RESUMEN
Nonimmune cells can have immunomodulatory roles that contribute to healthy development. However, the molecular and cellular mechanisms underlying the immunomodulatory functions of erythroid cells during human ontogenesis remain elusive. Here, integrated, single-cell transcriptomic studies of erythroid cells from the human yolk sac, fetal liver, preterm umbilical cord blood (UCB), term UCB and adult bone marrow (BM) identified classical and immune subsets of erythroid precursors with divergent differentiation trajectories. Immune-erythroid cells were present from the yolk sac to the adult BM throughout human ontogenesis but failed to be generated in vitro from human embryonic stem cells. Compared with classical-erythroid precursors, these immune-erythroid cells possessed dual erythroid and immune regulatory networks, showed immunomodulatory functions and interacted more frequently with various innate and adaptive immune cells. Our findings provide important insights into the nature of immune-erythroid cells and their roles during development and diseases.
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Células Precursoras Eritroides , Transcriptoma , Adulto , Diferenciación Celular/genética , Células Eritroides , Sangre Fetal , Humanos , Recién Nacido , Saco VitelinoRESUMEN
The discovery and application of genome editing introduced a new era of plant breeding by giving researchers efficient tools for the precise engineering of crop genomes1. Here we demonstrate the power of genome editing for engineering broad-spectrum disease resistance in rice (Oryza sativa). We first isolated a lesion mimic mutant (LMM) from a mutagenized rice population. We then demonstrated that a 29-base-pair deletion in a gene we named RESISTANCE TO BLAST1 (RBL1) caused broad-spectrum disease resistance and showed that this mutation caused an approximately 20-fold reduction in yield. RBL1 encodes a cytidine diphosphate diacylglycerol synthase that is required for phospholipid biosynthesis2. Mutation of RBL1 results in reduced levels of phosphatidylinositol and its derivative phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). In rice, PtdIns(4,5)P2 is enriched in cellular structures that are specifically associated with effector secretion and fungal infection, suggesting that it has a role as a disease-susceptibility factor3. By using targeted genome editing, we obtained an allele of RBL1, named RBL1Δ12, which confers broad-spectrum disease resistance but does not decrease yield in a model rice variety, as assessed in small-scale field trials. Our study has demonstrated the benefits of editing an LMM gene, a strategy relevant to diverse LMM genes and crops.
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Diacilglicerol Colinafosfotransferasa , Resistencia a la Enfermedad , Edición Génica , Oryza , Fitomejoramiento , Enfermedades de las Plantas , Resistencia a la Enfermedad/genética , Edición Génica/métodos , Genoma de Planta/genética , Oryza/enzimología , Oryza/genética , Oryza/microbiología , Fosfatidilinositoles/metabolismo , Fitomejoramiento/métodos , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Alelos , Fosfatidilinositol 4,5-Difosfato/metabolismo , Diacilglicerol Colinafosfotransferasa/genética , Diacilglicerol Colinafosfotransferasa/metabolismoRESUMEN
DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma, but the functional basis for this is unknown. Here, we show that loss-of-function DDX3X mutations are also enriched in MYC-translocated diffuse large B cell lymphoma and reveal functional cooperation between mutant DDX3X and MYC. DDX3X promotes the translation of mRNA encoding components of the core translational machinery, thereby driving global protein synthesis. Loss-of-function DDX3X mutations moderate MYC-driven global protein synthesis, thereby buffering MYC-induced proteotoxic stress during early lymphomagenesis. Established lymphoma cells restore full protein synthetic capacity by aberrant expression of DDX3Y, a Y chromosome homolog, the expression of which is normally restricted to the testis. These findings show that DDX3X loss of function can buffer MYC-driven proteotoxic stress and highlight the capacity of male B cell lymphomas to then compensate for this loss by ectopic DDX3Y expression.
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Linfocitos B/enzimología , ARN Helicasas DEAD-box/metabolismo , Linfoma de Células B/enzimología , Antígenos de Histocompatibilidad Menor/metabolismo , Proteínas de Neoplasias/biosíntesis , Proteínas Proto-Oncogénicas c-myc/metabolismo , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Animales , Linfocitos B/patología , Línea Celular Tumoral , Niño , Preescolar , ARN Helicasas DEAD-box/genética , Estrés del Retículo Endoplásmico , Femenino , Regulación Enzimológica de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Mutación con Pérdida de Función , Linfoma de Células B/genética , Linfoma de Células B/patología , Masculino , Ratones Transgénicos , Persona de Mediana Edad , Antígenos de Histocompatibilidad Menor/genética , Proteínas de Neoplasias/genética , Biosíntesis de Proteínas , Proteoma , Proteostasis , Proteínas Proto-Oncogénicas c-myc/genética , Adulto JovenRESUMEN
Invertebrates mainly rely on sequence-specific RNA interference (RNAi) to resist viral infections. Increasing studies show that double-stranded RNA (dsRNA) can induce sequence-independent protection and that Dicer-2, the key RNAi player that cleaves long dsRNA into small interfering RNA (siRNA), is necessary for this protection. However, how this protection occurs remains unknown. Herein, we report that it is caused by adenosine triphosphate (ATP)-hydrolysis accompanying the dsRNA-cleavage. Dicer-2 helicase domain is ATP-dependent; therefore, the cleavage consumes ATP. ATP depletion activates adenosine monophosphate-activated protein kinase (Ampk) and induces nuclear localization of Fork head box O (FoxO), a key transcriptional factor for dsRNA-induced genes. siRNAs that do not require processing cannot activate the transcriptional response. This study reveals a unique nonspecific antiviral mechanism other than the specific RNAi in shrimp. This mechanism is functionally similar to, but mechanistically different from, the dsRNA-activated antiviral response in vertebrates and suggests an interesting evolution of innate antiviral immunity.
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Proteínas Quinasas Activadas por AMP , Adenosina Trifosfato , ARN Bicatenario , Ribonucleasa III , Animales , ARN Bicatenario/metabolismo , Ribonucleasa III/metabolismo , Ribonucleasa III/genética , Proteínas Quinasas Activadas por AMP/metabolismo , Adenosina Trifosfato/metabolismo , Interferencia de ARN , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/metabolismo , Inmunidad Innata , Transcripción GenéticaRESUMEN
Beneficial bacteria remain largely unexplored. Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model-based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains-derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae's potential marker. In different health-disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model-based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https://github.com/zhenchengfang/metaProbiotics.
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Metagenoma , Probióticos , Humanos , Algoritmos , Metagenómica/métodos , Bacterias/genética , LenguajeRESUMEN
The arthropod exoskeleton provides protection and support and is vital for survival and adaption. The integrity and mechanical properties of the exoskeleton are often impaired after pathogenic infection; however, the detailed mechanism by which infection affects the exoskeleton remains largely unknown. Here, we report that the damage to the shrimp exoskeleton is caused by modulation of host lipid profiles after infection with white spot syndrome virus (WSSV). WSSV infection disrupts the mechanical performance of the exoskeleton by inducing the expression of a chitinase (Chi2) in the sub-cuticle epidermis and decreasing the cuticle chitin content. The induction of Chi2 expression is mediated by a nuclear receptor that can be activated by certain enriched long-chain saturated fatty acids after infection. The damage to the exoskeleton, an aftereffect of the induction of host lipogenesis by WSSV, significantly impairs the motor ability of shrimp. Blocking the WSSV-caused lipogenesis restored the mechanical performance of the cuticle and improved the motor ability of infected shrimp. Therefore, this study reveals a mechanism by which WSSV infection modulates shrimp internal metabolism resulting in phenotypic impairment, and provides new insights into the interactions between the arthropod host and virus.
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Exoesqueleto , Metabolismo de los Lípidos , Penaeidae , Virus del Síndrome de la Mancha Blanca 1 , Animales , Penaeidae/virología , Penaeidae/metabolismo , Exoesqueleto/metabolismo , Exoesqueleto/virología , Virus del Síndrome de la Mancha Blanca 1/fisiología , Metabolismo de los Lípidos/fisiología , Interacciones Huésped-Patógeno , Lipogénesis/fisiologíaRESUMEN
Recent studies show that antiviral systems are remarkably conserved from bacteria to mammals, demonstrating that unique insights into these systems can be gained by studying microbial organisms. Unlike in bacteria, however, where phage infection can be lethal, no cytotoxic viral consequence is known in the budding yeast Saccharomyces cerevisiae even though it is chronically infected with a double-stranded RNA mycovirus called L-A. This remains the case despite the previous identification of conserved antiviral systems that limit L-A replication. Here, we show that these systems collaborate to prevent rampant L-A replication, which causes lethality in cells grown at high temperature. Exploiting this discovery, we use an overexpression screen to identify antiviral functions for the yeast homologs of polyA-binding protein (PABPC1) and the La-domain containing protein Larp1, which are both involved in viral innate immunity in humans. Using a complementary loss of function approach, we identify new antiviral functions for the conserved RNA exonucleases REX2 and MYG1; the SAGA and PAF1 chromatin regulatory complexes; and HSF1, the master transcriptional regulator of the proteostatic stress response. Through investigation of these antiviral systems, we show that L-A pathogenesis is associated with an activated proteostatic stress response and the accumulation of cytotoxic protein aggregates. These findings identify proteotoxic stress as an underlying cause of L-A pathogenesis and further advance yeast as a powerful model system for the discovery and characterization of conserved antiviral systems.
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Virus Fúngicos , Proteínas de Saccharomyces cerevisiae , Humanos , Animales , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Antivirales , Virus Fúngicos/genética , Virus Fúngicos/metabolismo , ARN Bicatenario , Inmunidad Innata , Mamíferos/genética , Factores de Transcripción/genética , Proteínas Nucleares/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismoRESUMEN
Aberrant increase of arachidonic acid (ARA) has long been implicated in the pathology of Alzheimer's disease (AD), while the underlying causal mechanism remains unclear. In this study, we revealed a link between ARA mobilization and microglial dysfunction in Aß pathology. Lipidomic analysis of primary microglia from AppNL-GF mice showed a marked increase in free ARA and lysophospholipids (LPLs) along with a decrease in ARA-containing phospholipids, suggesting increased ARA release from phospholipids (PLs). To manipulate ARA-containing PLs in microglia, we genetically deleted lysophosphatidylcholine acyltransferase 3 (Lpcat3), the main enzyme catalyzing the incorporation of ARA into PLs. Loss of microglial Lpcat3 reduced the levels of ARA-containing PLs, free ARA and LPLs, leading to a compensatory increase in monounsaturated fatty acid (MUFA)-containing PLs in both male and female App NL-GF mice. Notably, the reduction of ARA in microglia significantly ameliorated oxidative stress and inflammatory responses while enhancing the phagocytosis of Aß plaques and promoting the compaction of Aß deposits. Mechanistically, scRNA seq suggested that LPCAT3 deficiency facilitates phagocytosis by facilitating de novo lipid synthesis while protecting microglia from oxidative damage. Collectively, our study reveals a novel mechanistic link between ARA mobilization and microglial dysfunction in AD. Lowering brain ARA levels through pharmacological or dietary interventions may be a potential therapeutic strategy to slow down AD progression.
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1-Acilglicerofosfocolina O-Aciltransferasa , Péptidos beta-Amiloides , Ácido Araquidónico , Microglía , Animales , Microglía/metabolismo , Ratones , Ácido Araquidónico/metabolismo , Masculino , Femenino , Péptidos beta-Amiloides/metabolismo , 1-Acilglicerofosfocolina O-Aciltransferasa/metabolismo , 1-Acilglicerofosfocolina O-Aciltransferasa/genética , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/patología , Enfermedad de Alzheimer/genética , Ratones Transgénicos , Peroxidación de Lípido , Ratones Endogámicos C57BL , Estrés Oxidativo/fisiología , Fosfolípidos/metabolismoRESUMEN
The cellular endosomal sorting complex required for transport (ESCRT) system comprises five distinct components and is involved in many different physiological processes. Recent studies have shown that different viruses rely upon the host ESCRT system for viral infection. However, whether this system is involved in white spot syndrome virus (WSSV) infection remains unclear. Here, we identified 24 homologs of ESCRT subunits in kuruma shrimp, Marsupenaeus japonicus, and found that some key components were strongly upregulated in shrimp after WSSV infection. Knockdown of key components of the ESCRT system using RNA interference inhibited virus replication, suggesting that the ESCRT system is beneficial for WSSV infection. We further focused on TSG101, a crucial member of the ESCRT-I family that plays a central role in recognizing cargo and activating the ESCRT-II and ESCRT-III complexes. TSG101 colocalized with WSSV in hemocytes. The addition of N16 (a TSG101 inhibitor) markedly decreased WSSV replication. TSG101 and ALIX of the ESCRT system interact with WSSV envelope proteins. The host proteins TSG101, RAB5, and RAB7, the viral protein VP28, and DNA were detected in endosomes isolated from hemocytes of WSSV-infected shrimp. Knockdown of Rab5 and Rab7 expression reduced viral replication. Taken together, these results suggest that the ESCRT system is hijacked by WSSV for transport through the early to late endosome pathway. Our work identified a novel requirement for the intracellular trafficking and infection of WSSV, and provided novel therapeutic targets for the prevention and control of WSSV in shrimp aquaculture. IMPORTANCE: Viruses utilize the ESCRT machinery in a variety of strategies for their replication and infection. This study revealed that the interaction of ESCRT complexes with WSSV envelope proteins plays a crucial role in WSSV infection in shrimp. The ESCRT system is conserved in the shrimp Marsupenaeus japonicus, and 24 homologs of the ESCRT system were identified in the shrimp. WSSV exploits the ESCRT system for transport and propagation via the interaction of envelope proteins with host TSG101 and ALIX in an endosome pathway-dependent manner. Understanding the underlying mechanisms of WSSV infection is important for disease control and breeding in shrimp aquaculture.
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Proteínas de Unión al ADN , Complejos de Clasificación Endosomal Requeridos para el Transporte , Penaeidae , Replicación Viral , Virus del Síndrome de la Mancha Blanca 1 , Animales , Virus del Síndrome de la Mancha Blanca 1/fisiología , Virus del Síndrome de la Mancha Blanca 1/metabolismo , Complejos de Clasificación Endosomal Requeridos para el Transporte/metabolismo , Penaeidae/virología , Penaeidae/metabolismo , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Endosomas/metabolismo , Endosomas/virología , Hemocitos/virología , Hemocitos/metabolismo , Interacciones Huésped-Patógeno , Proteínas del Envoltorio Viral/metabolismo , Proteínas del Envoltorio Viral/genética , Interferencia de ARNRESUMEN
Studies have confirmed that the occurrence of many complex diseases in the human body is closely related to the microbial community, and microbes can affect tumorigenesis and metastasis by regulating the tumor microenvironment. However, there are still large gaps in the clinical observation of the microbiota in disease. Although biological experiments are accurate in identifying disease-associated microbes, they are also time-consuming and expensive. The computational models for effective identification of diseases related microbes can shorten this process, and reduce capital and time costs. Based on this, in the paper, a model named DSAE_RF is presented to predict latent microbe-disease associations by combining multi-source features and deep learning. DSAE_RF calculates four similarities between microbes and diseases, which are then used as feature vectors for the disease-microbe pairs. Later, reliable negative samples are screened by k-means clustering, and a deep sparse autoencoder neural network is further used to extract effective features of the disease-microbe pairs. In this foundation, a random forest classifier is presented to predict the associations between microbes and diseases. To assess the performance of the model in this paper, 10-fold cross-validation is implemented on the same dataset. As a result, the AUC and AUPR of the model are 0.9448 and 0.9431, respectively. Furthermore, we also conduct a variety of experiments, including comparison of negative sample selection methods, comparison with different models and classifiers, Kolmogorov-Smirnov test and t-test, ablation experiments, robustness analysis, and case studies on Covid-19 and colorectal cancer. The results fully demonstrate the reliability and availability of our model.
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COVID-19 , Aprendizaje Profundo , Microbiota , Humanos , Reproducibilidad de los Resultados , Algoritmos , Biología Computacional/métodosRESUMEN
Although many single-cell computational methods proposed use gene expression as input, recent studies show that replacing 'unstable' gene expression with 'stable' gene-gene associations can greatly improve the performance of downstream analysis. To obtain accurate gene-gene associations, conditional cell-specific network method (c-CSN) filters out the indirect associations of cell-specific network method (CSN) based on the conditional independence of statistics. However, when there are strong connections in networks, the c-CSN suffers from false negative problem in network construction. To overcome this problem, a new partial cell-specific network method (p-CSN) based on the partial independence of statistics is proposed in this paper, which eliminates the singularity of the c-CSN by implicitly including direct associations among estimated variables. Based on the p-CSN, single-cell network entropy (scNEntropy) is further proposed to quantify cell state. The superiorities of our method are verified on several datasets. (i) Compared with traditional gene regulatory network construction methods, the p-CSN constructs partial cell-specific networks, namely, one cell to one network. (ii) When there are strong connections in networks, the p-CSN reduces the false negative probability of the c-CSN. (iii) The input of more accurate gene-gene associations further optimizes the performance of downstream analyses. (iv) The scNEntropy effectively quantifies cell state and reconstructs cell pseudo-time.
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Redes Reguladoras de Genes , Análisis de Secuencia de ARNRESUMEN
Atherosclerotic plaque formation is largely attributed to the impaired efferocytosis, which is known to be associated with the pathologic upregulation of cluster of differentiation 47 (CD47), a key antiphagocytic molecule. By gene expression omnibus (GEO) datasets analysis, we identified that four miRNAs are aberrantly downregulated in atherosclerosis, coronary artery disease, and obesity. Of them, hsa-miR-299-3p (miR-299-3p) was predicted to target the 3'UTR of human CD47 mRNA by bioinformatics analysis. Further, we demonstrated that miR-299-3p negatively regulates CD47 expression by binding to the target sequence "CCCACAU" in the 3'UTR of CD47 mRNA through luciferase reporter assay and site-directed mutagenesis. Additionally, we found that miR-299-3p was downregulated by ~32% in foam cells in response to oxidized low-density lipoprotein (ox-LDL) stimulation, thus upregulating CD47 and contributing to the impaired efferocytosis. Whereas, restoration of miR-299-3p reversed the ox-LDL-induced upregulation of CD47, thereby facilitating efferocytosis. In high-fat diet (HFD) fed ApoE-/- mice, we discovered that miR-299-3p was downregulated thus leading to upregulation of CD47 in abdominal aorta. Conversely, miR-299-3p restoration potently suppressed HFD-induced upregulation of CD47 and promoted phagocytosis of foam cells by macrophages in atherosclerotic plaques, thereby reducing necrotic core, increasing plaque stability, and mitigating atherosclerosis. Conclusively, we identify miR-299-3p as a negative regulator of CD47, and reveal a molecular mechanism whereby the ox-LDL-induced downregulation of miR-299-3p leads to the upregulation of CD47 in foam cells thus contributing to the impaired efferocytosis in atherosclerosis, and propose miR-299-3p can potentially serve as an inhibitor of CD47 to promote efferocytosis and ameliorate atherosclerosis.
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Aterosclerosis , Antígeno CD47 , Eferocitosis , MicroARNs , Animales , Humanos , Ratones , Regiones no Traducidas 3' , Aterosclerosis/metabolismo , Aterosclerosis/genética , Aterosclerosis/patología , Antígeno CD47/metabolismo , Antígeno CD47/genética , Dieta Alta en Grasa/efectos adversos , Células Espumosas/metabolismo , Células Espumosas/patología , Lipoproteínas LDL/metabolismo , Ratones Endogámicos C57BL , MicroARNs/genética , MicroARNs/metabolismoRESUMEN
Inflammation plays an important role in the initiation and progression of colorectal cancer (CRC) and leads to ß-catenin accumulation in colitis-related CRC. However, the mechanism remains largely unknown. Here, pancreatic progenitor cell differentiation and proliferation factor (PPDPF) is found to be upregulated in CRC and significantly correlated with tumor-node-metastasis (TNM) stages and survival time. Knockout of PPDPF in the intestinal epithelium shortens crypts, decreases the number of stem cells, and inhibits the growth of organoids and the occurrence of azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced CRC. Mechanistically, PPDPF is found to interact with Casein kinase 1α (CK1α), thereby disrupting its binding to Axin, disassociating the ß-catenin destruction complex, decreasing the phosphorylation of ß-catenin, and activating the Wnt/ß-catenin pathway. Furthermore, interleukin 6 (IL6)/Janus kinase 2 (JAK2)-mediated inflammatory signals lead to phosphorylation of PPDPF at Tyr16 and Tyr17, stabilizing the protein. In summary, this study demonstrates that PPDPF is a key molecule in CRC carcinogenesis and progression that connects inflammatory signals to the Wnt/ß-catenin signaling pathway, providing a potential novel therapeutic target.
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Neoplasias Colorrectales , Interleucina-6 , Humanos , Interleucina-6/efectos adversos , Interleucina-6/metabolismo , Fosforilación , beta Catenina/metabolismo , Vía de Señalización Wnt , Janus Quinasa 2/metabolismo , Neoplasias Colorrectales/genética , Proliferación Celular , Línea Celular Tumoral , Regulación Neoplásica de la Expresión GénicaRESUMEN
Studies have shown that protein glycosylation in cells reflects the real-time dynamics of biological processes, and the occurrence and development of many diseases are closely related to protein glycosylation. Abnormal protein glycosylation can be used as a potential diagnostic and prognostic marker of a disease, as well as a therapeutic target and a new breakthrough point for exploring pathogenesis. To address the issue of significant differences in the prediction results of previous models for different species, we constructed a hybrid deep learning model N-GlycoPred on the basis of dual-layer convolution, a paired attention mechanism and BiLSTM for accurate identification of N-glycosylation sites. By adopting one-hot encoding or the AAindex, we specifically selected the optimum combination of features and deep learning frameworks for human and mouse to refine the models. Based on six independent test datasets, our N-GlycoPred model achieved an average AUC of 0.9553, which is 0.23% higher than MusiteDeep. The comparison results indicate that our model can serve as a powerful tool for N-glycosylation site prescreening for biological researchers.
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Aprendizaje Profundo , Glicosilación , Humanos , Animales , RatonesRESUMEN
The bone marrow microenvironment has a key role in regulating haematopoiesis, but its molecular complexity and response to stress are incompletely understood. Here we map the transcriptional landscape of mouse bone marrow vascular, perivascular and osteoblast cell populations at single-cell resolution, both at homeostasis and under conditions of stress-induced haematopoiesis. This analysis revealed previously unappreciated levels of cellular heterogeneity within the bone marrow niche and resolved cellular sources of pro-haematopoietic growth factors, chemokines and membrane-bound ligands. Our studies demonstrate a considerable transcriptional remodelling of niche elements under stress conditions, including an adipocytic skewing of perivascular cells. Among the stress-induced changes, we observed that vascular Notch delta-like ligands (encoded by Dll1 and Dll4) were downregulated. In the absence of vascular Dll4, haematopoietic stem cells prematurely induced a myeloid transcriptional program. These findings refine our understanding of the cellular architecture of the bone marrow niche, reveal a dynamic and heterogeneous molecular landscape that is highly sensitive to stress and illustrate the utility of single-cell transcriptomic data in evaluating the regulation of haematopoiesis by discrete niche populations.
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Médula Ósea/irrigación sanguínea , Microambiente Celular , Hematopoyesis , Células Madre Hematopoyéticas , Análisis de la Célula Individual , Nicho de Células Madre , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Adipocitos/citología , Adipocitos/metabolismo , Animales , Proteínas de Unión al Calcio/metabolismo , Diferenciación Celular , Linaje de la Célula , Endotelio Vascular/citología , Femenino , Regulación de la Expresión Génica , Hematopoyesis/genética , Células Madre Hematopoyéticas/citología , Células Madre Hematopoyéticas/metabolismo , Masculino , Ratones , Células Mieloides/citología , Células Mieloides/metabolismo , Osteoblastos/citología , Osteoblastos/metabolismo , RNA-Seq , Receptores Notch/metabolismo , Nicho de Células Madre/genética , Estrés Fisiológico/genética , Transcriptoma/genéticaRESUMEN
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
RESUMEN
In chronic liver diseases, hepatic stellate cells (HSCs) are induced to form the myofibroblasts responsible for scar formation, leading to liver fibrosis and cirrhosis. Here, single-cell RNA sequencing with in vivo lineage tracing in nonalcoholic steatohepatitis (NASH) model mice reveals a subpopulation of HSCs transitioning back to a state resembling their developmental precursors, mesothelial cells (MCs), after liver injury. These damage-associated intermediates between HSCs and MCs (DIHMs) can be traced with a dual recombinase system by labeling Krt19-expressing cells within prelabeled Pdgfrb+ HSCs, and DIHMs highly express inflammation- and fibrosis-associated genes. Cre and Dre-inducible depletion of DIHMs by administering diphtheria toxin reduces liver fibrosis and alleviates liver damage in NASH model mice. Importantly, knockdown of Osr1, a zinc finger transcription factor of the OSR gene family, can block DIHM induction in vitro. Conditional knockout Osr1 in Pdgfrb-expressing mesenchymal cells in NASH model mice can reduce liver fibrosis in vivo. Our study collectively uncovers an injury-induced developmental reversion process wherein HSCs undergo what we call a mesenchymal-to-mesothelial transition, which can be targeted to develop interventions to treat chronic liver diseases.
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Current studies have indicated that insufficient trophoblast epithelial-mesenchymal transition (EMT), migration and invasion are crucial for spontaneous abortion (SA) occurrence and development. Exosomal miRNAs play significant roles in embryonic development and cellular communication. Hereon, we explored the roles of serum exosomes derived from SA patients on trophoblast EMT, migration and invasion. Exosomes were isolated from normal control (NC) patients with abortion for unplanned pregnancy and SA patients, then characterized by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA) and western blotting. Exosomal miRNA profiles were identified by miRNA sequencing. The effects of serum exosomes on trophoblast migration and invasion were detected by scratch wound healing and transwell assays, and other potential mechanisms were revealed by quantitative real-time PCR (RT-PCR), western blotting and dual-luciferase reporter assay. Finally, animal experiments were used to explore the effects of exosomal miR-410-3p on embryo absorption in mice. The serum exosomes from SA patients inhibited trophoblast EMT and reduced their migration and invasion ability in vitro. The miRNA sequencing showed that miR-410-3p was upregulated in SA serum exosomes. The functional experiments showed that SA serum exosomes restrained trophoblast EMT, migration and invasion by releasing miR-410-3p. Mechanistically, SA serum exosomal miR-410-3p inhibited trophoblast cell EMT, migration and invasion by targeting TNF receptor-associated factor 6 (TRAF6) at the post-transcriptional level. Besides, SA serum exosomal miR-410-3p inhibited the p38 MAPK signalling pathway by targeting TRAF6 in trophoblasts. Moreover, milk exosomes loaded with miR-410-3p mimic reached the maternal-fetal interface and aggravated embryo absorption in female mice. Clinically, miR-410-3p and TRAF6 expression were abnormal and negatively correlated in the placental villi of SA patients. Our findings indicated that exosome-derived miR-410-3p plays an important role between SA serum and trophoblasts in intercellular communication, suggesting a novel mechanism by which serum exosomal miRNA regulates trophoblasts in SA patients.
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Aborto Espontáneo , Exosomas , MicroARNs , Humanos , Femenino , Embarazo , Ratones , Animales , Exosomas/metabolismo , Factor 6 Asociado a Receptor de TNF/metabolismo , Placenta/metabolismo , MicroARNs/genética , Trofoblastos/metabolismo , Transición Epitelial-Mesenquimal/genética , Proliferación Celular , Movimiento Celular/genéticaRESUMEN
Two parallel pathways compartmentalized in the chloroplast and the endoplasmic reticulum contribute to thylakoid lipid synthesis in plants, but how these two pathways are coordinated during thylakoid biogenesis and remodeling remains unknown. We report here the molecular characterization of a homologous ADIPOSE TRIGLYCERIDE LIPASE-LIKE gene, previously referred to as ATGLL. The ATGLL gene is ubiquitously expressed throughout development and rapidly upregulated in response to a wide range of environmental cues. We show that ATGLL is a chloroplast non-regioselective lipase with a hydrolytic activity preferentially towards 16:0 of diacylglycerol (DAG). Comprehensive lipid profiling and radiotracer labeling studies revealed a negative correlation of ATGLL expression and the relative contribution of the chloroplast lipid pathway to thylakoid lipid biosynthesis. Additionally, we show that genetic manipulation of ATGLL expression resulted in changes in triacylglycerol levels in leaves. We propose that ATGLL, through affecting the level of prokaryotic DAG in the chloroplast, plays important roles in balancing the two glycerolipid pathways and in maintaining lipid homeostasis in plants.
Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Lipoproteína Lipasa/metabolismo , Cloroplastos/metabolismo , Tilacoides/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Plantas/metabolismo , LípidosRESUMEN
Our perception of objects depends on non-oculomotor depth cues, such as pictorial distance cues and binocular disparity, and oculomotor depth cues, such as vergence and accommodation. Although vergence eye movements are always involved in perceiving real distance, previous studies have mainly focused on the effect of oculomotor state via "proprioception" on distance and size perception. It remains unclear whether the oculomotor command of vergence eye movement would also influence visual processing. To address this question, we placed a light at 28.5 cm and a screen for stimulus presentation at 57 cm from the participants. In the NoDivergence condition, participants were asked to maintain fixation on the light regardless of stimulus presentation throughout the trial. In the WithDivergence condition, participants were instructed to initially maintain fixation on the near light and then turn their two eyes outward to look at the stimulus on the far screen. The stimulus was presented for 100 msec, entirely within the preparation stage of the divergence eye movement. We found that participants perceived the stimulus as larger but were less sensitive to stimulus sizes in the WithDivergence condition than in the NoDivergence condition. The earliest visual evoked component C1 (peak latency 80 msec), which varied with stimulus size in the NoDivergence condition, showed similar amplitudes for larger and smaller stimuli in the WithDivergence condition. These results show that vergence eye movement planning affects the earliest visual processing and size perception, and demonstrate an example of the effect of motor command on sensory processing.