A cell transcriptomic profile p ovides insights into adipocytes of porcine mammary gland across development

Background Studying the composition and developmental mechanisms in mammary gland is crucial for healthy growth of newborns. The mammary gland is inherently heterogeneous, and its physiological function dependents on the gene expression of multiple cell types. Most studies focused on epithelial cells, disregarding the role of neighboring adipocytes.Results Here, we constructed the largest transcriptomic dataset of porcine mammary gland cells thus far. The dataset captured 126,829 high-quality nuclei from physiological mammary glands across five developmental stages(d 90 of gestation, G90;d 0 after lactation, L0;d 20 after lactation, L20;2 d post natural involution, PI2;7 d post natural involution, PI7). Seven cell types were identified, including epithelial cells, adipocytes, endothelial cells, fibroblasts cells, immune cells, myoepithelial cells and precursor cells. Our data indicate that mammary glands at different developmental stages have distinct phenotypic and transcriptional signatures. During late gestation(G90), the differentiation and proliferation of adipocytes were inhibited. Meanwhile, partly epithelial cells were completely differentiated. Pseudo-time analysis showed that epithelial cells undergo three stages to achieve lactation, including cellular differentiation, hormone sensing, and metabolic activation. During lactation(L0 and L20), adipocytes area accounts for less than 0.5% of mammary glands. To maintain their own survival, the adipocyte exhibited a poorly differentiated state and a proliferative capacity. Epithelial cells initiate lactation upon hormonal stimulation. After fulfilling lactation mission, their undergo physiological death under high intensity lactation. Interestingly, the physiological dead cells seem to be actively cleared by immune cells via CCL21-ACKR4 pathway. This biological process may be an important mechanism for maintaining homeostasis of the mammary gland. During natural involution(PI2 and PI7), epithelial cell populations dedifferentiate into mesenchymal stem cells to maintain the lactation potential of mammary glands for the next lactation cycle.Conclusion The molecular mechanisms of dedifferentiation, proliferation and redifferentiation of adipocytes and epithelial cells were revealed from late pregnancy to natural involution. This cell transcriptomic profile constitutes an essential reference for future studies in the development and remodeling of the mammary gland at different stages.

SUMO1 regulates post-infarct cardiac repair based on cellular heterogeneity

Small ubiquitin-related modifier(SUMOylation)is a dynamic post-translational modification that maintains cardiac function and can protect against a hypertrophic response to cardiac pressure overload.However,the function of SUMOylation after myocardial infarction(MI)and the molecular details of heart cell responses to SUMO1 deficiency have not been determined.In this study,we demonstrated that SUMO1 protein was inconsistently abundant in different cell types and heart regions after MI.However,SUMO1 knockout significantly exacerbated systolic dysfunction and infarct size after myocardial injury.Single-nucleus RNA sequencing revealed the differential role of SUMO1 in regulating heart cells.Among cardiomyocytes,SUMO1 deletion increased the Nppa^(+)Nppb^(+)Ankrd1^(+)cardiomyocyte subcluster pro-portion after MI.In addition,the conversion of fibroblasts to myofibroblasts subclusters was inhibited in SUMO1 knockout mice.Importantly,SUMO1 loss promoted proliferation of endothelial cell subsets with the ability to reconstitute neovascularization and expressed angiogenesis-related genes.Computational analysis of ligand/receptor interactions suggested putative pathways that mediate cardiomyocytes to endothelial cell communication in the myocardium.Mice preinjected with cardiomyocyte-specific AAV-SUMO1,but not the endothelial cell-specific form,and exhibited ameliorated cardiac remodeling following MI.Collectively,our results identified the role of SUMO1 in cardiomyocytes,fibroblasts,and endothelial cells after MI.These findings provide new insights into SUMO1 involvement in the patho-genesis of MI and reveal novel therapeutic targets.

Cellular atlases of ovarian microenvironment alterations by diet and genetically-induced obesity

Obesity,which can arise from genetic or environmental factors,has been shown to cause serious damages to the reproductive system.The ovary,as one of the primary regulators of female fertility,is a complex organ comprised of heterogeneous cell types that work together to maintain a normal ovarian microenvironment(OME).Despite its importance,the effect of obesity on the entire ovary remains poorly documented.In this study,we performed ovary single-cell and nanoscale spatial RNA sequencing to investigate how the OME changed under different kinds of obesity,including high-fat diet(HFD)induced obesity and Leptin ablation induced obesity(OB).Our results demonstrate that OB,but not HFD,dramatically altered the proportion of ovarian granulosa cells,theca-interstitial cells,luteal cells,and endothelial cells.Furthermore,based on the spatial dynamics of follicular development,we defined four subpopulations of granulosa cell and found that obesity drastically disrupted the differentiation of mural granulosa cells from small to large antral follicles.Functionally,HFD enhanced follicle-stimulating hormone(FSH)sensitivity and hormone conversion,while OB caused decreased sensitivity,inadequate steroid hormone conversion,and impaired follicular development.These differences can be explained by the differential expression pattern of the transcription factor Foxo1.Overall,our study provides a powerful and high-resolution resource for profiling obesity-induced OME and offers insights into the diverse effects of obesity on female reproductive disorders.

A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean

Although root nodules are essential for biological nitrogen fixation in legumes,the cell types and molecular regulatory mechanisms contributing to nodule development and nitrogen fixation in determinate nodule legumes,such as soybean(Glycine max),remain incompletely understood.Here,we generated a single-nucleus resolution transcriptomic atlas of soybean roots and nodules at 14 days post inoculation(dpi)and annotated 17 major cell types,including six that are specific to nodules.We identified the specific cell types responsible for each step in the ureides synthesis pathway,which enables spatial compartmentalization of biochemical reactions during soybean nitrogen fixation.By utilizing RNA velocity analysis,we reconstructed the differentiation dynamics of soybean nodules,which differs from those of indeterminate nodules in Medicago truncatula.Moreover,we identified several putative regulators of soybean nodulation and two of these genes,GmbHLH93 and GmSCL1,were as-yet uncharacterized in soybean.Overexpression of each gene in soybean hairy root systems validated their respective roles in nodulation.Notably,enrichment for cytokinin-related genes in soybean nodules led to identification of the cytokinin receptor,GmCRE1,as a prominent component of the nodulation pathway.GmCRE1 knockout in soybean resulted in a striking nodule phenotype with decreased nitrogen fixation zone and depletion of leghemoglobins,accompanied by downregulation of nodule-specific gene expression,as well as almost complete abrogation of biological nitrogen fixation.In summary,this study provides a comprehensive perspective of the cellular landscape during soybean nodulation,shedding light on the underlying metabolic and developmental mechanisms of soybean nodule formation.

Single-nucleus RNA sequencing reveals heterogeneity among multiple white adipose tissue depots

Regardless of its anatomical site,adipose tissue shares a common energy-storage role but exhibits distinctive properties.Exploring the cellular and molecular heterogeneity of white adipose tissue(WAT)is crucial for comprehending its function and properties.However,existing single-nucleus RNA sequencing(snRNA-seq)studies of adipose tissue heterogeneity have examined only one or two depots.In this study,we employed snRNA-seq to test five representative depots including inguinal,epididymal,mesenteric,perirenal,and pericardial adipose tissues in mice under physiological conditions.By analyzing the contents of main cell catego-ries and gene profiles of various depots,we identified their distinctive physiological properties.Immune cells and fibro-adipogenic progenitor cells(FAPs)showed dramatic differences among WAT depots,while adipocytes seemed to be conserved.The heightened presence of regulatory macrophages and B cells in pericardial adipose tissues implied their potential contribution to the preservation of coronary vascular function.Moreover,the selective aggregation of pericytes within mesenteric adipose tissue was likely associated with the maintenance of intestinal barrier homeostasis.Using a combination of RNA sequencing and snRNA-seq analysis,the major subpopulations of FAPs derived from these depots determined the site characteristics of FAPs to a certain extent.Our work estab-lishes a systematic and reliable foundation for investigating the heterogeneity of WAT depots and elucidating the unique roles these depots play in coordinating the function of adjacent organs.

病毒和病毒病转录组学方法与应用

近年来,新型冠状病毒肺炎、流行性感冒、埃博拉出血热等病毒性疾病呈现愈演愈烈、愈发愈快的趋势。为保障人民健康和国民经济的稳定运行,研究病毒的致病机理与宿主免疫调控机制,解析病毒与宿主的基因表达调控规律,监测病原病毒与防治病毒病的重要性逐渐凸显。转录组测序是一类在RNA水平上关注基因在特定时空状态下表达特征的技术,是分析差异基因表达和研究mRNA差异剪接必不可少的工具。随着分子生物学实验技术的进步和生物信息学分析平台的成熟,转录组学研究向着低成本、低技术门槛的方向发展,逐渐从理论研究领域向临床实验室过渡,改变着临床工作人员对病毒与病毒病的传统认知,被越来越多的用于病毒转录机制、病毒与宿主的免疫互作、追踪疾病进展以及抗病毒药物研发等方面研究。本文主要对宏转录组的技术流程、常用软件以及病毒与病毒病方向的应用场景进行综述,并对细胞群转录组、单细胞转录组、单细胞核转录组以及空间转录组的方法与应用进行简要介绍,以期为病毒转录机制研究与病毒病的防控提供方法学参考。