Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 415 records · Page 23Linked to original sources

bioRxiv2024

IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming in a metabolic enzyme independent manner

Isocitrate dehydrogenase 1 (IDH1) is the key enzyme that was involved in the modulation of cellular metabolism, epigenetic modification and redox states homeostasis. Gain-of-function mutations and decreased expression of IDH1 have been demonstrated to be tightly associated with the pathogenesis of various myeloid malignancies characterized by ineffective erythropoiesis, such as acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). However, the function and mechanism of IDH1 in human erythropoiesis still remains to be further explored. Here, utilizing the human erythropoiesis system, we present an evidence of IDH1-mediated chromatin state reprogramming besides its well-characterized metabolism effects. We showed that knockdown of IDH1 induced chromatin reorganization and subsequently led to abnormalities of various key biological events in erythroid precursors, which could not be rescued by addition of reactive oxygen species (ROS) scavengers or supplementation of -ketoglutarate (-KG). We further revealed that deficiency of IDH1 induces genome-wide changes in distribution and intensity of multiple histone marks, among which H3K79me3 was identified as a critical factor in chromatin state reprogramming. Integrated analysis of ChIP-seq, ATAC-seq and RNA-seq recognized that SIRT1 was the key gene affected by IDH1 deficiency. Thus, our current work provided novel insights for further clarifying fundamental biological function of IDH1 which has substantial implications for an in-depth understanding of pathogenesis of diseases with IDH1 dysfunction and accordingly development of therapeutic strategies. Key PointsO_LIIDH1 deficiency impaired terminal erythropoiesis; C_LIO_LIIDH1 deficiency leads to chromatin states reprogramming by causing aberrant accumulation and genome-wide re-distribution of H3K79me3; C_LIO_LIDyserythropoiesis is caused by upregulation of SIRT1 induced by H3K79me3 accumulation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/599556v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@328986org.highwire.dtl.DTLVardef@1e2e8a0org.highwire.dtl.DTLVardef@166885org.highwire.dtl.DTLVardef@1283261_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model

Inspired by the advancements in pre-trained Large Language Models, there has been a surge of studies in the Life Sciences focusing on constructing foundation models with large scale single-cell RNA-seq data. These studies typically involve pre-training a transformer model on large-scale single-cell sequencing data, followed by fine-tuning for a variety of downstream tasks, achieving notable performance. However, these models all share a common short-coming: to utilize the transformer architecture, originally designed for textual data, they artificially impose a sequential structure on genes within cells, simplifying the complex interactions between genes. Furthermore, they focus solely on transcriptomic data, neglecting other relevant biological information. To address these issues, here we introduce Cell-Graph Compass (CGC), the first foundational model that leverages graph structures to model single cells and describes cells from multiple perspectives, including transcriptional profiles, gene text summaries, transcription factor regulatory networks, gene co-expression patterns, and gene positional relationships. By incorporating self-attention mechanisms, we pretrained the model on 50 million human single-cell sequencing data, resulting in a robust digital representation of cells. Extensive downstream experiments demonstrate that our approach can capture meaningful biological knowledge and achieve superior results in various problem scenarios, achieving the state-of-the-art (SOTA).

bioinformatics↗

bioRxiv2024

The Fem Cell-surface Signaling System is Regulated by ExsA in Pseudomonas aeruginosa and Affects Pathogenicity

Bacterial interspecies interactions shape the function and the structural dynamics of microbial communities and affect the progression of polymicrobial infections. The FemA-FemR-FemI (Fem) cell surface signaling system in Pseudomonas aeruginosa is known to be involved in the uptake of iron-chelating mycobactin produced by the Mycobacterium species. In this report, we present the data that indicates the femA-PA1909 operon was positively regulated by ExsA, a master regulator for the type three secretion system (T3SS), connecting the Fem system with T3SS. Intriguingly, the Fem system also influenced virulence factors in P. aeruginosa, including the quorum sensing systems, pyocyanin production, biofilm formation and the type six secretion systems (T6SSs). Using a Galleria mellonella infection model we observed that an femA deletion in PAO1 significantly increased the host survival rate while femI over-expression decreased it, suggesting a role for the Fem system in bacterial pathogenicity in vivo. Our data indicate the Fem system is a target of the T3SS master activator ExsA, and it affects P. aeruginosa pathogenicity.

microbiology↗

bioRxiv2024

Molecular effects of indoor tanning

BackgroundTanning bed users have a significantly increased risk of melanoma, but it remains unclear how indoor tanning drives melanomagenesis. Tanning bed radiation is often thought of as a substitute for natural UV radiation despite differences in the maximum doses, UV content, body sites exposed, and patterns of melanoma that arise. MethodsTo better understand the epidemiologic trends and etiology of melanoma associated with tanning bed use, we described the patterns of melanoma in patients with quantifiable tanning bed usage and performed exome sequencing of 182 melanocytes from normal skin of a subset of these patients. ResultsTanning bed users were more likely than non-users to have melanoma on body sites with low cumulative levels of sun damage and were more likely to have multiple melanomas. The melanocytes in normal appearing skin from tanning bed users had higher mutation burdens, a higher proportion of melanocytes with pathogenic mutations, and distinct mutational signatures. These differences were most prominent over body sites that experience comparatively less exposure to natural sunlight. ConclusionsWe conclude that tanning bed radiation induces melanoma by increasing the mutation burden of melanocytes and by mutagenizing a broader field of melanocytes than are typically exposed to natural sunlight. The unique signatures of mutations in skin cells of tanning users may be attributable to the distinct spectra of radiation emitted from solariums.

genomics↗

bioRxiv2024

Shiba: A unified computational method for robust identification of differential RNA splicing across platforms

Alternative pre-mRNA splicing (AS) is a fundamental regulatory process that generates transcript diversity and cell type variation. We developed Shiba, a comprehensive method that integrates transcript assembly, splicing event identification, read counting, and differential splicing analysis across RNA-seq platforms. Shiba excels in capturing annotated and unannotated AS events with superior accuracy, sensitivity, and reproducibility. It addresses the often-overlooked issue of junction read imbalance, significantly reducing false positives to aid target prioritization and downstream analyses. Unlike other tools that require large numbers of biological replicates or resulting in low sensitivity and high false positives, Shibas statistics framework is agnostic to sample size, as demonstrated by simulated data and its effective application to real n=1 RNA-seq datasets. To extend its utility to single-cell RNA-seq, we developed scShiba, which applies Shibas pseudobulk approach to analyze splicing at the cluster level. scShiba successfully revealed AS regulation in developmental dopaminergic neurons and differences between excitatory and inhibitory neurons. Both Shiba and scShiba are available in Docker/Singularity containers and Snakemake pipelines, ensuring reproducibility. With their comprehensive capabilities, Shiba and scShiba enable systematic quantification of alternative splicing events across various platforms, laying a solid foundation for mechanistic exploration of the functional complexity in RNA splicing.

bioinformatics↗

bioRxiv2024

Post-flowering photoperiod sensitivity of soybean in pod-setting responses

The development of soybean (Glycine max) is regulated by photoperiod, with genes related to photoperiod sensitivity primarily focused on flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to photoperiod. Long-day (LD) conditions tend to extend the time from flowering to pod formation (R1 to R3 stage), and the first wave of flowers tends to fall off. Additionally, photoperiod affects pistil morphology; under short-day (SD) conditions, the stigma has a curved hook-like structure that facilitates better interaction with the filaments when pollen is released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex genes, showed no difference in pod formation time under LD or SD conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, ROS signals, and the application of sucrose solution in vitro might influence floral organ abscission. HighlightPhotoperiod sensitivity after flowering affects the pod-setting time in soybean.

plant biology↗

bioRxiv2024

Molecular and circuit determinants in the globus pallidus mediating control of cocaine-induced behavioral plasticity

The globus pallidus externus (GPe) is a central component of the basal ganglia circuit, receiving strong input from the indirect pathway and regulating a variety of functions, including locomotor output and habit formation. We recently showed that it also acts as a gatekeeper of cocaine-induced behavioral plasticity, as inhibition of parvalbumin-positive cells in the GPe (GPePV) prevents the development of cocaine-induced reward and sensitization. However, the molecular and circuit mechanisms underlying this function are unknown. Here we show that GPePV cells control cocaine reward and sensitization by inhibiting GABAergic neurons in the substantia nigra pars reticulata (SNrGABA), and ultimately, selectively modulating the activity of ventral tegmental area dopamine (VTADA) cells projecting to the lateral shell of the nucleus accumbens (NAcLat). A major input to GPePV cells is the indirect pathway of the dorsomedial striatum (DMSD2), which receives DAergic innervation from collaterals of VTADA[->]NAcLat cells, making this a closed-loop circuit. Cocaine likely facilitates reward and sensitization not directly through actions in the GPe, but rather in the upstream DMS, where the cocaine-induced elevation of DA triggers a depression in DMSD2 cell activity. This cocaine-induced elevation in DA levels can be blocked by inhibition of GPePV cells, closing the loop. Interestingly, the level of GPePV cell activity prior to cocaine administration is correlated with the extent of reward and sensitization that animals experience in response to future administration of cocaine, indicating that GPePV cell activity is a key predictor of future behavioral responses to cocaine. Single nucleus RNA-sequencing of GPe cells indicated that genes encoding voltage-gated potassium channels KCNQ3 and KCNQ5 that control intrinsic cellular excitability are downregulated in GPePV cells following a single cocaine exposure, contributing to the elevation in GPePV cell excitability. Acutely activating channels containing KCNQ3 and/or KCNQ5 using the small molecule carnosic acid, a key psychoactive component of Salvia rosmarinus (rosemary) extract, reduced GPePV cell excitability and also impaired cocaine reward, sensitization, and volitional cocaine intake, indicating its potential as a therapeutic to counteract psychostimulant use disorder. Our findings illuminate the molecular and circuit mechanisms by which the GPe orchestrates brain-wide changes in response to cocaine that are required for reward, sensitization, and self-administration behaviors.

neuroscience↗

bioRxiv2024

Molecular Specializations Underlying Phenotypic Differences in Inner Ear Hair Cells of Zebrafish and Mice

Hair cells (HCs) are the sensory receptors of the auditory and vestibular systems in the inner ears of vertebrates that selectively transduce mechanical stimuli into electrical activity. Although all HCs have the hallmark stereocilia bundle for mechanotransduction, HCs in non-mammals and mammals differ in their molecular specialization in the apical, basolateral and synaptic membranes. HCs of non-mammals, such as zebrafish (zHCs), are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals. Mammalian cochlear HCs, in contrast, are not electrically tuned and achieve amplification by somatic motility of outer HCs (OHCs). To understand the genetic mechanisms underlying differences among adult zebrafish and mammalian cochlear HCs, we compared their RNA-seq-characterized transcriptomes, focusing on protein-coding orthologous genes related to HC specialization. There was considerable shared expression of gene orthologs among the HCs, including those genes associated with mechanotransduction, ion transport/channels, and synaptic signaling. For example, both zebrafish and mouse HCs express Tmc1, Lhfpl5, Tmie, Cib2, Cacna1d, Cacnb2, Otof, Pclo and Slc17a8. However, there were some notable differences in expression among zHCs, OHCs, and inner HCs (IHCs), which likely underlie the distinctive physiological properties of each cell type. Tmc2 and Cib3 were not detected in adult mouse HCs but tmc2a and b and cib3 were highly expressed in zHCs. Mouse HCs express Kcna10, Kcnj13, Kcnj16, and Kcnq4, which were not detected in zHCs. Chrna9 and Chrna10 were expressed in mouse HCs. In contrast, chrna10 was not detected in zHCs. OHCs highly express Slc26a5 which encodes the motor protein prestin that contributes to OHC electromotility. However, zHCs have only weak expression of slc26a5, and subsequently showed no voltage dependent electromotility when measured. Notably, the zHCs expressed more paralogous genes including those associated with HC-specific functions and transcriptional activity, though it is unknown whether they have functions similar to their mammalian counterparts. There was overlap in the expressed genes associated with a known hearing phenotype. Our analyses unveil substantial differences in gene expression patterns that may explain phenotypic specialization of zebrafish and mouse HCs. This dataset also includes several protein-coding genes to further the functional characterization of HCs and study of HC evolution from non-mammals to mammals.

neuroscience↗

bioRxiv2024

Decreased cellular excitability of pyramidal tract neurons in primary motor cortex leads to paradoxically increased network activity in simulated parkinsonian motor cortex

Primary motor cortex (M1) layer 5B pyramidal tract (PT5B) neurons develop intrinsic pathology in rodent and primate Parkinsons disease (PD) models. We used computer simulation to predict how decreased PT5B neuron excitability, identified with current injection in vitro, would change activity patterns of the M1 network. Using NEURON/NetPyNE, we implemented computer simulations of PT5B neurons based on control and 6-OHDA-treated mouse slice data. Parkinsonian PT5B neurons, in an otherwise unmodified simulated M1 network, produced major changes in LFP oscillatory power: an order of magnitude increase in beta band power around 15 Hz in the rest state. This demonstrated that relatively small changes in PT5B neuron excitability would alter oscillatory patterns of activity throughout the M1 circuit, increasing beta band power, a signature of PD pathophysiology. Dysfunction in PT5B neurons, the final-common-pathway to brainstem and spinal cord, provides a new target to treat PD motor symptoms.

neuroscience↗

bioRxiv2024

From gene to structure: Unraveling genomic dark matter in Ca. Accumulibacter

Candidatus Accumulibacter is a unique and pivotal genus of polyphosphate-accumulating organisms (PAOs) prevalent in wastewater treatment plants, and plays mainstay roles in the global phosphorus cycle. Whereas, the efforts toward a complete understanding of their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods, leaving more than half of their protein-encoding genes unannotated. To address the challenge, we developed a comprehensive approach integrating pangenome analysis, gene-based protein structure and function prediction, and metatranscriptomic analysis, extending beyond the constraints of sequence-centric methodologies. The application to Ca. Accumulibacter allowed the establishment of the pan-Ca. Accumulibacter proteome structure database, providing references for >200,000 proteins. Benchmarking on 28 Ca. Accumulibacter genomes showed major increases in the average annotation coverage from 51% to 83%. Genetic and metabolic characteristics that had eluded exploration via conventional methods were unraveled. For instance, the identification of a previously unknown phosphofructokinase gene suggests that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A previously defined homolog of phosphate-specific transport system accessory protein (PhoU) was actually an inorganic phosphate transport (Pit) accessory protein, regulating Pit instead of the high-affinity phosphate transport (Pst), a key to the emergence of the polyphosphate-accumulating trait of Ca. Accumulibacter. Additional lineage members were found encoding complete denitrification pathways. This study offers a readily usable and transferable tool for the establishment of high-coverage annotation reference databases for diverse cultured and uncultured bacteria, facilitating the exploration and understanding of genomic dark matter in the bacterial domain. SynopsisA integrated and advanced approach unraveling key genomic dark matter in Ca. Accumulibacter and readily applicable to diverse bacteria for customerized high-coverage annotation reference database establishment

genomics↗

bioRxiv2024

Construction of a breast cancer predictive nomogram based on diverse cell death methods and reveal tumor microenvironment characterization

ObjectiveTo develop a robust predictive model and nomogram for breast cancer (BC) linked to genes associated with diverse cell death methods. MethodsThe prognostic model was constructed using the LASSO Cox method. Model performance was assessed using K-M analysis, ROC curves, and independent prognostic analysis. Subsequently, we constructed a nomogram and analyzed differences in tumor microenvironment and drug sensitivity between different subgroups. The enrichment of differentially expressed genes between different subgroups was assessed. Additionally, we overexpressed CD24 in BC cell lines to assess its impact on cellular proliferation using CCK8 assays, migration through scratch and transwell assays, and apoptosis via flow cytometry. ResultsA prognostic model comprising twelve genes (CREB3L1, SFRP1, SHARPIN, AIFM1, IL-18, CD24, EDA2R, CRIP1, XBP1, BCL2A1, NKX3-1, and NME5) was constructed. BC patients were categorized into different subgroups, with the low-risk subgroup demonstrating superior survival. Additionally, we constructed a nomogram. The nomogram was validated as a reliable independent predictor of outcome. The enrichment analyses imply a connection between patient risk and immune response. The low-risk subgroup had a higher TME score. Patients in the high-risk group had improved responses to lapatinib, BI-2536, OSI-027, and SB505124, while those in the low-risk subgroup showed improved sensitivity to axitinib, epirubicin, fulvestrant, and olaparib. Furthermore, CD24 overexpression was found to promote proliferation and migration, while inhibiting apoptosis. ConclusionThese findings contribute to the individualization of treatment and aid in uncovering the tumor microenvironment characterization for BC patients.

cancer biology↗

bioRxiv2024

Roles and mechanisms of leptomeningeal collaterals in human distal MCA territory ischemia

BackgroundLeptomeningeal collaterals (LMCs) provided hemodynamic support and reperfusion during acute ischemic stroke (AIS). Although regulation details have been deeply acquired from animal models, human cortex may share limited hemodynamic patterns due to larger physical scale that needs further investigation. MethodsWe performed sequential hierarchical blocking during awake craniotomy on fourteen human subjects to mimic AIS in middle cerebral artery (MCA) M4 segment territory. Widefield microscope was applied to reveal microcirculation of LMCs. Relative flow rate (RFR) was measured to evaluate the impact of LMCs hierarchy on microcirculation maintenance. Single-cell sequencing and spatial transcriptomics were further performed to analyze the mechanism of different LMCs recruitment abilities. ResultsLMCs RFR decreased to 30.75% immediately (95% CI, 6.64 - 54.86%, P < 0.001), and about 80.25% RFR was finally recovered within 5 minutes (95% CI, 55.2 - 105.3%, P = 0.0034) during M4 occlusion. For M5 and pial branches occlusion, RFR decreased to 55.78% with no further recovery (95% CI, 22.50-89.05%, P = 0.014), and 4 in 11 subjects had no valid microcirculation. For subjects with better recruitment ability, the proportion of arteriole is much higher in leptomeninx (76 - 79% vs. 36 - 56%). There were more significant interaction pairs associated with key signaling pathways between arteriole and neuron/astrocyte (TGF-beta signaling pathway, ECM-receptor interaction) ConclusionsAbundant LMCs supported hemodynamic stability during AIS in human subjects. The proportion of arteriole is much higher in leptomeninx for subjects with better recruitment ability. The Active neuron/astrocyte - arteriole interaction may improve LMCs recruitment. GRAPH ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/594043v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@eb7fb8org.highwire.dtl.DTLVardef@10e10aforg.highwire.dtl.DTLVardef@6954c7org.highwire.dtl.DTLVardef@13ceb98_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Gradual labeling with fluorogenic probes for MINFLUX nanoscopy of densely packed structures

Single-molecule localization in densely packed structures represents a formidable challenge in nanoscopy. Here we develop a gradual labeling method with fluorogenic probes for MINFLUX nanoscopy (GLF-MINFLUX), with which individual proteins in packed structures can be sequential illuminated and quantitatively localized at the nanoscale solely by adjusting probe concentration. With a 1.7-fold localization precision improvement and 2.2-fold faster acquisition, GLF-MINFLUX enables dual-channel nanoscale imaging of densely neuronal microtubules and microfilaments, and three-dimensional quantitative mapping of individual TOM20 proteins in mitochondrial clusters.

biophysics↗

bioRxiv2024

Intracranial neurophysiological correlates of rumination

Rumination is a transdiagnostic psychological process that plays a prominent role in many common psychiatric disorders, albeit its neurophysiological basis remains elusive. Existing neuroimaging studies have highlighted the precuneus and hippocampus as two essential brain regions in ruminations neural underpinnings. Here, we examined the intracranial electroencephalogram (iEEG) recordings from 21 patients with epilepsy during a naturalistic, continuous, active rumination state and measured the slow frequency (1-8 Hz) and high gamma (70-150 Hz) band oscillation powers. We observed enhanced slow frequency power in the precuneus and reduced high gamma power in the hippocampus during the rumination condition compared to the control condition. The hippocampal high gamma power reduction was associated with the self-reported reflection tendency. Our findings provided the first empirical evidence of the neurophysiological underpinnings of rumination and implicated a precuneus-hippocampus coupling across neural oscillation bands during an active rumination state.

neuroscience↗

bioRxiv2024

A timed epigenetic switch balances T and ILC lineage proportions in the thymus

How stem and progenitor cells give rise to multiple cell types in defined numbers and proportions is a central question in developmental biology. Epigenetic switches, acting at single gene loci, can generate extended delays in the activation timing of lineage-specifying genes, and thereby impact lineage decisions and cell type output of progenitors. Here, we analyzed a timed epigenetic switch controlling Bcl11b, a transcription factor that drives T cell lineage commitment, but only after a long multi-day time delay in expression. To investigate roles for this delay in controlling lineage decision making, we analyzed progenitors with a deletion in a distal Bcl11b enhancer, that further extends this delay by [~]3 days. Strikingly, delaying Bcl11b activation reduces T cell output but enhances ILC generation in the thymus, and does so by redirecting progenitors to the ILC lineages at the T and ILC developmental branchpoint. Mechanistically, delaying Bcl11b activation promoted ILC redirection by up-regulating a PLZF-dependent ILC transcriptional program in progenitors. Despite up-regulating PLZF, committed ILC progenitors were still capable of later activating Bcl11b, which is also needed for specification of type 2 ILCs. These results show that epigenetic switches, by controlling the activation timing and order of lineage-specifying genes within regulatory networks, can modulate population sizes and proportions of differentiated cell types.

developmental biology↗

bioRxiv2024

Optimizing ex vivo CAR-T cell-mediated cytotoxicity assay through multimodality imaging

CAR-T cell-based therapies have demonstrated remarkable efficacy in treating malignant cancers, especially liquid tumors, and are increasingly being evaluated in clinical trials for solid tumors. With the FDAs initiative for advancing alternative methods for drug discovery and development, full human ex vivo assays are increasingly essential for precision CAR-T development. However, prevailing ex vivo CAR-T cell-mediated cytotoxicity assays are limited by their use of radioactive materials, lack of real-time measurement, low throughput, and inability to automate, among others. To address these limitations, we optimized the assay using multimodality imaging methods, including bioluminescence, impedance tracking, phase contrast, and fluorescence, to track CAR-T cells co-cultured with CD19, CD20, and HER2 luciferase reporter cancer cells in real-time. Additionally, we varied the ratio of CAR-T cells to cancer cells to determine optimal cytotoxicity readouts. Our findings demonstrated that the CAR-T cell group effectively attacked cancer cells, and the optimized assay provided superior temporal and spatial precision measurements of ex vivo CAR-T killing of cancer cells, confirming the reliability, consistency, and high throughput of the optimized assay.

immunology↗

bioRxiv2024

High glucose treatment induced nuclei aggregation of microvascular endothelial cells via foxo1a-klf2a pathway

BACKGROUNDHyperglycemia is a major contributor to endothelial dysfunction and blood vessel damage, leading to severe diabetic microvascular complications. Despite the growing body of research on the underlying mechanisms of endothelial cell dysfunction, the available drugs based on current knowledge fall short of effectively alleviating these complications. Therefore, our endeavor to explore novel insights into the cellular and molecular mechanisms of endothelial dysfunction is crucial for the field. METHODSIn this study, we carried out a high-resolution imaging and time-lapse imaging analysis of the behavior of endothelial cells in Tg(kdrl:ras-mCherry::fli1a:nEGFP) zebrafish embryos upon high glucose treatment. Genetic manipulation and chemical biology approaches were utilized to analyze the underlying mechanism of high-glucose-induced nuclei aggregation and aberrant migration of zebrafish endothelial cells and cultured human endothelial cells. Bioinformatical analysis of single-cell RNA sequencing data and molecular biological techniques to identify the target genes of Foxo1a. RESULTSIn this study, we observed that the high glucose treatment resulted in nuclei aggregation of endothelial cells in zebrafish intersegmental vessels (ISVs). Additionally, the aberrant migration of microvascular endothelial cells in high glucose-treated embryos, which might be a cause of nuclei aggregation, was discovered. High glucose-induced aggregation of vascular endothelial nuclei via foxo1a downregulation in zebrafish embryos. Then, we revealed that high glucose resulted in the downregulation of foxo1a expression and increased the expression of its direct downstream effector, klf2a, through which the aberrant migration and aggregation of vascular endothelial nuclei were caused. CONCLUSIONSHigh glucose treatment caused the nuclei of endothelial cells to aggregate in vivo, which resembles the crowded nuclei of endothelial cells in microaneurysms. High glucose suppresses foxo1a expression and increases the expression of its downstream effector, klf2a, thereby causing the aberrant migration and aggregation of vascular endothelial nuclei. Our findings provide a novel insight into the mechanism of microvascular complications in hyperglycemia.

cell biology↗

bioRxiv2024

Multiple Omics Find New Cecal Microbial Features Associated with Feed Efficiency in Ducks

As the global population continues to grow exponentially, the competition for resources between livestock and humans has become increasingly intense. Breeding efficient animal breeds, fully utilizing feed resources, and reducing environmental damage are major challenges facing the livestock industry. To address these issues, enhancing the feed utilization efficiency in the poultry industry is crucial. Recent studies have elucidated the pivotal role of gut microbiota in modulating the feeding behavior of their host organisms. Thus, we used metagenomics, transcriptomics, and metabolomics to explore how the intestinal microbiome affects the feed utilization efficiency in ducks. Our metagenomic analysis revealed a significant up-regulation of Elusimicrobiota at the phylum level within the high residual feed intake (HRFI) group, in comparison to the low residual feed intake (LRFI) group. Additionally, functional analysis using Clusters of Orthologous Groups of proteins (COG) indicated prominent disparities in the category of secondary metabolites biosynthesis, transport, and catabolism between the HRFI and LRFI groups. Furthermore, our metabolomics investigation identified an upregulated expression of the secondary metabolite 15-deoxy-{Delta}12,14-prostaglandin J2 (15d-PGJ2) in the HRFI group compared to the LRFI group. Liver transcriptome analysis identified prostaglandin-endoperoxide synthase 2 (PTGS2) as a key hub gene, exerting significant regulatory influence within the arachidonic acid pathway. Notably, the metabolite 15d-PGJ2 is a terminal product in the metabolic pathway of arachidonic acid. The correlation analysis between the cecal microbiota and differential metabolites revealed a significant negative correlation between Elusimicrobiota and the metabolite 15d-PGJ2. In summary, we assumed that the intestinal microbiome Elusimicrobiota regulates the expression of the PTGS2 gene, consequently inducing variations in PTGS2 efficiency between the HRFI and LRFI groups, ultimately leading to diverse residual feed intake levels in ducks. IMPORTANCEThis investigation utilizes metabolomics to elucidate the interplay between genes and microbiome communities. We present evidence of disparities in the composition of microbial consortia among ducks RFI, alongside identification of pivotal genes within the liver that potentially modulate RFI. These results provide novel perspectives on the processes through which the cecum and liver influence RFI.

microbiology↗