Biology subjects

Ma, Q.

Publications and source records attributed to Ma, Q..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Axenisation of oleaginous microalgal cultures via anoxic photosensitisation.

Growing interest in sustainable biofuel research has necessitated high quality axenic oleaginous microalgal strains. Unfortunately, most strains available in culture banks contain commensal microbes such as bacteria and the default decontamination method involves antibiotic treatment which has begun to exacerbate the emergence of antibiotic resistance. To overcome this problem, anoxic photosensitisation was investigated as an alternate approach. Four oleaginous microalgal species (Tetradesmus obliquus, Desmodesmus armatus, Chlorella vulgaris and Nannochloropsis limnetica) were incubated in varying concentrations of Rose Bengal (0 {micro}M, 1 {micro}M, 3 {micro}M and 9 {micro}M) either in normal (oxic) or anoxic conditions, for 72 h under light (8.85 {+/-} 0.40 W m-2) in a specially designed heterotrophic growth complex (HGC) medium, followed by 72 h in standard Bolds Basal Medium (BBM). Commonly used antibiotics-based protocol was used as the control method. Post treatment, cell numbers and percentage populations were counted with Flow cytometry, and viability was tested using standard plating methods using BBM and LB. Additionally, the contaminating microbes in the cultures were profiled using 16s rRNA sequencing. Anoxic conditions were able to significantly decrease bacterial content, albeit with an equally detrimental effect on the microalgal population. Although the responses differed between the microalgae, anoxic incubation along with Rose Bengal at 3 {micro}M was able to completely decontaminate N. limnetica and C. vulgaris, while D. armatus and T. obliquus could be decontaminated with an additional streak-plating step. None of the cultures could be decontaminated using antibiotics treatment owing to the presence of gram-negative, multi-drug resistant bacteria such as S. maltophilia, M. foliorum and S. chilensis. These results suggest that decontamination of xenic microalgal cultures was largely due to anoxy, that was synergistically enhanced by Rose Bengal at a concentration of [≥]3 {micro}M. HighlightsO_LIRose Bengal at 3 {micro}M in anoxic conditions can help achieve axenic microalgal cultures. C_LIO_LIStandard antibiotics were unable to decontaminate any of the cultures owing to the presence of multi-drug resistant bacteria. C_LIO_LIStandard antibiotics treatment was deleterious to D. armatus cultures. C_LIO_LIStreak plating may be required for D. armatus and T. obliquus after anoxic Rose Bengal treatment to obtain individual colonies for further inoculation. C_LI

microbiology↗

bioRxiv2024

Xenosiderophore transporter gene expression and clade-specific filamentation in Candida auris killifish infection

Candida auris is a critical priority fungal pathogen (World Health Organization). Clinical management is challenging due to a high mortality rate, rapidly increasing antifungal resistance, and frequent nosocomial outbreaks. A critical bottleneck in understanding virulence is the lack of gene expression profiling models during infection. We developed a fish embryo yolk-sac microinjection model using Aphanius dispar (Arabian killifish; AK) at human body temperature. This enabled interrogation of infection dynamics via dual host-pathogen RNA-seq across five major clades of C. auris (I-V). Host responses included heat shock, complement activation, and nutritional immunity, notably haem oxygenase (HMOX) expression during clade IV infection. We identified a pathogen transcriptional signature across all five clades of C. auris strongly enriched for putative xenosiderophore transmembrane transporters. We describe this novel family and a sub-clade of five putative haem transport-related (HTR) genes. Only the basal clade V isolate formed filaments, associated with canonical and atypical regulators of morphogenesis. Clades I and IV demonstrated increased virulence, accompanied by up-regulation of three HTR genes in clade IV, and the non-mating mating-type locus (MTL) gene PIKA in both clades. Our study provides new insight into C. auris pathogenesis, highlighting species-wide in vivo up-regulation of XTC genes during host tissue infection. Significance statementCandida auris is an emerging human fungal pathogen and global public health threat, yet in vivo transcriptomic analysis of tissue infection has remained elusive. Using yolk-sac infection in Arabian killifish, we profiled gene expression across five major C. auris clades. We found that the basal clade V uniquely undergoes filamentation during infection, while all clades upregulate members of a large, expanded family of xenosiderophore transporter candidate genes. These findings highlight the important roles for iron acquisition and morphological switching in pathogenesis, revealing potential mechanisms of immune evasion and fungal persistence, and identifying candidate targets for antifungal therapy.

microbiology↗

bioRxiv2024

scGNN+: Adapting ChatGPT for Seamless Tutorial and Code Optimization

Foundation models have transformed AI by leveraging large-scale data to efficiently perform diverse tasks, and their applications in bioinformatics are primarily focused on data-centric tasks like cell type annotation and gene expression analysis. However, their potential extends beyond data analysis, offering significant opportunities in software development and optimization, such as code refinement, tutorial generation, and advanced visualization. For example, models like OpenAI Codex can suggest optimized code snippets and generate well-documented, reproducible workflows, enhancing accessibility and reducing computational complexity. Despite these advantages, the use of foundation models for improving computational tool engineering in single-cell research remains underutilized. To address this gap, we developed scGNN+, a web-based platform that combines the power of graph neural networks with the capabilities of ChatGPT to enhance reproducibility, code optimization, and visualization. scGNN+ further simplifies the process for users by generating standardized, well-annotated code, making complex procedures more accessible to non-programmers. Additionally, ChatGPT integration allows users to create high-quality, customizable visualizations through natural language prompts, improving data interpretation and presentation. Ultimately, scGNN+ offers a user-friendly, reproducible, and optimized solution for single-cell research, leveraging the full potential of foundation models in bioinformatics. scGNN+ is publicly available at https://bmblx.bmi.osumc.edu/scgnn+.

bioinformatics↗

bioRxiv2024

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

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

bioinformatics↗

bioRxiv2024

A multidimensional Pan-cancer analysis of CDKN1A identifies CDKN1A as an Immunological and Prognostic Biomarker

CDKN1A/p21 is well recognized for its role in cell cycle regulation and genomic stability. However, its functions in the Tumor microenvironment (TME) and tumor immunity are not yet fully understood. Hereby, we explored CDKN1A expression and immunological/prognostic values via various databases and analytical methods including cBioPortal, Kaplan-Meier, UCSCXenaShiny, TIMER, Single-cell RNA sequencing (scRNA-seq) analysis, etc. In addition, we explored different approaches including CCK8, EdU, Colony formation, Drug sensitivity and Annixin-V assay to explore the influence of p21 in proliferative capacity in cancer cells. We found that CDKN1A is lowly expressed in BLCA, BRCA, COAD, KICH, LUAD, LUSC, PRAD, READ and STAD compared to normal samples, whereas it is highly expressed in CHOL, HNSC, KIRC, KIRP and THCA compared to normal cohorts. CDKN1A expression is significantly correlated with overall survival, disease-specific survival, disease-free survival and progression-free interval different cancer types. Additionally, CDKN1A is associated with CD4+ T cell, CD8+ T cell, Neutrophil, Macrophage and Myeloid dendritic cell infiltration in diverse cancer types. Functional experiments reveal that p21 overexpression leads to a significant reduction in proliferative capacity, facilitates cell apoptosis and senescence in multiple cancer cell lines. In contrast, silenced p21 facilitates cell growth and wound closure, prevent cell senescence in different cancer cell lines. In conclusion, our findings suggest that CDKN1A may serve as a valuable prognostic and immunotherapeutic marker in diverse cancer.

cancer biology↗

bioRxiv2024

Phase-separating MoSpa2 Complex Organizes Actin Nucleation Center for M.oryzae Plant Infection

Polarized actin cable from Spitzenkorper at the hyphal tip fuels filamentous growth in diverse biphasic fungal pathogens. This multi-component complex, featuring the actin nucleator Bni1 and other factors, initiates actin polymerization, guiding biphasic fungal growth and host infection. How dynamic assembly of Spitzenkorper and actin cable are achieved to support filamentous fungi that undergo multistage morphogenesis for host invasion remains unclear, including Magnaporthe oryzae, which undergoes multistage morphological transition during rice infection. Here, we identified that the scaffolder MoSpa2 remodeling actin cable networks, in space and time, by assembling the polarisome complex via phase separation, supporting Magnaporthe oryzaes polarized growth. Via N-terminal intrinsically disordered regions (IDRs), MoSpa2 first stimulates actin cable assembly through multivalent interactions with MoBni1 nucleator, and then also creates polarized actin cable bundles by F-actin association and a concurrent inhibition of cofilin-mediated F-actin depolymerization. MoSpa2 mutants exhibit impaired hyphal growth and reduced rice infection, underling its significance. This work elucidates the fundamental mechanisms underlying fungal morphogenesis, offering the potential for targeted interventions in pathogenesis.

pathology↗

bioRxiv2024

Neural correlates of device-based sleep characteristics in adolescents

Understanding the brain mechanisms underlying objective sleep patterns in adolescents and their implications for psychophysiological development is a complex challenge. Here, we applied sparse canonical correlation (sCCA) analysis on 3300 adolescents from Adolescent Brain Cognitive Development (ABCD) study, integrating extensive device-based sleep characteristics and multimodal imaging data. We revealed two sleep-brain dimensions: one characterized by later being asleep and shorter duration, linked to decreased subcortical-cortical network functional connectivities; the other showed higher heart rate and shorter light sleep duration, associated with lower brain volumes and decreased functional connectivities. Hierarchical clustering based on brain dimension associated with sleep characteristics revealed three biotypes of adolescents, marked by unique sleep profiles: biotype 1 exhibited delayed and shorter sleep, coupled with higher heart rate during sleep; biotype 3 with earlier and longer sleep, accompanied by lower heart rate; and biotype 2 with intermediate pattern. This biotypic differences also extended to cognition, academic attainment, brain structure and function in a gradient order. Longitudinal analysis demonstrated consistent biotypic differences from ages 9 to14, highlighting enduring cognitive and academic advantages in biotype3. The linked sleep-brain dimensions and the associated biotypes were well replicated in a longitudinal sample of 1271 individuals. Collectively, our novel findings delineate a linkage between objective sleep characteristics and developing brain in adolescents, underscoring their significance in cognitive development and academic attainment, which could serve as references for individuals with sleep difficulties and offer insights for optimizing sleep routines to enhance better cognitive development and school achievement.

neuroscience↗

bioRxiv2024

Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells

Although mitochondrial DNA (mtDNA) variants hold promise as endogenous barcodes for tracking human cell lineages, their efficacy as reliable lineage markers is hindered by the complex dynamics of mtDNA in somatic tissues. Here, we utilized computational modeling and single-cell genomics to thoroughly interrogate the origin and clonal dynamics of mtDNA lineage markers across various biological settings. Our findings revealed the majority of purported "clone informative variants (CIVs)" were pre-existing heteroplamies in the first cell instead of de novo somatic mutations during divisions. Moreover, CIVs demonstrated limited discriminatory power among different lineages during normal development; however, certain CIVs with consistently high allele frequencies proved capable of faithfully labeling cell lineages in scenarios of stringent clonal expansion. Inspired by our simulations, we introduced a lineage informative (LI) score, facilitating the identification of reliable mitochondrial lineage markers across different modalities of single-cell genomic data.

bioinformatics↗

bioRxiv2024

Gucy1α1 specifically marks kidney, heart, lung and liver fibroblasts

Fibrosis is a common outcome of numerous pathologies, including chronic kidney disease (CKD), a progressive renal function deterioration. Current approaches to target activated fibroblasts, key effector contributors to fibrotic tissue remodeling, lack specificity. Here, we report Gucy11 as a specific kidney fibroblast marker. Gucy11 levels significantly increased over the course of two clinically relevant murine CKD models and directly correlated with established fibrosis markers. Immunofluorescent (IF) imaging showed that Gucy11 comprehensively labelled cortical and medullary quiescent and activated fibroblasts in the control kidney and throughout injury progression, respectively. Unlike traditionally used markers platelet derived growth factor receptor beta (Pdgfr{beta}) and vimentin (Vim), Gucy11 did not overlap with off-target populations such as podocytes. Notably, Gucy11 labelled kidney fibroblasts in both male and female mice. Furthermore, we observed elevated GUCY11 expression in the human fibrotic kidney and lung. Studies in the murine models of cardiac and liver fibrosis revealed Gucy11 elevation in activated Pdgfr{beta}-, Vim- and alpha smooth muscle actin (Sma)-expressing fibroblasts paralleling injury progression and resolution. Overall, we demonstrate Gucy11 as an exclusive fibroblast marker in both sexes. Due to its multiorgan translational potential, GUCY11 might provide a novel promising strategy to specifically target and mechanistically examine fibroblasts.

molecular biology↗

bioRxiv2024

scBSP: A fast and accurate tool for identifying spatially variable genes from spatial transcriptomic data

Spatially resolved transcriptomics have enabled the inference of gene expression patterns within two and three-dimensional space, while introducing computational challenges due to growing spatial resolutions and sparse expressions. Here, we introduce scBSP, an open-source, versatile, and user-friendly package designed for identifying spatially variable genes in large-scale spatial transcriptomics. scBSP implements sparse matrix operation to significantly increase the computational efficiency in both computational time and memory usage, processing the high-definition spatial transcriptomics data for 19,950 genes on 181,367 spots within 10 seconds. Applied to diverse sequencing data and simulations, scBSP efficiently identifies spatially variable genes, demonstrating fast computational speed and consistency across various sequencing techniques and spatial resolutions for both two and three-dimensional data with up to millions of cells. On a sample with hundreds of thousands of sports, scBSP identifies SVGs accurately in seconds to on a typical desktop computer.

bioinformatics↗

bioRxiv2024

Singular Odorant Receptor Expression Orchestrated by Promoter Activation Specificity in Apis Mellifera Olfactory Sensory Neurons

Honeybee, positioned as an outgroup of flies and mosquitos, have exhibited intriguing duplications and expansions of OR genes in genomic studies. However, little is known about how the OR genes are expressed and regulated in honeybee olfactory sensory neurons (OSNs). In this study, we utilized a single-cell multi-omics approach to profile the transcriptome and chromatin accessibility in Apis mellifera antennal nuclei, aiming to elucidate OR gene expression and its underlying regulatory mechanisms. Our systematical analysis unveiled a similar singular expression pattern of ligand-specific receptors in Apis mellifera OSNs, parallel with those observed in Drosophila melanogaster. Mechanistically, we discovered that promoter activation of OR genes orchestrates receptor expression patterns. For instance, although multiple adjacent OR genes are co-expressed with a single active promoter through polycistronic transcription, only the first OR gene could produce functional receptor protein, as supported by transcriptome quantification in OSNs. Additionally, we found that co-expression of receptor proteins might occur only when co-expressed OR genes possess multiple accessible promoters. This scenario is less common than expected, considering the number and evolutionary age of OR genes in Apis mellifera, suggesting a selection favoring the specialization of rapidly expanded OR genes in Apis mellifera. Overall, our study provides significant insights into the insect olfaction system and the regulatory mechanisms of OR genes expression.

neuroscience↗

bioRxiv2024

Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women

The human uterus is a complex and dynamic organ whose lining grows, remodels, and regenerates in every menstrual cycle or upon tissue damage. Here we applied single-cell RNA sequencing to profile more the 50,000 uterine cells from both the endometrium and myometrium of 5 healthy premenopausal individuals, and jointly analyzed the data with a previously published dataset from 15 subjects. The resulting normal uterus cell atlas contains more than 167K cells representing the lymphatic endothelium, blood endothelium, stromal, ciliated epithelium, unciliated epithelium, and immune cell populations. Focused analyses within each major cell type and comparisons with subtype labels from prior studies allowed us to document supporting evidence, resolve naming conflicts, and to propose a consensus annotation system of 39 subtypes. We release their gene expression centroids, differentially expressed genes, and mRNA patterns of literature-based markers as a shared community resource. We find many subtypes show dynamic changes over different phases of the cycle and identify multiple potential progenitor cells: compartment-wide progenitors for each major cell type, transitional cells that are upstream of other subtypes, and potential cross-lineage multipotent stromal progenitors that may be capable of replenishing the epithelial, stromal, and endothelial compartments. When compared to the healthy premenopausal samples, a postpartum and a postmenopausal uterus sample revealed substantially altered tissue composition, involving the rise or fall of stromal, endothelial, and immune cells. The cell taxonomy and molecular markers we report here are expected to inform studies of both basic biology of uterine function and its disorders. SIGNIFICANCEWe present single-cell RNA sequencing data from seven individuals (five healthy pre-menopausal women, one post-menopausal woman, and one postpartum) and perform an integrated analysis of this data alongside 15 previously published scRNA-seq datasets. We identified 39 distinct cell subtypes across four major cell types in the uterus. By using RNA velocity analysis and centroid-centroid comparisons we identify multiple computationally predicted progenitor populations for each of the major cell compartments, as well as potential cross-compartment, multi-potent progenitors. While the function and interactions of these cell populations remain to be validated through future experiments, the markers and their "dual characteristics" that we describe will serve as a rich resource to the scientific community. Importantly, we address a significant challenge in the field: reconciling multiple uterine cell taxonomies being proposed. To achieve this, we focused on integrating historical and contemporary knowledge across multiple studies. By providing detailed evidence used for cell classification we lay the groundwork for establishing a stable, consensus cell atlas of the human uterus.

cell biology↗

bioRxiv2024

Myc Dysregulation in Activated Macrophages Initiates Iron-Mediated Lipid Peroxidation that Fuels Type I Interferon and Compromises TB Resistance

A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop pulmonary TB. We developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining feature of human TB: the development of necrotic lung granulomas and determined that the sst1-susceptible phenotype was driven by the aberrant macrophage activation. This study demonstrates that the aberrant response of the sst1-susceptible macrophages to prolonged stimulation with TNF is primarily driven by conflicting Myc and antioxidant response pathways leading to a coordinated failure 1) to properly sequester intracellular iron and 2) to activate ferroptosis inhibitor enzymes. Consequently, iron-mediated lipid peroxidation fueled Ifn{beta} superinduction and sustained the Type I Interferon (IFN-I) pathway hyperactivity that locked the sst1-susceptible macrophages in a state of unresolving stress and compromised their resistance to Mtb. The accumulation of the aberrantly activated, stressed, macrophages within granuloma microenvironment led to the local failure of anti-tuberculosis immunity and tissue necrosis. The upregulation of Myc pathway in peripheral blood cells of human TB patients was significantly associated with poor outcomes of TB treatment. Thus, Myc dysregulation in activated macrophages results in an aberrant macrophage activation and represents a novel target for host-directed TB therapies.

immunology↗

bioRxiv2024

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown, in part due to technical barriers in dissecting the tumor microenvironment (TME) in high detail. Herein, we applied multiplexed ion beam imaging (MIBI) spatial pro-teomics on 6 EBV-positive and 14 EBV-negative cHL samples. We identify key TME features that distinguish between EBV-positive and EBV-negative cHL, including the relative predominance of memory CD8 T cells and increased T-cell dysfunction as a function of spatial proximity to HRS cells. Building upon a larger multi-institutional cohort of 22 EBV-positive and 24 EBV-negative cHL samples, we orthogonally validated our findings through a spatial multi-omics approach, coupling whole transcriptome capture with antibody-defined cell types for tu-mor and T-cell populations within the cHL TME. We delineate contrasting transcriptomic immunological signatures between EBV-positive and EBV-negative cases that differently impact HRS cell proliferation, tumor-immune interactions, and mecha-nisms of T-cell dysregulation and dysfunction. Our multi-modal framework enabled a comprehensive dissection of EBV-linked reorganization and immune evasion within the cHL TME, and highlighted the need to elucidate the cellular and molecular fac-tors of virus-associated tumors, with potential for targeted therapeutic strategies.

cancer biology↗

bioRxiv2024

Spiking GABAergic OPC tumor cells prolong survival in IDH1 mutant glioma

Prior studies have described the complex interplay that exists between glioma cells and neurons, however, the electrophysiological properties endogenous to tumor cells remain obscure. To address this, we employed Patch-sequencing on human glioma specimens and found that one third of patched cells in IDH mutant (IDHmut) tumors demonstrate properties of both neurons and glia by firing single, short action potentials. To define these hybrid cells (HCs) and discern if they are tumor in origin, we developed a computational tool, Single Cell Rule Association Mining (SCRAM), to annotate each cell individually. SCRAM revealed that HCs represent tumor and non-tumor cells that feature GABAergic neuron and oligodendrocyte precursor cell signatures. These studies are the first to characterize the combined electrophysiological and molecular properties of human glioma cells and describe a new cell type in human glioma with unique electrophysiological and transcriptomic properties that are likely also present in the non-tumor mammalian brain.

cancer biology↗

bioRxiv2024

Identification of RACK1A as a component of the auxin-ethylene crosstalk regulating apical hook development in Arabidopsis thaliana

Apical hook development is an ideal model for studying differential growth in plants, and is controlled by complex hormonal crosstalk, with auxin and ethylene being the major players. Here, we identified a bioactive small molecule that decelerates apical hook opening in Arabidopsis thaliana. Our genetic studies suggest that this molecule enhances or maintains the auxin maximum found in the inner hook side and requires certain auxin and ethylene signaling components to modulate apical hook opening. Using biochemical approaches, we then revealed the WD40 repeat scaffold protein RECEPTOR FOR ACTIVATED C KINASE 1A (RACK1A) as a direct target of this compound. We present data in support of RACK1A playing a positive role in apical hook opening by negatively regulating the differential auxin response gradient across the hook via specific auxin and ethylene signaling mechanisms and thereby adjusting differential cell growth, an essential process for organ structure and function in plants. We have thus identified a role for RACK1A and auxin-ethylene crosstalk in negatively regulating differential cell growth to promote apical hook opening. Significance StatementDifferential growth, or the growth of cells at different rates across tissues, is essential for providing shape and structure during plant development. The apical hook is a transient structure formed by differential cell growth across the hypocotyl tip in dark-grown seedlings, which protects the underlying tissues, and which opens during seedling development. We identified a small molecule that decelerates hook opening and discovered that it targets the protein RECEPTOR FOR ACTIVATED C KINASE 1A (RACK1A). We then showed that RACK1A promotes apical hook opening at the level of crosstalk between the plant hormones auxin and ethylene, by adjusting differential cell growth. Our work paves the way to a better understanding of how plants regulate and adapt their growth during development.

plant biology↗

bioRxiv2024

A 10-valent composite mRNA vaccine against both influenza and COVID-19

The COVID-19 pandemic caused by SARS-CoV-2 viruses has had a persistent and significant impact on global public health for four years. Recently, there has been a resurgence of seasonal influenza transmission worldwide. The co-circulation of SARS-CoV-2 and seasonal influenza viruses results in a dual burden on communities. Additionally, the pandemic potential of zoonotic influenza viruses, such as avian Influenza A/H5N1 and A/H7N9, remains a concern. Therefore, a combined vaccine against all these respiratory diseases is in urgent need. mRNA vaccines, with their superior efficacy, speed in development, flexibility, and cost-effectiveness, offer a promising solution for such infectious diseases and potential future pandemics. In this study, we present FLUCOV-10, a novel 10-valent mRNA vaccine created from our proven platform. This vaccine encodes hemagglutinin (HA) proteins from four seasonal influenza viruses and two avian influenza viruses with pandemic potential, as well as spike proteins from four SARS-CoV-2 variants. A two-dose immunization with the FLUCOV-10 elicited robust immune responses in mice, producing IgG antibodies, neutralizing antibodies, and antigen-specific cellular immune responses against all the vaccine-matched viruses of influenza and SARS-CoV-2. Remarkably, the FLUCOV-10 immunization provided complete protection in mouse models against both homologous and heterologous strains of influenza and SARS-CoV-2. These results highlight the potential of FLUCOV-10 as an effective vaccine candidate for the prevention of influenza and COVID-19. Author summaryAmidst the ongoing and emerging respiratory viral threats, particularly the concurrent and sequential spread of SARS-CoV-2 and influenza, our research introduces FLUCOV-10. This novel mRNA-based combination vaccine, designed to counteract both influenza and COVID-19, by incorporating genes for surface glycoproteins from various influenza viruses and SARS-CoV-2 variants. This combination vaccine showed highly effective in preclinical trials, generating strong immune responses, and ensuring protection against both matching and heterologous strains of influenza and SARS-CoV-2. FLUCOV-10 represents a significant step forward in our ability to address respiratory viral threats, showcasing potential as a singular, adaptable vaccine solution for global health challenges.

microbiology↗

bioRxiv2023

In vivo proximity proteomics uncovers palmdelphin (PALMD) as a Z-line-associated mitigator of isoproterenol-induced cardiac injury

Z-lines are core ultrastructural organizers of cardiomyocytes that modulate many facets of cardiac pathogenesis. Yet a comprehensive proteomic atlas of Z-line-associated components remain incomplete. Here, we established an adeno-associated virus (AAV)-delivered, cardiomyocyte-specific, proximity-labeling approach to characterize the Z-line proteome in vivo. We found palmdelphin (PALMD) as a novel Z-line-associated protein in both adult murine cardiomyocytes and human pluripotent stem cell-derived cardiomyocytes. Germline and cardiomyocyte-specific palmd knockout mice were grossly normal at baseline but exhibited compromised cardiac hypertrophy and aggravated cardiac injury upon long-term isoproterenol treatment. By contrast, cardiomyocyte-specific PALMD overexpression was sufficient to mitigate isoproterenol-induced cardiac injury. PALMD ablation perturbed transverse tubules (T-tubules) and their association with sarcoplasmic reticulum, which formed the Z-line-associated junctional membrane complex (JMC) essential for calcium handling and cardiac function. These phenotypes were associated with disrupted localization of T-tubule markers caveolin-3 (CAV3) and junctophilin-2 (JPH2) and the reduction of nexilin (NEXN) protein, a crucial Z-line-associated protein that is essential for both Z-line and JMC structures and functions. PALMD was found to interact with NEXN and enhance its protein stability while the Nexn mRNA level was not affected. Together, this study discovered PALMD as a potential target for myocardial protection and highlighted in vivo proximity proteomics as a powerful approach to nominate novel players regulating cardiac pathogenesis. HighlightsO_LIIn vivo proximity proteomics uncover novel Z-line components that are undetected in in vitro proximity proteomics in cardiomyocytes. C_LIO_LIPALMD is a novel Z-line-associated protein that is dispensable for baseline cardiomyocyte function in vivo. C_LIO_LIPALMD mitigates cardiac dysfunction and myocardial injury after repeated isoproterenol insults. C_LIO_LIPALMD stabilizes NEXN, an essential Z-line-associated regulator of the junctional membrane complex and cardiac systolic function. C_LI

molecular biology↗