., tau accumulation, hyperphosphorylation, and spreading) is exacerbated in APOE4 versus APOE3 mice. Moreover, APOE4 animals exhibit underlying mitochondrial dysfunction and enhanced glucocorticoid receptor activation in the hippocampus, factors that likely contribute to tau pathogenesis in both the presence and absence of stress/glucocorticoids. Supporting this concept, we show that opening of the mitochondrial permeability transition pore drives mitochondrial dysfunction and tau pathology in APOE4 mice, and that pharmacological inhibition of pore opening is protective against ApoE4-mediated mitochondrial damage, tau phosphorylation and spreading, and downstream hippocampal synapse loss. These findings shed light on the mechanisms of stress vulnerability in APOE4 carriers and identify the mitochondrial permeability transition pore as a potential therapeutic target for ameliorating Alzheimers pathogenesis in this population.

neuroscience↗

bioRxiv2025

Ustilaginoidea virens suppresses floral immunity through promoting GA biosynthesis by the effector SCRE9

Rice false smut caused by Ustilaginoidea virens has become one of the most important rice diseases. U. virens specifically infects rice florets through stamen filaments. However, it is mysterious how U. virens inhibits floral immunity for successful colonization. Here, we show that a small cysteine-rich effector SCRE9 is a key virulence factor in U. virens. Expression of SCRE9 in rice not only suppresses immune responses and false smut resistance, but also significantly increases expression of expansin and gibberellin (GA) biosynthetic genes and GA content in young rice panicles. We further demonstrate that OsSIP1 (SCRE9-interacting protein 1) in rice is targeted by SCRE9 and interacts with the OsMADS63 and OsMADS68 transcription factors that transcriptionally regulate the GA synthesis gene GA3ox1. Interestingly, the chloroplast-localized OsSIP1 recruits OsMADS63/68 into the chloroplast. SCRE9 causes OsSIP1 to be translocated into the nucleus, thereby releasing OsMADS63/68 from the chloroplast into the nucleus to promote GA3ox1 transcription. Therefore, SCRE9 promotes GA biosynthesis and expression of expansins in rice florets, thus loosening cell walls and overcoming the physical barrier during U. virens infection. The finding uncovers an unidentified floret infection strategy that offsets the deficiency in cell wall degrading ability in the unique floret colonizing fungus.

plant biology↗

bioRxiv2024

Secretory leukocyte protease inhibitor influences periarticular joint inflammation in B. burgdorferi-infected mice

Lyme disease, caused by Borrelia burgdorferi, is the most common tick-borne infection in the United States. Arthritis is a major clinical manifestation of infection, and synovial tissue damage has been attributed to the excessive pro-inflammatory responses. The secretory leukocyte protease inhibitor (SLPI) promotes tissue repair and exerts anti-inflammatory effects. The role of SLPI in the development of Lyme arthritis in C57BL/6 mice, which can be infected with B. burgdorferi, but only develop mild joint inflammation, was therefore examined. SLPI-deficient C57BL/6 mice challenged with B. burgdorferi had a higher infection load in the tibiotarsal joints and marked periarticular swelling, compared to infected wild type control mice. The ankle joint tissues of B. burgdorferi-infected SLPI-deficient mice contained significantly higher percentages of infiltrating neutrophils and macrophages. B. burgdorferi-infected SLPI-deficient mice also exhibited elevated serum levels of IL-6, neutrophil elastase, and MMP-8. Moreover, using a recently developed BASEHIT (BActerial Selection to Elucidate Host-microbe Interactions in high Throughput) library, we found that SLPI directly interacts with B. burgdorferi. These data demonstrate the importance of SLPI in suppressing periarticular joint inflammation in Lyme disease.

microbiology↗

bioRxiv2024

VIRALpre: Genomic Foundation Model Embedding Fused withK-mer Feature for Virus Identification

Virus, a submicroscopic infectious agent, influences all life forms. Identifying viral sequences is essential to understand their biological functions and then analyze their impacts on public health, and the development of microbial communities. For its significance, tools are developed based on various mathematical methods and algorithms. However, previous methods struggle to identify viral sequences, especially short contigs accurately since the limited information and small-scale close-set dataset. Here we propose VIRALpre, a hybrid framework combined with genomic foundation model (GFM) embedding and K-mer feature of sequences to precisely recognize viral genomic fragments. VIRALpre is empowered by the generalization competencies of GFMs, which have proven their strength in various downstream tasks, thanks to newly established large-scale training databases and Attention mechanism. On the other hand, K-mer features provide additional biological information to bridge the limitation of GFMs in classification tasks. Comprehensive experimental results demonstrate that VIRALpre significantly outperforms all the previous methods on virus identification performance by 4% in accuracy. To prove that this model is qualified when facing unique contigs to training data, BLASTn-based similarity cut-off test(setting e-value as 10-5) is done and it achieves about 10% F1-score improvement. More than well-built test datasets, new zero-shot cross-dataset tests on benchmark datasets sampling from natural environments are conducted, VIRALpre performs identify almost most viral sequences while keeping a very low False Positive Rate. Based on these solid experiments, VIRALpre has the ability to manage short-contig virus identification by truly learning the distinctions of viral sequences and hopefully act as an adviser to promote virus-related research.

bioinformatics↗

bioRxiv2024

PMAIP1-Mediated Glucose Metabolism and its Impact on the Tumor Microenvironment in Breast Cancer: Integration of Multi-Omics Analysis and Experimental Validation

BackgroundGlucose metabolism in breast cancer has a potential effect on tumor progression and is related to the immune microenvironment. Thus, this study aimed to develop a glucose metabolism- tumor microenvironment score to provide new perspectives on breast cancer treatment. MethodData were acquired from the Gene Expression Omnibus and UCSC Xena databases, and glucose-metabolism-related genes were acquired from the Gene Set Enrichment Analysis database. Genes with significant prognostic value were identified, and immune infiltration analysis was conducted, and a prognostic model was constructed based on the results of these analyses. The results were validated by in vitro experiments with MCF-7 and MCF-10A cell lines, including expression validation, functional experiments, and bulk sequencing. Single-cell analysis was also conducted to explore the role of specific cell clusters in breast cancer, and Bayes deconvolution was used to further investigate the associations between cell clusters and tumor phenotypes of breast cancer. ResultsFour significant prognostic genes (PMAIP1, PGK1, SIRT7, and SORBS1) were identified, and, through immune infiltration analysis, a combined prognostic model based on glucose metabolism and immune infiltration was established. The model was used to classify clinical subtypes of breast cancer, and PMAIP1 was identified as a potential critical gene related to glucose metabolism in breast cancer. Single-cell analysis and Bayes deconvolution jointly confirmed the protective role of the PMAIP1+ luminal cell cluster.

bioinformatics↗

bioRxiv2024

Comet fragment-ion indexing for enhanced peptide sequencing

Fragment ion indexing has significantly improved the efficiency of proteomics database search tools. This work implements fragment ion indexing in Comet, a widely-used, open-source search engine. We demonstrate that this enhancement maintains scoring and identification accuracy while substantially increasing peptide spectral matching speeds across multiple applications, including open modification searches, immunopeptidomics, and real-time searches. Comet-FI reduced search speeds by up to 94%, enabling the rapid analysis of complex data types like immunopeptidomes. Fragment-ion indexing enables Comet to keep pace with modern instrumentation and expanding applications in proteomics, reinforcing its utility in diverse proteomics workflows and its integration with a wide range of proteomics tools and platforms.

bioinformatics↗

bioRxiv2024

DNA/polysome phase separation and cell width confinement couple nucleoid segregation to cell growth in Escherichia coli

Chromosome segregation is essential for cellular proliferation. Unlike eukaryotes, bacteria lack cytoskeleton-based machinery to segregate their chromosomal DNA (nucleoid). The bacterial ParABS system segregates the duplicated chromosomal regions near the origin of replication. However, this function does not explain how bacterial cells partition the rest (bulk) of the chromosomal material. Furthermore, some bacteria, including Escherichia coli, lack a ParABS system. Yet, E. coli faithfully segregates nucleoids across various growth rates. Here, we provide theoretical and experimental evidence that polysome production during chromosomal gene expression helps compact, split, segregate, and position nucleoids in E. coli through out-of-equilibrium dynamics and polysome exclusion from the DNA meshwork, inherently coupling these processes to biomass growth across nutritional conditions. Halting chromosomal gene expression and thus polysome production immediately stops sister nucleoid migration while ensuing polysome depletion gradually reverses nucleoid segregation. Redirecting gene expression away from the chromosome and toward plasmids causes ectopic polysome accumulations that are sufficient to drive aberrant nucleoid dynamics. Cell width enlargement suggest that the proximity of the DNA to the membrane along the radial axis is important to limit the exchange of polysomes across DNA-free regions, ensuring nucleoid segregation along the cell length. Our findings suggest a self-organizing mechanism for coupling nucleoid segregation to cell growth.

microbiology↗

bioRxiv2024

Mapping and engineering RNA-controlled architecture of the multiphase nucleolus

Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a layered multiphase liquid-like structure and the site of ribosome biogenesis. In the nucleolus, ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps that ultimately result in formation of the ribosomal small subunit (SSU) and large subunit (LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic de novo nucleoli through an engineered rDNA plasmid system in cells, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.

cell biology↗

bioRxiv2024

Borrelia burgdorferi Secretes c-di-AMP as an Extracellular Pathogen-Associated Molecular Pattern to Elicit Type I Interferon Responses in Mammalian Hosts

Borrelia burgdorferi (B. burgdorferi), an extracellular spirochetal pathogen, elicits a type-I interferon (IFN-I) response that contributes to the pathology of Lyme disease, including the development and severity of Lyme arthritis. However, the specific Pathogen-Associated Molecular Patterns (PAMPs) of B. burgdorferi responsible for triggering the IFN-I response are not well understood. Previous studies have identified an unknown, nuclease-resistant component in B. burgdorferi culture supernatants that significantly stimulates the IFN-I response, but its identity remains unknown. In this study, we reveal that B. burgdorferi secretes cyclic-di-adenosine monophosphate (c-di-AMP) as a key extracellular PAMP, inducing the host IFN-I response in macrophages. Using genetically manipulated B. burgdorferi strains, we demonstrate a requirement of c-di-AMP for stimulating IFN-I response by macrophages ex vivo. Additionally, infecting mice with B. burgdorferi alongside exogenous c-di-AMP resulted in a markedly increased IFN-I response in mouse tissues. Furthermore, inactivation or inhibition of the host STING signaling pathway significantly reduced the IFN-I response, indicating that c-di-AMP-induced IFN-I production is STING-dependent. Our findings identify c-di-AMP as a crucial PAMP secreted by B. burgdorferi to elicit the host IFN-I response via activation of STING signaling pathway, suggesting that targeting c-di-AMP production could represent a novel therapeutic strategy against Lyme arthritis. SUMMARYBorrelia burgdorferi, the bacteria that causes Lyme disease, induces a robust host immune response, including the production of type-I interferon (IFN-I). While this response helps combat the infection, it also contributes to complications such as Lyme arthritis. Our research aimed to identify the specific bacterial component that triggers the IFN-I response. We discovered that Borrelia burgdorferi releases a second messenger molecule, cyclic-di-adenosine monophosphate (c-di-AMP), which is recognized by host immune cells and subsequently triggers IFN-I production. This finding is significant as it advances our understanding of Lyme disease pathogenesis and offers a new strategy to tackle Lyme disease by targeting the production of c-di-AMP, in which we may be able to reduce the severity of the disease and mitigate long-term tissue damage. One sentence summaryBorrelia burgdorferi c-di-AMP induces Type I IFN response

immunology↗

bioRxiv2024

High-Resolution Genome Assembly and Population Genetic Study of the Endangered Maple Acer pentaphyllum (Sapindaceae): Implications for Conservation Strategies

Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to dry-hot valleys of the Yalong River in western Sichuan, China, requires urgent conservation efforts due to its extremely rarity and restricted distribution. In this study, we present a high-quality chromosome-level reference genome of A. pentaphyllum (626 Mb, 2n = 26), comprising 70.64% repetitive sequences and 38,540 protein-coding genes. Phylogenetic analysis shows that A. pentaphyllum diverged from a clade consisting of A. yangbiense and A. saccharum in the late Eocene ([~]37.83 Ma). In the genome of A. pentaphyllum, genes involved in responding to external environmental change have undergone expansion and positive selection, potentially reflecting its adaptive strategies. While no recent independent whole-genome duplication events were detected, a recent rapid amplification of transposable elements was observed. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 {+/-} 0.97 x 10-3) compared to other woody species. Phylogeographic patterns suggest an upstream colonization along the Yalong River, with two severe population bottlenecks correlating with major Pleistocene climatic transitions. In addition, most populations exhibit high inbreeding and genetic load, particularly those at range edges (TKX, CDG, TES). Based on these genomic insights, we propose targeted conservation strategies, including genetic rescue measures, to safeguard this unique maple species. These findings not only contribute to the preservation of A. pentaphyllum but also enhance our understanding of plant adaptation to extreme environments and the impacts of climate change on species with restricted distributions.

genetics↗

bioRxiv2024

Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition

Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome assembly algorithms, high-quality chromosome-level assemblies of polyploid genomes have become increasingly attainable. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in case where known diploid ancestors are absent. In this study, we introduce a novel approach that leverages long terminal repeat retrotransposons (LTR-RTs) coupled with the Serial Similarity Matrix (SSM) method to assign genome assemblies to subgenomes, particularly beneficial for those without known diploid progenitor genomes. The SSM method helps identify subgenome-specific LTRs and facilitates the inference of the timing of allopolyploidization events. We validated the efficacy of the SSM approach using well-studied allopolyploidy genomes, Eragrostis tef and Gossypium hirsutum, alongside an artificially created allotetraploid genome by merging two closely related diploid species, Glycine max and G. soja. Our results demonstrated the robustness of the method and its effectiveness in assigning chromosomes to subgenomes. We then applied the SSM method to the octoploid strawberry genome. Our analysis revealed three allopolyploidization events in the evolutionary trajectory of the octoploid strawberry genome, shedding light on the evolutionary process of the origin of the octoploid strawberry genome and enhancing our understanding of allopolyploidization in this complex species.

bioinformatics↗

bioRxiv2024

Modulation Of SUDEP By Central Serotonergic Cooperating with Noradrenergic Circuits: A Synergistic-Dependent Manner

Sudden unexpected death in epilepsy (SUDEP) is the leading cause of death in refractory epilepsy patients. Despite previous accumulating evidence has shown that seizure-induced respiratory arrest (S-IRA) may play the main contributor to SUDEP as an initiating event preeminent cause of mortality, the specific underlying mechanism of action remains unclear. Based on our previous work, serotonin (5-HT) signaling in the dorsal raphe nucleus (DRN) is strongly implicated in S-IRA in animal models, including the DBA/1 mice, on the meanwhile, norepinephrine (NE) neurons of the locus coeruleus (LC) also plays a vital role in regulating respiratory function on its own. Superficially, monoaminergic neuron, as important neurotransmitters in the central nervous system, have similar modes of action in the maintenance of nervous system balance, and each of them has a regulatory effect on SUDEP. However, it remains to be investigated whether monoaminergic neuron family (NE and 5-HT) are related in the mechanism of regulating SUDEP, what is even more curious is whether the two are intrinsically linked. Thus, we hypothesize neural mechanism of central noradrenergic and serotonergic circuits in modulating SUDEP in a synergistic-dependent manner, this endeavor will culminate in a significant breakthrough in elucidating the precise mechanism of action underlying SUDEP. In our study, we will use chemogenetics, optogenetics, calcium signal recording, and bidirectional tracing to explore the internal mechanism of DR-LC regulating the occurrence of SUDEP, and by specifically injecting 5-HT2AR antagonist Ketanserin (KET) and/or NE-1R antagonist Prazosin into the pre-Botzinger complex (PBC), it was finally elucidate that the DR-LC-PBC network can effectively reduce the incidence of SIRA. We firstly proposed a powerful target for exploring the reduction of the incidence of SUDEP, which has great clinical translation potential.

neuroscience↗

bioRxiv2024

Neisseria gonorrhoeae induces local secretion of IL-10 at the human cervix to promote asymptomatic colonization

Gonorrhea, caused by the human-restricted pathogen Neisseria gonorrhoeae, is a commonly reported sexually transmitted infection. Since most infections in women are asymptomatic, the true number of infections is likely much higher than reported. How gonococci (GC) colonize womens vaginocervix without triggering symptoms remains elusive. Using a human cervical tissue explant model, we found that GC inoculation increased the local secretion of both pro- (IL-1{beta} and TNF-) and anti-inflammatory (IL-10) cytokines during the first 24-h. Cytokine induction required GC expression of an Opa isoform that binds the host receptors carcinoembryonic antigen-related cell adhesion molecules (CEACAMs). GC inoculation induced NF-{kappa}B activation in both cervical epithelial and subepithelial cells. However, inhibition of NF-{kappa}B activation, which reduced GC-induced IL-1{beta} and TNF-, did not affect GC colonization. Neutralizing IL-10 or blocking IL-10 receptors by antibodies reduced GC colonization by increasing epithelial shedding and epithelial cell-cell junction disassembly. Inhibition of the CEACAM downstream signaling molecule SHP1/2, which reduced GC colonization and increased epithelial shedding, reduced GC-induced IL-10 secretion. These results show that GC induce local IL-10 secretion at the cervix by engaging the host CEACAMs to prevent GC-colonizing epithelial cells from shedding while suppressing inflammation activation, providing a potential mechanism for GC asymptomatic infection in women.

cell biology↗

bioRxiv2024

De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting in pancreatic cancer

Oncogenic KRAS, the genetic driver of 90% of pancreatic adenocarcinoma (PDAC), induces a metabolic rewiring characterized, in part, by dependency on de novo pyrimidine biosynthesis. Pharmacologic inhibition of dihydroorotate dehydrogenase (DHODH), an enzyme in the de novo pyrimidine synthesis pathway, delays pancreatic tumor growth in vivo; however, limited monotherapy efficacy suggests compensatory pathways and that combinatorial strategies are required for enhanced efficacy. Here, we use an integrated metabolomic, quantitative temporal proteomic and in vitro and in vivo DHODH inhibitor anchored CRISPR/Cas9 genetic screening approach to identify compensatory pathways to DHODH inhibition (DHODHi) and targets for combination strategies. We demonstrate that DHODHi alters the apoptotic regulatory proteome thereby enhancing sensitivity to inhibitors of the anti-apoptotic BCL2L1 (BCL-XL) protein. Combinatorial regimens with DHODH and BCL-XL inhibition synergistically induce apoptosis in PDAC cell lines and patient-derived PDAC organoids. In vivo DHODH inhibition with Brequinar and BCL-XL degradation with DT2216, a proteolysis targeting chimera (PROTAC), significantly inhibits the growth of PDAC tumors. Our data defines mechanisms of adaptation to DHODH inhibition and identifies a combination therapy strategy in PDAC.

cancer biology↗

bioRxiv2024

NK Cell Exhaustion in Wilson's Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

Metabolic abnormalities associated with liver disease have a significant impact on the risk and prognosis of cholecystitis. However, the underlying mechanism is complicated and remains to be elucidated. In particular, the effect of metabolic abnormalities on the progression of cholecystitis through the regulation of immune cell function is poorly understood. In this study, we investigated this issue using Wilsons disease (WD) as a model. Wilsons disease is a genetic disorder characterized by impaired mitochondrial function and abnormal copper metabolism. Our retrospective clinical study of over 600 patients with WD found that they have a significantly higher incidence of cholecystitis and a poorer prognosis. The immune cell landscape in the hepatic mesenchymal stromal microenvironment of WD patients was shown using single-cell RNA. A major change is the constitution and function of the innate immune system, including enhanced antigen presentation process, activation of the immune response, and activation of lymphocytes. The proportion of mononuclear phagocytes and natural killer (NK) cells is increased, and the primary characteristic and function of macrophage, Kupffer cell, neutrophil, and NK cell are altered. Exhaustion of NK cell is the fundamental factor, supported by an increase in the expression of the inhibitory receptors KLRC1 and TIGIT and a decrease in the expression of cytotoxic molecules. Clinical tissue and blood samples verified increased KLRC1+ and TIGIT+ NK cells and decreased IFN{gamma}+ NK cells in WD. Further bioinformatic analysis has confirmed a positive correlation between NK cell exhaustion and poor prognosis in cholecystitis and other inflammatory diseases. The study demonstrated abnormal function of liver mesenchymal immune cells triggered by specific metabolic dysfunction in WD, with a focus on the correlation between NK cell exhaustion and poor healing of cholecystitis. Our findings highlight the immune cell dysfunction due to metabolic changes in hepatocytes and provide new insights into the improvement of inflammatory diseases by assessing immune cell function.

immunology↗

bioRxiv2024

Mitigation of Stress-induced Structural Remodeling and Functional Deficiency in iPSC-CMs with PLN R9C Mutation by Promoting Autophagy

BackgroundPhospholamban (PLN) is a key regulator of cardiac function connecting adrenergic signaling and calcium homeostasis. The R9C mutation of PLN is known to cause early onset dilated cardiomyopathy (DCM) and premature death, yet the detailed mechanisms underlie the pathologic remodeling process are not well defined in human cardiomyocytes. The aim of this study is to unravel the role of PLN R9C in DCM and identify potential therapeutic targets. MethodsPLN R9C knock-in (KI) and patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated and comprehensively examined for their expression profile, contractile function, and cellular signaling under both baseline conditions and following functional challenges. ResultsPLN R9C KI iPSC-CMs exhibited near-normal morphology and calcium handling, slightly increased contractility, and an attenuated response to {beta}-adrenergic activation compared to wild-type (WT) cells. However, treatment with a maturation medium (MM) has induced fundamentally different remodeling in the two groups: while it improved the structural integrity and functional performance of WT cells, the same treatment result in sarcomere disarrangement, calcium handling deficiency, and further disrupted adrenergic signaling in PLN R9C KI cells. To understand the mechanism, transcriptomic analysis showed the enrichment of protein homeostasis signaling pathways specifically in PLN R9C KI cells in response to the MM treatment and increased contractile demands. Further studies also indicated elevated ROS levels, interrupted autophagic flux, and increased pentamer PLN aggregation in functionally challenged KI cells. These results were further confirmed in patient-specific iPSC-CM models, suggesting that functional stresses exacerbate the deficiencies in PLN R9C cells through disrupting protein homeostasis. Indeed, treating stressed patient cells with autophagy-accelerating reagents, such as metformin and rapamycin, has restored autophagic flux, mitigated sarcomere disarrangement, and partially rescued {beta}-adrenergic signaling and cardiac function. ConclusionsPLN R9C leads to a mild increase of calcium recycling and contractility. Functional challenges further enhanced contractile and proteostasis stress, leading to autophagic overload, structural remodeling, and functional deficiencies in PLN R9C cardiomyocytes. Activation of autophagy signaling partially rescues these effects, revealing a potential therapeutic target for DCM patients with the PLN R9C mutation. Graphic abstractsA graphic abstract is available for this article.

molecular biology↗