Biology subjects

Wu, M.

Publications and source records attributed to Wu, M..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia

The {beta}-catenin-dependent canonical Wnt signaling is pivotal in organ development, tissue homeostasis, and cancer. Here we identified an upstream enhancer of Ctnnb1 - the coding gene for {beta}-catenin, named ieCtnnb1 (intestinal enhancer of Ctnnb1), which is crucial for intestinal homeostasis. ieCtnnb1 is predominantly active in the base of small intestinal crypts and throughout the epithelia of large intestine. Knockout of ieCtnnb1 led to a reduction in Ctnnb1 transcription, compromising the canonical Wnt signaling in intestinal crypts. Single-cell sequencing revealed that ieCtnnb1 knockout altered epithelial compositions and potentially compromised functions of small intestinal crypts. While deletion of ieCtnnb1 hampered epithelial turnovers in physiologic conditions, it prevented occurrence and progression of Wnt/{beta}-catenin-driven colorectal cancers. Human ieCTNNB1 drove reporter gene expression in a pattern highly similar to mouse ieCtnnb1. ieCTNNB1 contains a single-nucleotide polymorphism associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues was stronger than that in adjacent normal tissues. HNF4 and phosphorylated CREB1 were identified as key trans-factors binding to ieCTNNB1 and regulating CTNNB1 transcription. Together, these findings unveil an enhancer-dependent mechanism controlling the dosage of Wnt signaling and homeostasis in intestinal epithelia.

cell biology↗

bioRxiv2024

Metabolic analysis in intact human-derived cerebral organoids by high-resolution magic-angle spinning NMR spectroscopy

Human-derived cerebral organoids (COs) are an emerging model system for the study of human neural development and physiology. Here, we describe the assessment of metabolism in human-derived COs using high-resolution magic-angle spinning (HR-MAS) NMR spectroscopy. Metabolic changes during development are assessed by studying COs at various stages of maturity. Our results suggest that COs exhibit a metabolic profile similar to in vivo human brain metabolism, albeit with a few notable metabolic differences.

biophysics↗

bioRxiv2024

Transcranial Direct Current Stimulation over the Posterior Parietal Cortex Increases Non-target Retrieval during Visual Working Memory

Accurate visual working memory (VWM) requires precise content-context binding. Previous studies have revealed a close relationship between the posterior parietal cortex (PPC) and feature binding during VWM, this study further examined their causal relationship through three transcranial direct current stimulation (tDCS) experiments. In Experiment 1 (N = 57), participants underwent three sessions of tDCS separately, including PPC stimulation, occipital cortex stimulation, and sham stimulation, and completed a series of delayed estimation tasks for orientations before and after stimulation. Results showed that tDCS over PPC selectively prolonged recall response time (RT) and increased the probability of non-target responses (a.k.a. failure of feature binding). In Experiment 2 (N = 29), combining metacognition estimation during the task, we further investigated whether the effects of PPC stimulation on RT and increased probability of non-target responses were attributed to more mis-binding (i.e., participants self-reported "remembered" in non-target responses) or informed guessing (participants self-reported "forgotten" in non-target responses). We replicated the main findings in Experiment 1, and we also observed greater tDCS effects of PPC on RT in informed guessing trials than mis-binding trials while comparable effects on non-target response rates in these two types of trials. In Experiment 3 (N = 28), we then examined whether the effects of tDCS over PPC specifically influenced the memory retrieval process by using a change detection task. We found that PPC stimulation did not influence the recognition RT or accuracy. Together, this study provides causal evidence supporting the involvement of PPC in feature binding during VWM retrieval. Significance StatementVisual working memory (VWM) enables humans to temporarily store and process visual information, which requires accurate binding of items to their unique context. Accumulating studies posited that the posterior parietal cortex (PPC) is closely related to this binding process, the current study further examined their causal relationship. Through three strictly within-subject well-designed non-invasive neural stimulation experiments, we found that PPC stimulation selectively increased response time (RT) and binding error during VWM. Moreover, we found these changes were modulated by individual metacognition and only occurred during memory recall instead of recognition. Together, our results provided strong evidence that PPC is causally involved in the binding process during visual working memory retrieval.

neuroscience↗

bioRxiv2024

Weighted variance component test for the integrative multi-omics analysis of microbiome data

Metabolic dysregulation and alterations have been linked to various diseases and conditions. Innovations in high-throughput technology now allow rapid profiling of the metabolome and metagenome -- often the gene content of bacterial populations -- for characterizing metabolism. Due to the small sample sizes and high dimensionality of the data, pathway analysis (wherein the effect of multiple genes or metabolites on an outcome is cumulatively assessed) of metabolomic data is commonly conducted and also represents a standard for metagenomic analysis. However, how to integrate both data types remains unclear. Recognizing that a metabolic pathway can be complementarily characterized by both metagenomics and metabolomics, we propose a weighted variance components framework to test if the joint effect of genes and metabolites in a biological pathway is associated with outcomes. The approach allows analytic p-value calculation, correlation between data types, and optimal weighting. Power simulations show that our approach often outperforms other strategies while maintaining type I error. The approach is illustrated on real data.

bioinformatics↗

bioRxiv2024

A unifying model of species abundance distribution

The species abundance distribution (SAD) is one of the most fundamental and best-studied macroecological patterns at the core of any biodiversity theory. Remarkably, almost every community investigated to date shows a hollow curve, indicative of the presence of many rare species and a few abundant species. While the precise nature of SAD is believed to reflect fundamental ecological processes underlying community assembly, ecologists have yet to identify a single model that comprehensively explains all SADs. Recent studies using large datasets suggested that logseries best describes animal and plant communities1,2 while lognormal is the best model for microbes3, thereby challenging the notion of a unifying SAD model across the tree of life. Using a large dataset of [~]30,000 globally distributed communities spanning animals, plants and microbes from diverse environments, here we show that powerbend distribution, predicted by a maximum information entropy-based theory of ecology, emerges as a unifying model that accurately captures SADs of all life forms, habitats and abundance scales, supporting the existence of universal ecological principles. Our findings reject the notion of pure neutrality and support the idea that community assembly is driven by both random fluctuations and deterministic mechanisms, such as interspecific trait variation and resource competition. We also show that the previously estimated one trillion microbial species existing on Earth might be orders of magnitude off.

ecology↗

bioRxiv2024

Occurrence, risk assessment of antibiotics and antimicrobial resistance in Escherichia coli in typical rivers of Sichuan

Worldwide interest has been generated by the presence and distribution of antibiotics and antibiotic resistance genes (ARGs) in rivers. However, there was a dearth of research on the contamination of Sichuan provinces typical rivers with antibiotics. In this study, the residual level of antibiotics in 42 national/provincial sites of 9 rivers was analyzed by UPLC-MS/MS, the ecological risk level was evaluated using risk assessment method, and the drug resistance of E. coli in water was evaluated by Kirby-Bauer method. Redundancy analysis demonstrated how residual antibiotics affect the structure of the microbial community in the Minjiang River basin (RDA). Nine rivers all contained antibiotics. Among them, the MinJiang, TuoJiang, and JiaLingJiang rivers were severely contaminated with antibiotic concentrations ranging from 0.29 to 2233.71 ng/L. The Sichuan Basins antibiotic pollution level was significantly higher when compared to other Sichuan zones, which was consistent with the regions high population density. Additionally, it was discovered that 9.77% of the E. coli isolated from 9 rivers had antibiotic resistance, and more than 5.8% of them had multidrug resistance. Moreover, Norfloxacin, amoxicillin, ampicillin, and tetracycline were the main risk factors for high ecological risk in 26 of the 42 monitoring sites. Additionally, there is a strong correlation between the microbial community change and residual antibiotic. These results offered some reference information regarding the distribution of antibiotics and ARGs in typical rivers in the Chinese province of Sichuan, and this study showed that more attention needs to be paid to antibiotic pollution in Sichuans typical rivers.

microbiology↗

bioRxiv2024

Direct Genome-Scale Screening of Gluconobacter oxydans B58 for Rare Earth Element Bioleaching

The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REE). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole genome knockout collection for the bioleaching microbe Gluconobacter oxydans B58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in bioleaching by up to 111% (G. oxydans {delta}GO_1598, a disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% ({delta}GO_1096, a disruption of the gene encoding the GTP-binding protein TypA). Notable changes in biolixiviant pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching by G. oxydans through targeted genetic engineering.

synthetic biology↗

bioRxiv2024

HIF1α controls adipose tissue growth through metabolic rechanneling

Excessive expansion of white adipose tissue occurs when energy intake exceeds demand. It creates a state of relative hypoxia that is directly linked to activation of the hypoxia-inducible factor (HIF) in obese human subjects and mouse models of obesity. Whether HIF1 function is important for the development of basal adiposity and diet-induced obesity remains unclear. In the present study, we genetically ablated Hif1 in adipocytes and analyzed the corresponding mice for both basal and diet-induced obesity-associated visceral white adipose tissue mass as well as parameters of systemic glucose homeostasis and peripheral insulin sensitivity. We found that inactivation of Hif1 in mouse adipocytes inhibited basal adiposity and suppressed nutrient-overload-induced adipose tissue growth. These changes in adiposity were associated with improved systemic glucose homeostasis and peripheral insulin sensitivity. Mechanistically, Hif1 mediated effects on adipocyte metabolism by re-routing glycolytic intermediates into the glycerolipid shunt, leading to increased de novo triacylglyceride synthesis in hypertrophic adipocytes. Our results have established key roles for HIif1 in controlling adipocyte growth and metabolism and adipose tissue expansion under basal conditions and in response to a high-fat diet, highlighting the central role of hypoxia and HIF1 in the development of obesity. Article HighlightsO_LIHif1 function is critical for basal adipose tissue mass expansion, and is also required for fat accumulation in response to high fat diet. C_LIO_LICo-option and co-activation of the glycerolipid biosynthetic pathway by glycolysis is an important modulator of visceral adiposity. C_LIO_LIThese findings reveal an important role of Hif1 in the adipose tissue through the coupling of glycolysis and lipid anabolism in response to HFD, which may provide a potential therapeutic target for type 2 diabetes in the future. C_LI

cell biology↗

bioRxiv2024

Deletion of adipocyte Sine Oculis Homeobox Homolog 1 prevents lipolysis and attenuates skin fibrosis.

Dermal fibrosis is a cardinal feature of systemic sclerosis (SSc) for which there are limited treatment strategies. This is in part due to our fragmented understanding of how dermal white adipose tissue (DWAT) contributes to skin fibrosis. We identified elevated sine oculis homeobox homolog 1 (SIX1) expression in SSc skin samples from the GENISOS and PRESS cohorts, the expression of which correlated with adipose-associated genes and molecular pathways. SIX1 localization studies identified increased signals in the DWAT area in SSc and in experimental models of skin fibrosis. Global and adipocyte specific Six1 deletion abrogated end-stage fibrotic gene expression and dermal adipocyte shrinkage induced by SQ bleomycin treatment. Further studies revealed a link between elevated SIX1 and increased expression of SERPINE1 and its protein PAI-1 which are known pro-fibrotic mediators. However, SIX1 deletion did not appear to affect cellular trans differentiation. Taken together these results point at SIX1 as a potential target for dermal fibrosis in SSc. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSkin thickening and tightening are leading causes of morbidity in systemic sclerosis (SSc). The authors previously reported that the aberrantly expressed developmental transcription factor sine oculis homeobox homology 1 (SIX1) drives pulmonary fibrosis. However, the contribution of SIX1 to skin fibrosis and associated dermal fat loss remains unknown. Added value of this studyThe role of dermal fat loss in skin fibrosis is not fully understood. Studies have shown that adipocytes can transition to mesenchymal cells promoting fibrosis, consistent with loss of the dermal white adipose layer. Our research provides insight into a novel molecular mechanism of lipodystrophy important for skin fibrosis in SSc. We identified the upregulation of SIX1 in adipocytes in skin from patients with SSc which was associated with the progression of skin fibrosis. We found elevated Six1 in mouse dermal adipocytes of early fibrotic skin. Ubiquitous and adipose-specific loss of Six1 decreased markers of experimental skin fibrosis in mice which recapitulate cardinal features of SSc dermal fibrosis. Increased SIX1 expression is linked with elevated levels of Serpine1 the gene that codes for the protein plasminogen activator inhibitor (PAI)-1. This is important since PAI-1 is a known pro-fibrotic agent in the skin that contributes to the deposition of extracellular matrix (ECM) products. Implications of all the available evidenceFat atrophy may represent a targetable contributor to early systemic sclerosis manifestations. This is as it precedes skin fibrosis and the use of topical agent which are usually lipophilic can help us target dermal adipocytes. Our results show that SIX1 could be an important early marker for skin fibrosis in SSc that can also be targeted therapeutically.

molecular biology↗

bioRxiv2024

An integrated microfluidic and fluorescence platform for probing in vivo neuropharmacology

Neurotechnologies and genetic tools for dissecting neural circuit functions have advanced rapidly over the past decade, although the development of complementary pharmacological method-ologies has comparatively lagged. Understanding the precise pharmacological mechanisms of neuroactive compounds is critical for advancing basic neurobiology and neuropharmacology, as well as for developing more effective treatments for neurological and neuropsychiatric disorders. However, integrating modern tools for assessing neural activity in large-scale neural networks with spatially localized drug delivery remains a major challenge. Here, we present a dual microfluidic-photometry platform that enables simultaneous intracranial drug delivery with neural dynamics monitoring in the rodent brain. The integrated platform combines a wireless, battery-free, miniaturized fluidic microsystem with optical probes, allowing for spatially and temporally specific drug delivery while recording activity-dependent fluorescence using genetically encoded calcium indicators (GECIs), neurotransmitter sensors GRABNE and GRABDA, and neuropeptide sensors. We demonstrate the performance this platform for investigating neuropharmacological mechanisms in vivo and characterize its efficacy in probing precise mechanistic actions of neuroactive compounds across several rapidly evolving neuroscience domains.

neuroscience↗

bioRxiv2024

Mining the biosynthetic landscape of lactic acid bacteria unearths a new family of RiPPs assembled by a novel type of ThiF-like adenylyltransferases

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are chemically diverse natural products of ribosomal origin. These peptides, which frequently act as signals or antimicrobials, are biosynthesized by conserved enzymatic machineries, making genome mining a powerful strategy for unearthing previously uncharacterized members of their class. Herein, we investigate the untapped biosynthetic potential of Lactobacillales (i.e. lactic acid bacteria) - an order of Gram-positive bacteria closely associated with human life, including pathogenic species and industrially-relevent fermenters of dairy products. Through genome mining methods, we systematically explored the distribution and diversity of ThiF-like adenylyltransferases-utilizing RiPP systems in lactic acid bacteria and identified a number of unprecedented biosynthetic gene clusters. In one of these clusters, we found a previously undescribed group of macrocyclic imide biosynthetic pathways containing multiple transporters and may be involved in potential quorum sensing (QS) system. Through in vitro assays, we determined that one such adenylyltranferase specifically catalyzes the intracyclization of its precursor peptide through macrocyclic imide formation. Incubating the enzyme with various primary amines revealed it could effectively amidate the C-terminus of the precursor peptide. This new transformation adds to the growing list of Natures peptide macrocyclization strategies and expands the impressive catalytic repertoire of the adenylyltransferase family. The diverse RiPP systems identified herein represent a vast, unexploited landscape for discovery of novel class of natural products and potential QS systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/593846v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1cd3125org.highwire.dtl.DTLVardef@55a546org.highwire.dtl.DTLVardef@d5a325org.highwire.dtl.DTLVardef@1c9e1f3_HPS_FORMAT_FIGEXP M_FIG C_FIG (For Table of Contents use only)

biochemistry↗

bioRxiv2024

Enhanced extracellular matrix remodeling due to embedded spheroid fluidization

Tumor spheroids are in vitro three-dimensional, cellular collectives consisting of cancerous cells. Embedding these spheroids in an in vitro fibrous environment, such as a collagen network, to mimic the extracellular matrix (ECM) provides an essential platform to quantitatively investigate the biophysical mechanisms leading to tumor invasion of the ECM. To understand the mechanical interplay between tumor spheroids and the ECM, we computationally construct and study a three-dimensional vertex model for a tumor spheroid that is mechanically coupled to a cross-linked network of fibers. In such a vertex model, cells are represented as deformable polyhedrons that share faces. Some fraction of the boundary faces of the tumor spheroid contain linker springs connecting the center of the boundary face to the nearest node in the fiber network. As these linker springs actively contract, the fiber network remodels. By toggling between fluid-like and solid-like spheroids via changing the dimensionless cell shape index, we find that the spheroid rheology affects the remodeling of the fiber network. More precisely, fluid-like spheroids displace the fiber network more on average near the vicinity of the spheroid than solid-like spheroids. We also find more densification of the fiber network near the spheroid for the fluid-like spheroids. These spheroid rheology-dependent effects are the result of cellular motility due to active cellular rearrangements that emerge over time in the fluid-like spheroids to generate spheroid shape fluctuations. These shape fluctuations lead to emergent feedback between the spheroid and the fiber network to further remodel the fiber network with, for example, lower radial alignment of the higher-tensioned fibers given the breaking of spheroidal radial symmetry, which can then further remodel the spheroid. Our results uncover intricate morphological-mechanical interplay between an embedded spheroid and its surrounding fiber network with both spheroid contractile strength and spheroid shape fluctuations playing important roles in the pre-invasion stages of tumor invasion.

biophysics↗

bioRxiv2024

CLigOpt: Controllable Ligand Design through Target-Specific Optimisation

AO_SCPCAPBSTRACTC_SCPCAPO_ST_ABSMotivationC_ST_ABSKey challenge in deep generative models for molecular design is to navigate random sampling of the vast molecular space, and produce promising molecules that compromise property controls across multiple chemical criteria. Fragment-based drug design (FBDD), using fragments as starting points, is an effective way to constrain chemical space and improve generation of biologically active molecules. Furthermore, optimisation approaches are often implemented with generative models to search through chemical space, and identify promising samples which satisfy specific properties. Controllable FBDD has promising potential in efficient target-specific ligand design. ResultsWe propose a controllable FBDD model, CLigOpt, which can generate molecules with desired properties from a given fragment pair. CLigOpt is a Variational AutoEncoder-based model which utilises co-embeddings of node and edge features to fully mine information from molecular graphs, as well as a multi-objective Controllable Generation Module to generate molecules under property controls. CLigOpt achieves consistently strong performance in generating structurally and chemically valid molecules, as evaluated across six metrics. Applicability is illustrated through ligand candidates for hDHFR and it is shown that the proportion of feasible active molecules from the generated set is increased by 10%. Molecular docking and synthesisability prediction tasks are conducted to prioritise generated molecules to derive potential lead compounds. Availability and ImplementationThe source code is available via https://github.com/yutongLi1997/CLigOpt-Controllable-Ligand-Design-through-Target-Specific-Optimisation.

bioinformatics↗

bioRxiv2024

Host evolution improves genetic circuit function in complex growth environments

Genetically engineered bacteria have become an attractive platform for numerous biomedical and industrial applications. Despite genetic circuitry functioning predictably under favorable growth conditions in the lab, the same cannot be said when placed in more complex environments for eventual deployment. Here, we used a combination of evolutionary and rational engineering approaches to enhance E. coli for robust genetic circuit behavior in non-traditional growth environments. We utilized adaptive laboratory evolution (ALE) on E. coli MG1655 in a minimal media with a sole carbon source and saw improved dynamics of a population-lysis-based circuit after host evolution. Additionally, we improved lysis circuit tolerance of a more clinically relevant strain, the probiotic E. coli Nissle, using ALE of the host strain in a more complex media environment with added reactive oxygen species (ROS) stress. We observed improved recovery from circuit-induced lysis in the evolved Nissle strain, and in combination with directed mutagenesis, recovered circuit function in the complex media. These findings serve as a proof-of-concept that relevant strains of bacteria can be optimized for improved growth and performance in complex environments using ALE and that these changes can modify and improve synthetic gene circuit function for real-world applications.

synthetic biology↗

bioRxiv2024

The impact of Bacillus coagulans X3 on available nitrogen content, bacterial community composition, and nitrogen functional gene levels when composting cattle manure

This study was designed to probe available nitrogen levels, bacterial community composition, and the levels of nitrogen functional genes present when composting cattle manure with or without the addition of Bacillus coagulans X3. Bacterial supplementation was associated with the prolongation of the thermophilic stage and improved maturity of the resultant compost. At the maturity stage, samples to which B. coagulans X3 had been added exhibited significant increases in ammonium nitrogen, nitrate nitrogen, and total nitrogen levels. The dominant bacterial phyla observed in these composting samples were Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteriota, and Chloroflexi.B. coagulans X3 addition resulted in significant increases in relative Firmicutes abundance during the thermophilic and cooling stages, while also increasing amoA and nosZ gene abundance and reducing nirS gene levels over the course of composting. Together, these data suggest that B. coagulans X3 supplementation provides an effective means of enhancing nitrogen content in the context of cattle manure composting through the regulation of nitrification and denitrification activity.

microbiology↗

bioRxiv2024

High-resolution single particle imaging at 100-200 keV with the Gatan Alpine direct electron detector.

Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these voltages, specifically a ~4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 [A] resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope. We also achieved a ~3.2 [A] resolution reconstruction for a 115 kDa asymmetric protein complex, proving its effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpines capability for high-resolution data acquisition and screening on lower-end systems by obtaining ~3 [A] resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, possibly bringing smaller sized particles within the scope of cryo-EM.

biophysics↗

bioRxiv2024

Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16

Osteogenic differentiation is essential for bone development, metabolism, and repair; however, the underlying regulatory relationships among genes remain poorly understood. To elucidate the transcriptomic changes and identify novel regulatory genes involved in osteogenic differentiation, we differentiated mesenchymal stem cells (MSCs) derived from 20 human iPSC lines into preosteoblasts (preOBs) and osteoblasts (OBs). We then performed transcriptome profiling of MSCs, preOBs and OBs. The iPSC-derived MSCs and OBs showed similar transcriptome profiles to those of primary human MSCs and OBs, respectively. Differential gene expression analysis revealed global changes in the transcriptomes from MSCs to preOBs, and then to OBs, including the differential expression of 840 genes encoding transcription factors (TFs). TF regulatory network analysis uncovered a network comprising 451 TFs, organized into five interactive modules. Multiscale embedded gene co-expression network analysis (MEGENA) identified gene co-expression modules and key network regulators (KNRs). From these analyses, KLF16 emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of Klf16 in vitro inhibited osteogenic differentiation and mineralization, while Klf16+/- mice exhibited increased bone mineral density, trabecular number, and cortical bone area. Our study underscores the complexity of osteogenic differentiation and identifies novel regulatory genes such as KLF16, which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.

molecular biology↗

bioRxiv2024

PRMT5 deficiency disturbs Nur77 methylation to inhibit endometrial stromal cell differentiation in recurrent implantation failure

Various posttranslational modifications (PTMs) have been implicated in endometrial stromal cell (EnSC) differentiation, but the potential role of PTM crosstalk has not been identified. Here, we report that protein arginine methyltransferase 5 (PRMT5) is indispensable for human endometrial decidualization, functioning as a key regulator of decidualization defect in recurrent implantation failure (RIF) patients. Uterine-selective deletion of Prmt5 led to defective embryo implantation in mice due to impaired EnSC decidualization. Mechanistically, we find that PRMT5 catalyzes symmetric dimethylation of orphan nuclear receptor Nur77 at arginine 346, which in turn promotes Nur77 nuclear localization and increases its transcriptional activity in EnSC. Moreover, we demonstrate that PRMT5-mediated Nur77 methylation antagonizes AKT-induced phosphorylation of Nur77 at serine 351 in the transition from proliferation to differentiation of EnSC and disruption of the balance between methylation and phosphorylation of Nur77 is essentially involved in the endometrium of RIF patients. Furthermore, by modulating the methylation-phosphorylation of Nur77 and its transcriptional activity, we rescued impaired decidualization in RIF, further highlighting the critical role of the PRMT5/AKT/Nur77 complex in uterine receptivity to embryo implantation.

cell biology↗