Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocyt...Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.展开更多
Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In t...Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In this study,a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues,including stems,roots,leaves,and hypocotyls.Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity.Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination.We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway.The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.展开更多
Neonatal hypoxic-ischemic encephalopathy(HIE),resulting from perinatal asphyxia-induced hypoxic-ischemic brain damage(HIBD),is a severe neurological disorder that impairs neurodevelopment,and no definitive therapies a...Neonatal hypoxic-ischemic encephalopathy(HIE),resulting from perinatal asphyxia-induced hypoxic-ischemic brain damage(HIBD),is a severe neurological disorder that impairs neurodevelopment,and no definitive therapies are available.The polyphenolic natural compound salvianolic acid C(SAC)exhibits antioxidant,anti-inflammatory,and antiapoptotic properties.In this study,we evaluated the efficacy of SAC in treating HIE via animal and human brain organoid experiments.Human brain organoids served as a translational platform for assessing natural product efficacy and clinical effect prediction.Rat brain tissues were harvested at two time points(24 h and 7 d after HIBD and SAC administration)for single-nucleus RNA sequencing.In vitro and in vivo experiments,including microarrays and gene silencing,were employed to confirm the sequencing findings.Our findings demonstrated that during the acute phase of HIBD,SAC suppressed signal transducer and activator of transcription 3+(Stat3+)astrocyte-driven acute neuroinflammation,decreased inflammatory factor release,and maintained glial-immune homeostasis.During the subacute phase,SAC promoted oligodendrocyte differentiation and facilitated crosstalk between anti-inflammatory microglia and myelinating oligodendrocytes,establishing a regenerative microenvironment and enhancing neuregulin 3(NRG3)-receptor tyrosine-protein kinase erbB-4(ErbB4)signaling axis activity.These coordinated mechanisms highlight the dual capacity of SAC in mitigating early injury and driving structural repair in the later stages.This study revealed the pathophysiology of HIE and the multitarget neuroprotective effects of SAC against this disorder at single-cell resolution,advancing the mechanistic foundations for SAC-based therapies in neonatal brain injury.展开更多
Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infe...Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000single-nucleus transcriptomes of the lung, liver,kidney, and cerebral cortex in rhesus macaques(Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multiorgan dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019(COVID-19).Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway,which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy(an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection,which may facilitate the development of therapeutic interventions for COVID-19.展开更多
Single-nucleus RNA-sequencing technology has revolutionized understanding of nuanced changes in gene expression between cell types within tissues.Unfortunately,our understanding of regulatory RNAs,such as microRNAs(mi...Single-nucleus RNA-sequencing technology has revolutionized understanding of nuanced changes in gene expression between cell types within tissues.Unfortunately,our understanding of regulatory RNAs,such as microRNAs(miRNAs),is limited through both single-cell and single-nucleus techniques due to the short length of miRNAs in the cytoplasm and the incomplete reference of longer primary miRNA(pri-miRNA)transcripts in the nucleus.We build a custom reference to align and count pri-miRNA sequences in singlenucleus data.Using young and aged subventricular zone(SVZ)nuclei,we show differential expression of pri-miRNAs targeting genes involved in neural stem cells(NSC)differentiation in the aged SVZ.Furthermore,using wild-type and 5XFAD mouse model cortex nuclei,to validate the use of primiReference,we find cell-type-specific expression of pri-miRNAs known to be involved in Alzheimer’s disease(AD).pri-miRNAs likely contribute to NSC dysregulation with age and AD pathology.primiReference is paramount in capturing a global profile of gene expression and regulation in single-nucleus data and can provide key insights into cell-type-specific expression of pri-miRNAs,paving the way for future studies of regulation and pathway dysregulation.By looking at pri-miRNA abundance and transcriptional differences,regulation of gene expression by miRNAs in disease and aging can be further explored.展开更多
Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)n...Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)neurons,and accumulating evidence suggests that glia play prominent roles in nicotine addiction.However,VTA neurons and glia have yet to be characterized at the transcriptional level during the progression of nicotine self-administration.Here,a male mouse model of nicotine self-administration is established and the timing of three critical phases(pre-addiction,addicting,and post-addiction phase)is characterized.Single-nucleus RNA sequencing in the VTA at each phase is performed to comprehensively classify specific cell subtypes.Adaptive changes occurred during the addicting and post-addiction phases,with the addicting phase displaying highly dynamic neuroplasticity that profoundly impacts the transcription in each cell subtype.Furthermore,significant transcriptional changes in energy metabolism-related genes are observed,accompanied by notable structural alterations in neuronal mitochondria during the progression of nicotine self-administration.The results provide insights into mechanisms underlying the progression of nicotine addiction,serving as an important resource for identifying potential molecular targets for nicotine cessation.展开更多
Background:Hypoplastic left heart syndrome(HLHS)is one of the most challenging congenital heart diseases in clinical treatment.In cardiac tissues,resident macrophages fulfill critical functions in maintaining a stable...Background:Hypoplastic left heart syndrome(HLHS)is one of the most challenging congenital heart diseases in clinical treatment.In cardiac tissues,resident macrophages fulfill critical functions in maintaining a stable cardiac state and have strong regenerative capacity and organ specificity.However,the molecular mechanisms of macro-phages in HLHS remained unclear.Methods:Single-nucleus RNA sequencing(snRNA-seq)data of HLHS and healthy control(donors)samples obtained from the Gene Expression Omnibus(GEO)database were normalized and clustered using the Seurat package.The“FindMarkers”function was used to screen differentially expressed genes(DEGs)between the HLHS and donor groups and to analyze the functional enrichment of the set of genes of interest.Finally,cell-cell communication,pseudotime,and single-cell regulatory network inference and cluster-ing(SCENIC)analyses were used to study the mechanisms of macrophages in HLHS.Results:Based on the snRNA-seq data of HLHS and donors,we identified a total of 9 cell clusters,among which the proportion of macrophages was significantly less in the HLHS group than in the control group.Subdivision of macrophage subpopulations(Macrophages 1,2,and 3)showed that Macrophages 1 was mainly involved in nervous system development,angiogenesis,and apoptotic processes.In addition,analysis of communication between Macro-phages 1 and cardiomyocytes revealed that ligand-acceptor pairs such as GAS6/AXL,IL6,IGF1,THY1,and L1CAM were present only in the donor group.Finally,pesudotime and SCENIC analyses demonstrated that FOXO3 and ELF2 played a critical role for Macrophages 1 to maintain cardiac function in patients with HLHS.Conclusion:Our study improved the current understanding of the molecular mechanisms of macrophage devel-opment in HLHS,showing that manipulating the regulatory role of macrophages in the heart can be a novel treat-ment for HLHS.展开更多
Marchantia polymorpha,a model liverwort,provides a valuable system for investigating the evolution of plant sexual reproduction.To explore the cellular landscape of its reproductive structures,we generate a single-nuc...Marchantia polymorpha,a model liverwort,provides a valuable system for investigating the evolution of plant sexual reproduction.To explore the cellular landscape of its reproductive structures,we generate a single-nucleus transcriptomic atlas of the antheridiophore,archegoniophore,and sporophyte.Using singlenucleus RNA sequencing(snRNA-seq),we capture over 30,000 high-quality nuclei and identify distinct cel populations.In the male organ,we characterize stages of spermatogenesis from early antheridium cells to mature sperm,revealing dynamic transcriptional programs including cell cycle regulation,chromatin remodeling,and calcium signaling.In the female organ,we define cell types including archegonial layers and secondary central cells.Sporophyte clusters are annotated as spores,elaters,capsule wall,foot,and seta cells,with transcriptional signatures related to structural support,stress response,and reproductive functions.Cross-species analysis indicates that capsule wall cells in liverworts are similar to tapetum cells.Notably,foot cells exhibit high expression of genes involved in sporopollenin biosynthesis and signaling pathways,serving as a central hub that mediates communication between the maternal gametophyte and the developing sporophyte.This study provides a comprehensive cellular and molecular map of M.polymorpha reproductive organs and sporophyte,establishing a framework for investigating the development and evolution of sexual reproduction in early land plants.展开更多
Lumbar disc(LD)herniation and aging are prevalent conditions that can result in substantial morbidity.This study aimed to clarify the mechanisms connecting the LD aging and herniation,particularly focusing on cellular...Lumbar disc(LD)herniation and aging are prevalent conditions that can result in substantial morbidity.This study aimed to clarify the mechanisms connecting the LD aging and herniation,particularly focusing on cellular senescence and molecular alterations in the nucleus pulposus(NP).We performed a detailed analysis of NP samples from a diverse cohort,including individuals of varying ages and those with diagnosed LD herniation.Our methodology combined histological assessments with single-nucleus RNA sequencing to identify phenotypic and molecular changes related to NP aging and herniation.We discovered that cellular senescence and a decrease in nucleus pulposus progenitor cells(NPPCs)are central to both processes.Additionally,we found an age-related increase in NFAT1 expression that promotes NPPC senescence and contributes to both aging and herniation of LD.This research offers fresh insights into LD aging and its associated pathologies,potentially guiding the development of new therapeutic strategies to target the root causes of LD herniation and aging.展开更多
Intramuscular fat(IMF)is a complex adipose tissue within skeletal muscle,appearing specially tissue heterogeneous,and the factors influencing its formation remain unclear.In conditions such as diabetes,aging,and muscl...Intramuscular fat(IMF)is a complex adipose tissue within skeletal muscle,appearing specially tissue heterogeneous,and the factors influencing its formation remain unclear.In conditions such as diabetes,aging,and muscle wasting,IMF was deposited in abnormal locations in skeletal muscle,damaged the normal physiological functions of skeletal muscle.Here,we used Longissimus dorsi muscles from pigs with different IMF contents as samples and adopted a method combining spatial transcriptome(ST)and single-nucleus RNA-seq to identify the spatial heterogeneity of IMF.ST revealed that genes involved in TGF-βsignaling pathways were specifically highly enriched in IMF.In lean pigs,IMF autocrine produces more TGF-β2,while in obese pigs,IMF received more endothelial-derived TGF-β1.In vitro experiments have proven that porcine endothelial cells in a simulated high-fat environment released more TGF-β1 than TGF-β2.Moreover,under obesity mice,the addition of TGF-βafter muscle injury abolished IMF production and slowed muscle repair,whereas TGF-βinhibition accelerated muscle repair.Our findings demonstrate that the TGF-βpathway specifically regulates these processes,suggesting it as a potential therapeutic target for managing muscle atrophy in obese patients and enhancing muscle repair while reducing IMF deposition.展开更多
As a maternal nutrient-storage tissue in seeds, the endosperm is a drought-responsive compartment that influences seed development and crop yield through structural and compositional changes. However, the mechanisms t...As a maternal nutrient-storage tissue in seeds, the endosperm is a drought-responsive compartment that influences seed development and crop yield through structural and compositional changes. However, the mechanisms that regulate these adaptive responses in soybean endosperm remain unclear owing to the complexity of this tissue. In this study, we performed single-nucleus multiomics analysis across three key developmental stages of soybean seeds, generating a high-resolution map that identified 10 major cell types, as expected, and revealed that the endosperm is one of the main sites for drought response. Further sub-clustering delineated 12 distinct sub-populations representing five previously uncharacterized endosperm sub-cell types. Notably, the peripheral endosperm (PEN) showed the strongest drought response, with trajectory analysis revealing changes in PEN differentiation pathways and associated tran-scription factor (TF) networks under drought conditions. Moreover, analysis of cell-type-specific transcriptional regulatory networks demonstrated increased binding activity of drought-responsive TFs during stress. This study presents a single-nucleus atlas of drought-stressed soybean endosperm, offering molecular and cellular insights into drought tolerance mechanisms for soybean breeding.展开更多
The gut is not only used by insects as an organ for the digestion of food and absorption of nutrients but also as an important barrier against the invasion and proliferation of pathogenic microorganisms.Bombyx mori cy...The gut is not only used by insects as an organ for the digestion of food and absorption of nutrients but also as an important barrier against the invasion and proliferation of pathogenic microorganisms.Bombyx mori cytoplasmic polyhedrosis virus(BmCPV),an insect-specific virus,predominantly colonizes the midgut epithelial cells of the silkworm,thereby jeopardizing its normal growth.However,there is limited knowledge of the cellular immune responses to viral infection and whether the infection is promoted or inhibited by different types of cells in the silkworm midgut.In this study,we used single-nucleus RNA sequencing to identify representative enteroendocrine cells,enterocytes,and muscle cell types in the silkworm midgut.In addition,by analyzing the transcriptional profiles of various subpopulations in the infected and uninfected groups,we found that BmCPV infection suppresses the response of the antiviral pathways and induces the expression of BmHSP70,which plays a role in promoting BmCPV replication.However,certain immune genes in the midgut of the silkworm,such as BmLebocin3,were induced upon viral infection,and downregulation of BmLEB3 using RNA interference promoted BmCPV replication in the midgut of B.mori.These results suggest that viral immune evasion and active host resistance coexist in BmCPV-infected silkworms.We reveal the richness of cellular diversity in the midgut of B.mori larvae by single-nucleus RNA sequencing analysis and provide new insights into the complex interactions between the host and the virus at the single-cell level.展开更多
Peanut(Arachis hypogaea L.)is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground.Subterranean fruit-pod development,which significantly affects peanut production,inv...Peanut(Arachis hypogaea L.)is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground.Subterranean fruit-pod development,which significantly affects peanut production,involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues.To investigate the molecular mechanisms that underlie peanut fruitpod development,we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing(snRNA-seq)and single-nucleus assay for transposase-accessible chromatin with sequencing(snATAC-seq)data at the single-cell level.We identified distinct cell types,such as meristem,embryo,vascular tissue,cuticular layer,and stele cells within the shell wall.These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development.snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA.For instance,we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells,indicating an essential role for the vascular cells in peg gravitropism.Overall,our single-nucleus analysis provides comprehensive and novel information on specific cell types,gene expression,and chromatin accessibility during the early stages of fruit-pod development.This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.展开更多
Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecifi...Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.展开更多
Aging increases the risk ofliver diseases and systemic susceptibility to aging-related diseases.However,cell type-specific changes and the underlying mechanism of liver aging in higher vertebrates remain incompletely ...Aging increases the risk ofliver diseases and systemic susceptibility to aging-related diseases.However,cell type-specific changes and the underlying mechanism of liver aging in higher vertebrates remain incompletely characterized.Here,we constructed the first single-nucleus transcriptomic landscape of primate liver aging,in which we resolved cell type-specific gene expression fluctuation in hepatocytes across three liver zonations and detected aberrant cell-cell interactions between hepatocytes and niche cells.Upon in-depth dissection of this rich dataset,we identifed impaired lipid metabolism and upregulation of chronic inflammation-related genes prominently associated with declined liver functions during aging.In particular,hyperactivated sterol regulatory element-binding protein(SREBP)signaling was a hallmark of the aged liver,and consequently,forced activation of SREBP2 in human primary hepatocytes recapitulated in vivo aging phenotypes,manifesting as impaired detoxification and accelerated cellular senescence.This study expands our knowledge of primate liver aging and informs the development of diagnostics and therapeutic interventions for liver aging and associated diseases.展开更多
Age-dependent loss of skeletal muscle mass and function is a feature of sarcopenia,and increases the risk of many aging-related metabolic diseases.Here,we report phenotypic and single-nucleus transcriptomic analyses o...Age-dependent loss of skeletal muscle mass and function is a feature of sarcopenia,and increases the risk of many aging-related metabolic diseases.Here,we report phenotypic and single-nucleus transcriptomic analyses of non-human primate skeletal muscle aging.A higher transcriptional fluctuation was observed in myonuclei relative to other interstitial cell types,indicating a higher susceptibility of skeletal muscle fiber to aging.We found a downregulation of Foxo3 in aged primate skeletal muscle,and identi-fied FOxo3 as a hub transcription factor maintaining skeletal muscle homeostasis.Through the establishment of a complementary experimental pipeline based on a human pluripotent stem cell-derived myotube model,we revealed that silence of Foxo3 accelerates human myotube senescence,whereas genetic activation of endogenous FOxO3 alleviates human myotube aging.Altogether,based on a combination of monkey skeletal muscle and human myotube aging research models,we unraveled the pivotal role of the FOxO3 in safeguarding primate skeletal muscle from aging,providing a comprehensive resource for the development of clinical diagnosis and targeted therapeutic interventions against human skeletal muscle aging and the onset of sarcopenia along with aging-relateddisorders.展开更多
The testis is pivotal for male reproduction,and its progressive functional decline in aging is associated with infertility.However,the regulatory mechanism underlying primate testicular aging remains largely elusive.H...The testis is pivotal for male reproduction,and its progressive functional decline in aging is associated with infertility.However,the regulatory mechanism underlying primate testicular aging remains largely elusive.Here,we resolve the aging-related cellular and molecular alterations of primate testicular aging by establishing a single-nucleus transcriptomic atlas.Gene-expression patterns along the spermatogenesis trajectory revealed molecular programs associated with attrition of spermatogonial stem cell reservoir,disturbed meiosis and impaired spermiogenesis along the sequential continuum.Remarkably,Sertoli cell was identified as the cell type most susceptible to aging,given its deeply perturbed age-associated transcriptional profiles.Concomitantly,downregulation of the transcription factor Wilms'Tumor 1(WTi),essential for Sertoli cell homeostasis,was associated with accelerated cellular senescence,disrupted tight junctions,and a compromised cell identity signature,which altogether may help create a hostile microenvironment for spermatogenesis.Collectively,our study depicts in-depth transcriptomic traits of non-human primate(NHP)testicular aging at single-cell resolution,providing potential diagnostic biomarkers and targets for therapeutic interventions against testicular aging and age-related male reproductive diseases.展开更多
Aging poses a major risk factor for cardiovascular diseases,the leading cause of death in the aged population.However,the cell type-specific changes underlying cardiac aging are far from being clear.Here,we performed ...Aging poses a major risk factor for cardiovascular diseases,the leading cause of death in the aged population.However,the cell type-specific changes underlying cardiac aging are far from being clear.Here,we performed single-nucleus RNA-sequencing analysis of left ventricles from young and aged cynomolgus monkeys to define cell composition changes and transcriptomic alterations across different cell types associated with age.We found that aged cardiomyocytes underwent a dramatic loss in cell numbers and profound fluctuations in transcriptional profles.Via transcription regulatory network analysis,we identified FOxP1,a core transcription factor in organ development,as a key downregulated factor in aged cardiomyocytes,concomitant with the dysregulation of FoxP1 target genes associated with heart function and cardiac diseases.Consistently,the deficiency of FOxP1 led to hypertrophic and senescent phenotypes in human embryonic stem cell-derived cardiomyocytes.Altogether,our findings depict the celiular and molecular landscape of ventricular aging at the single-cell resolution,and identify drivers for primate cardiac aging and potential targets for intervention against cardiac aging and associated diseases.展开更多
Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis,a worldwide prevalent inflammatory disease.However,a systematic characterization and comprehensive understandi...Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis,a worldwide prevalent inflammatory disease.However,a systematic characterization and comprehensive understanding of the regulatory mechanism underlying gingival aging is still lacking.Here,we systematically dissected the phenotypic characteristics of gingiva during aging in primates and constructed the first single-nucleus transcriptomic landscape of gingival aging,by which a panel of cell type-specific signatures were elucidated.Epithelial cells were identified as the most affected cell types by aging in the gingiva.Further analyses pinpointed the crucial role of YAP in epithelial self-renew and homeostasis,which declined during aging in epithelial cells,especially in basal cells.The decline of YAP activity during aging was confrmed in the human gingival tissues,and downregulation of YAP in human primary gingival keratinocytes recapitulated the major phenotypic defects observed in the aged primate gingiva while overexpression of YAP showed rejuvenation effects.Our work provides an in-depth understanding of gingival aging and serves as a rich resource for developing novel strategies to combat aging-associated gingival diseases,with the ultimate goal of advancing periodontal health and promoting healthy aging.展开更多
To uncover the role of satellite cells(SCs)in paravertebral muscle development and aging,we constructed a single-nucleus transcriptomic atlas of mouse paravertebral muscle across seven timepoints spanning the embryo(d...To uncover the role of satellite cells(SCs)in paravertebral muscle development and aging,we constructed a single-nucleus transcriptomic atlas of mouse paravertebral muscle across seven timepoints spanning the embryo(day 16.5)to old(month 24)stages.Eight cell types,including SCs,fast muscle cells,and slow muscle cells,were identified.An energy metabolism-related gene set,TCA CYCLE IN SENESCENCE,was enriched in SCs.Forty-two skeletal muscle disease-related genes were highly expressed in SCs and exhibited similar expression patterns.Among them,Pdha1 was the core gene in the TCA CYCLE IN SENESCENCE;Pgam2,Sod1,and Suclg1 are transcription factors closely associated with skeletal muscle energy metabolism.Transcription factor enrichment analysis of the 42 genes revealed that Myod1 and Mef2a were also highly expressed in SCs,which regulated Pdha1 expression and were associated with skeletal muscle development.These findings hint that energy metabolism may be pivotal in SCs development and aging.Three ligand-receptor pairs of extracellular matrix(ECM)-receptor interactions,Lamc1-Dag1,Lama2-Dag1,and Hspg2-Dag1,may play a vital role in SCs interactions with slow/fast muscle cells and SCs self-renewal.Finally,we built the first database of a skeletal muscle single-cell transcriptome,the Musculoskeletal Cell Atlas(http://www.mskca.tech),which lists 630,040 skeletal muscle cells and provides interactive visualization,a useful resource for revealing skeletal muscle cellular heterogeneity during development and aging.Our study could provide new targets and ideas for developing drugs to inhibit skeletal muscle aging and treat skeletal muscle diseases.展开更多
基金supported by the National Natural Science Foundation of China,No.82301403(to DZ)。
文摘Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.
基金supported by the Guangdong Provincial Key Research and Development Program-Modern Seed Industry(2022B0202060004)National Key Research and Development Project(2023YFD1202800)+9 种基金National Natural Science Foundation of China(32272121,32172051,32301869,32000471)Guangdong Science and Technology Plan Project(2023B1212060038)Guangdong Basic and Applied Basic Research Foundation(2021A1515010811,2023A1515010098,2023A1515010569)China Agriculture Research System of MOF and MARA(CARS-13)Guangzhou Basic and Applied Basic Research Foundation(2023A04J0776)Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science(R2020PY-JX004,R2020PY-JG005,R2021PY-QY003,R2022YJYB3025)the Foundation of the Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences(202201,202306)Special Funds for the Revitalization of Agriculture through Seed Industry under the Provincial Rural Revitalization Strategy(2022-NPY-00-022)the Project of Collaborative Innovation Center of GDAAS(XTXM202203)Science and Technology Planning Project of Heyuan City(Heyuan She Nong Da Zhuan Xiang 2022002).
文摘Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In this study,a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues,including stems,roots,leaves,and hypocotyls.Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity.Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination.We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway.The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.
基金supported by the Zhejiang Province Traditional Chinese Medicine Science and Technology Project(GZY-ZJKJ-24076)the High-level Talents Special Support Program of Zhejiang Province(2024-KYY-GXJS-0026)+3 种基金the‘Pioneer’Research and Development Program of Zhejiang(2023C03004)the Transverse Research Project of Zhejiang University(2023-KYY-A070350007)the Theme-base Research Scheme,Research Grants Committee(T13-602/21-N)the Starlit South Lake Leading Elite Program(2023A303005).
文摘Neonatal hypoxic-ischemic encephalopathy(HIE),resulting from perinatal asphyxia-induced hypoxic-ischemic brain damage(HIBD),is a severe neurological disorder that impairs neurodevelopment,and no definitive therapies are available.The polyphenolic natural compound salvianolic acid C(SAC)exhibits antioxidant,anti-inflammatory,and antiapoptotic properties.In this study,we evaluated the efficacy of SAC in treating HIE via animal and human brain organoid experiments.Human brain organoids served as a translational platform for assessing natural product efficacy and clinical effect prediction.Rat brain tissues were harvested at two time points(24 h and 7 d after HIBD and SAC administration)for single-nucleus RNA sequencing.In vitro and in vivo experiments,including microarrays and gene silencing,were employed to confirm the sequencing findings.Our findings demonstrated that during the acute phase of HIBD,SAC suppressed signal transducer and activator of transcription 3+(Stat3+)astrocyte-driven acute neuroinflammation,decreased inflammatory factor release,and maintained glial-immune homeostasis.During the subacute phase,SAC promoted oligodendrocyte differentiation and facilitated crosstalk between anti-inflammatory microglia and myelinating oligodendrocytes,establishing a regenerative microenvironment and enhancing neuregulin 3(NRG3)-receptor tyrosine-protein kinase erbB-4(ErbB4)signaling axis activity.These coordinated mechanisms highlight the dual capacity of SAC in mitigating early injury and driving structural repair in the later stages.This study revealed the pathophysiology of HIE and the multitarget neuroprotective effects of SAC against this disorder at single-cell resolution,advancing the mechanistic foundations for SAC-based therapies in neonatal brain injury.
基金supported by the National Basic Research Program of China(2020YFA0804000,2020YFC0842000,2020YFA0112200,2021YFC2301703)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB32010100)+6 种基金Special Associate Research Program of the Chinese Academy of Sciences(E1290601)National Natural Science Foundation of China(32122037,81891001,32192411,32100512,U1902215)Collaborative Research Fund of the Chinese Institute for Brain Research,Beijing(2020-NKX-PT-03)CAS Project for Young Scientists in Basic Research(YSBR-013)Young Elite Scientist Sponsorship Program by the China Association for Science and Technology(2020QNRC001)National Resource Center for Non-Human Primates。
文摘Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000single-nucleus transcriptomes of the lung, liver,kidney, and cerebral cortex in rhesus macaques(Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multiorgan dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019(COVID-19).Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway,which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy(an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection,which may facilitate the development of therapeutic interventions for COVID-19.
基金provided by T32AG041688 and P20GM119943 from the National Institutes of Healthprovided by P20GM119943 from the National Institutes of Health.
文摘Single-nucleus RNA-sequencing technology has revolutionized understanding of nuanced changes in gene expression between cell types within tissues.Unfortunately,our understanding of regulatory RNAs,such as microRNAs(miRNAs),is limited through both single-cell and single-nucleus techniques due to the short length of miRNAs in the cytoplasm and the incomplete reference of longer primary miRNA(pri-miRNA)transcripts in the nucleus.We build a custom reference to align and count pri-miRNA sequences in singlenucleus data.Using young and aged subventricular zone(SVZ)nuclei,we show differential expression of pri-miRNAs targeting genes involved in neural stem cells(NSC)differentiation in the aged SVZ.Furthermore,using wild-type and 5XFAD mouse model cortex nuclei,to validate the use of primiReference,we find cell-type-specific expression of pri-miRNAs known to be involved in Alzheimer’s disease(AD).pri-miRNAs likely contribute to NSC dysregulation with age and AD pathology.primiReference is paramount in capturing a global profile of gene expression and regulation in single-nucleus data and can provide key insights into cell-type-specific expression of pri-miRNAs,paving the way for future studies of regulation and pathway dysregulation.By looking at pri-miRNA abundance and transcriptional differences,regulation of gene expression by miRNAs in disease and aging can be further explored.
基金supported by the Major Project of Tobacco Biological Effects(552022AK0070,110202102014)。
文摘Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)neurons,and accumulating evidence suggests that glia play prominent roles in nicotine addiction.However,VTA neurons and glia have yet to be characterized at the transcriptional level during the progression of nicotine self-administration.Here,a male mouse model of nicotine self-administration is established and the timing of three critical phases(pre-addiction,addicting,and post-addiction phase)is characterized.Single-nucleus RNA sequencing in the VTA at each phase is performed to comprehensively classify specific cell subtypes.Adaptive changes occurred during the addicting and post-addiction phases,with the addicting phase displaying highly dynamic neuroplasticity that profoundly impacts the transcription in each cell subtype.Furthermore,significant transcriptional changes in energy metabolism-related genes are observed,accompanied by notable structural alterations in neuronal mitochondria during the progression of nicotine self-administration.The results provide insights into mechanisms underlying the progression of nicotine addiction,serving as an important resource for identifying potential molecular targets for nicotine cessation.
基金supported by Jiangsu Province Postgraduate Practice Innovation Program(SJCX22_0766)Natural Science Foundation of Jiangsu Province(BK20231378)Leader of Geriatric Clinical Technology Application Research Project of Jiangsu Provincial Health Commission(LR2022002)。
文摘Background:Hypoplastic left heart syndrome(HLHS)is one of the most challenging congenital heart diseases in clinical treatment.In cardiac tissues,resident macrophages fulfill critical functions in maintaining a stable cardiac state and have strong regenerative capacity and organ specificity.However,the molecular mechanisms of macro-phages in HLHS remained unclear.Methods:Single-nucleus RNA sequencing(snRNA-seq)data of HLHS and healthy control(donors)samples obtained from the Gene Expression Omnibus(GEO)database were normalized and clustered using the Seurat package.The“FindMarkers”function was used to screen differentially expressed genes(DEGs)between the HLHS and donor groups and to analyze the functional enrichment of the set of genes of interest.Finally,cell-cell communication,pseudotime,and single-cell regulatory network inference and cluster-ing(SCENIC)analyses were used to study the mechanisms of macrophages in HLHS.Results:Based on the snRNA-seq data of HLHS and donors,we identified a total of 9 cell clusters,among which the proportion of macrophages was significantly less in the HLHS group than in the control group.Subdivision of macrophage subpopulations(Macrophages 1,2,and 3)showed that Macrophages 1 was mainly involved in nervous system development,angiogenesis,and apoptotic processes.In addition,analysis of communication between Macro-phages 1 and cardiomyocytes revealed that ligand-acceptor pairs such as GAS6/AXL,IL6,IGF1,THY1,and L1CAM were present only in the donor group.Finally,pesudotime and SCENIC analyses demonstrated that FOXO3 and ELF2 played a critical role for Macrophages 1 to maintain cardiac function in patients with HLHS.Conclusion:Our study improved the current understanding of the molecular mechanisms of macrophage devel-opment in HLHS,showing that manipulating the regulatory role of macrophages in the heart can be a novel treat-ment for HLHS.
基金supported by the 10 KP project(https://db.cngb.org/1Okp/)and the Scientific Foundation of the Urban Management Bureau of Shenzhen(202403).
文摘Marchantia polymorpha,a model liverwort,provides a valuable system for investigating the evolution of plant sexual reproduction.To explore the cellular landscape of its reproductive structures,we generate a single-nucleus transcriptomic atlas of the antheridiophore,archegoniophore,and sporophyte.Using singlenucleus RNA sequencing(snRNA-seq),we capture over 30,000 high-quality nuclei and identify distinct cel populations.In the male organ,we characterize stages of spermatogenesis from early antheridium cells to mature sperm,revealing dynamic transcriptional programs including cell cycle regulation,chromatin remodeling,and calcium signaling.In the female organ,we define cell types including archegonial layers and secondary central cells.Sporophyte clusters are annotated as spores,elaters,capsule wall,foot,and seta cells,with transcriptional signatures related to structural support,stress response,and reproductive functions.Cross-species analysis indicates that capsule wall cells in liverworts are similar to tapetum cells.Notably,foot cells exhibit high expression of genes involved in sporopollenin biosynthesis and signaling pathways,serving as a central hub that mediates communication between the maternal gametophyte and the developing sporophyte.This study provides a comprehensive cellular and molecular map of M.polymorpha reproductive organs and sporophyte,establishing a framework for investigating the development and evolution of sexual reproduction in early land plants.
基金supported by the National Key Research and Development Program of China(2022YFA1103800,2020YFA0804000,2022YFA1103700,the STI2030-Major Projects-2021ZD0202400)Non-Communicable Chronic Diseases-National Science and Technology Major Project(2024ZD0530400)+15 种基金the National Natural Science Foundation of China(82488301,82125011,92168201,82361148131,82322025,82422031,82330044,32341001,32121001,82192863,82361148130,8231101626,82271600,82471586,92468303)the Program of the Beijing Natural Science Foundation(F251011,JQ24044,Z240018,Z230011)Shenzhen Medical Research Fund(C2406001)CAS Project for Young Scientists in Basic Research(YSBR-076,YSBR-012)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA0460403,XDC0200000)the Informatization Plan of Chinese Academy of Sciences(CAS-WX2022SDC-XK14)New Cornerstone Science Foundation through the XPLORER PRIZE(2021-1045)Beijing Municipal Public Welfare Development and Reform Pilot Project for Medical Research Institutes(JYY2023-13)CAS Youth Interdisciplinary Team,Space Medical Experiment Project of CMSP(HYZHXMH01012)Key Laboratory of Alzheimer’s Disease of Zhejiang Province(ZJAD-2024001)Initiative Scientific Research Program,Institute of Zoology,CAS(2023IOZ0202,2024IOZ0103,2023IOZ0102)Beijing Anzhen Hospital High Level Research Funding(2024AZB3002)Excellent Young Talents Program of Capital Medical University(12300927)Excellent Young Talents Training Program for the Construction of Beijing Municipal University Teacher Team(BPHR202203105)Young Elite Scientists Sponsorship Program by CAST(2021QNRC001)Youth Innovation Promotion Association of CAS(2022083).
文摘Lumbar disc(LD)herniation and aging are prevalent conditions that can result in substantial morbidity.This study aimed to clarify the mechanisms connecting the LD aging and herniation,particularly focusing on cellular senescence and molecular alterations in the nucleus pulposus(NP).We performed a detailed analysis of NP samples from a diverse cohort,including individuals of varying ages and those with diagnosed LD herniation.Our methodology combined histological assessments with single-nucleus RNA sequencing to identify phenotypic and molecular changes related to NP aging and herniation.We discovered that cellular senescence and a decrease in nucleus pulposus progenitor cells(NPPCs)are central to both processes.Additionally,we found an age-related increase in NFAT1 expression that promotes NPPC senescence and contributes to both aging and herniation of LD.This research offers fresh insights into LD aging and its associated pathologies,potentially guiding the development of new therapeutic strategies to target the root causes of LD herniation and aging.
基金supported by the National Natural Science Foundation of China(323B2058)Selection and Breeding of New Local Pig Breeds and Promotion of Industrialization(2022-440000-43010101-9501)+2 种基金Selection and Breeding of Guangdong Small-ear Spotted Pig(2022-440000-4301030202-9510)China Agriculture Research System(CASR-35)the Key Scientific Research Project of Education Department of Shaanxi(22JS033).
文摘Intramuscular fat(IMF)is a complex adipose tissue within skeletal muscle,appearing specially tissue heterogeneous,and the factors influencing its formation remain unclear.In conditions such as diabetes,aging,and muscle wasting,IMF was deposited in abnormal locations in skeletal muscle,damaged the normal physiological functions of skeletal muscle.Here,we used Longissimus dorsi muscles from pigs with different IMF contents as samples and adopted a method combining spatial transcriptome(ST)and single-nucleus RNA-seq to identify the spatial heterogeneity of IMF.ST revealed that genes involved in TGF-βsignaling pathways were specifically highly enriched in IMF.In lean pigs,IMF autocrine produces more TGF-β2,while in obese pigs,IMF received more endothelial-derived TGF-β1.In vitro experiments have proven that porcine endothelial cells in a simulated high-fat environment released more TGF-β1 than TGF-β2.Moreover,under obesity mice,the addition of TGF-βafter muscle injury abolished IMF production and slowed muscle repair,whereas TGF-βinhibition accelerated muscle repair.Our findings demonstrate that the TGF-βpathway specifically regulates these processes,suggesting it as a potential therapeutic target for managing muscle atrophy in obese patients and enhancing muscle repair while reducing IMF deposition.
基金supported by the National Natural Science Foundation of China,China(grant number 31970344)the Joint Funds of the Natural Science Foundation of Hainan Province,China(grant number 2021JJLH0065).
文摘As a maternal nutrient-storage tissue in seeds, the endosperm is a drought-responsive compartment that influences seed development and crop yield through structural and compositional changes. However, the mechanisms that regulate these adaptive responses in soybean endosperm remain unclear owing to the complexity of this tissue. In this study, we performed single-nucleus multiomics analysis across three key developmental stages of soybean seeds, generating a high-resolution map that identified 10 major cell types, as expected, and revealed that the endosperm is one of the main sites for drought response. Further sub-clustering delineated 12 distinct sub-populations representing five previously uncharacterized endosperm sub-cell types. Notably, the peripheral endosperm (PEN) showed the strongest drought response, with trajectory analysis revealing changes in PEN differentiation pathways and associated tran-scription factor (TF) networks under drought conditions. Moreover, analysis of cell-type-specific transcriptional regulatory networks demonstrated increased binding activity of drought-responsive TFs during stress. This study presents a single-nucleus atlas of drought-stressed soybean endosperm, offering molecular and cellular insights into drought tolerance mechanisms for soybean breeding.
基金supported by the National Natural Science Foundation of China(No.32372951)。
文摘The gut is not only used by insects as an organ for the digestion of food and absorption of nutrients but also as an important barrier against the invasion and proliferation of pathogenic microorganisms.Bombyx mori cytoplasmic polyhedrosis virus(BmCPV),an insect-specific virus,predominantly colonizes the midgut epithelial cells of the silkworm,thereby jeopardizing its normal growth.However,there is limited knowledge of the cellular immune responses to viral infection and whether the infection is promoted or inhibited by different types of cells in the silkworm midgut.In this study,we used single-nucleus RNA sequencing to identify representative enteroendocrine cells,enterocytes,and muscle cell types in the silkworm midgut.In addition,by analyzing the transcriptional profiles of various subpopulations in the infected and uninfected groups,we found that BmCPV infection suppresses the response of the antiviral pathways and induces the expression of BmHSP70,which plays a role in promoting BmCPV replication.However,certain immune genes in the midgut of the silkworm,such as BmLebocin3,were induced upon viral infection,and downregulation of BmLEB3 using RNA interference promoted BmCPV replication in the midgut of B.mori.These results suggest that viral immune evasion and active host resistance coexist in BmCPV-infected silkworms.We reveal the richness of cellular diversity in the midgut of B.mori larvae by single-nucleus RNA sequencing analysis and provide new insights into the complex interactions between the host and the virus at the single-cell level.
基金supported by grants from the Taishan Scholar Foundation of Shandong Province(tsqn202103161)the Natural Science Foundation of Shandong Province(ZR202103010405)+3 种基金the Key R&D Program of Shandong Province,China(ZR202211070163)the Foundation of President of the Peking University Institute of Advanced Agricultural Sciences(ZR202211070163)the Peanut Seed Industry Project in Shandong Province,China(2022LZGC007)to X.LIt was also funded by the National Natural Science Foundation of China(NSFC)Key Program(32230006)to X.W.D.
文摘Peanut(Arachis hypogaea L.)is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground.Subterranean fruit-pod development,which significantly affects peanut production,involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues.To investigate the molecular mechanisms that underlie peanut fruitpod development,we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing(snRNA-seq)and single-nucleus assay for transposase-accessible chromatin with sequencing(snATAC-seq)data at the single-cell level.We identified distinct cell types,such as meristem,embryo,vascular tissue,cuticular layer,and stele cells within the shell wall.These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development.snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA.For instance,we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells,indicating an essential role for the vascular cells in peg gravitropism.Overall,our single-nucleus analysis provides comprehensive and novel information on specific cell types,gene expression,and chromatin accessibility during the early stages of fruit-pod development.This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.
基金This work was supported by a grant to M.L.from the U.S.National Science Foundation(IOS#1339194 and 1854326)by grants to J.S.from the U.S.National Science Foundation(IOS#1923589)+1 种基金the Department of Energy(DE-SC0020358)by the Center for Plant Science Innovation,and by the Department of Agronomy and Horticulture at the University of Nebraska-Lincoln.
文摘Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.
基金supported by the National Key Research and Development Program of China (Grant Nos.2022YFA1103700,2020YFA0804000,2020YFA0112200,2021YFF1201000,2022YFA1103800,2021YFA1101401,the STI2030-Major Projects-2021ZD0202400)the National Natural Science Foundation of China (Grant Nos.92049116,81921006,82125011,92149301,92168201,91949209,92049304,32121001,82192863,82122024,82071588,32000500,82271600)+9 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16000000)CAS Project for Young Scientists in Basic Research (YSBR-076,YSBR-012)the Program of the Beijing Natural Science Foundation (Z190019)the Pilot Project for Public Welfare Development and Reform of Beijing-affiliated Medical Research Institutes (No.11000022T000000461062)Youth Innovation Promotion Association of CAS (E1CAZW0401,2023092,2022083)Young Elite Scientists Sponsorship Program by CAST (YESS20200012,YESS20210002)the Informatization Plan of Chinese Academy of Sciences (CAS-WX2021SF-0301,CAS-WX2022SDC-XK14,CAS-WX2021SF-0101)New Cormerstone Science Foundation through the XPLORER PRIZE (2021-1045)Excellent Young Talents Program of Capital Medical University (No.12300927)Excellent Young Talents Training Program for the Construction of Beijing Municipal University Teacher Team (BPHR202203105).
文摘Aging increases the risk ofliver diseases and systemic susceptibility to aging-related diseases.However,cell type-specific changes and the underlying mechanism of liver aging in higher vertebrates remain incompletely characterized.Here,we constructed the first single-nucleus transcriptomic landscape of primate liver aging,in which we resolved cell type-specific gene expression fluctuation in hepatocytes across three liver zonations and detected aberrant cell-cell interactions between hepatocytes and niche cells.Upon in-depth dissection of this rich dataset,we identifed impaired lipid metabolism and upregulation of chronic inflammation-related genes prominently associated with declined liver functions during aging.In particular,hyperactivated sterol regulatory element-binding protein(SREBP)signaling was a hallmark of the aged liver,and consequently,forced activation of SREBP2 in human primary hepatocytes recapitulated in vivo aging phenotypes,manifesting as impaired detoxification and accelerated cellular senescence.This study expands our knowledge of primate liver aging and informs the development of diagnostics and therapeutic interventions for liver aging and associated diseases.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA16000000)the National Natural Science Foundation of China(Nos.82071588,81921006,82125011,92149301,92168201,92049116,32121001,82192863,91949209,92049304,82122024,82001477,31900523,81861168034,32000500,82271600,82201714)+10 种基金the National Key Research and Development Program of China(Nos.2018YFC2000100,2020YFA0804000,2018YFA0107203,2020YFA0112200,2021YFF1201005,2021ZD0202401,2018YFC2000400,2020YFA0113400,2021YFE0111800,2022YFA1103700)the Program of the Beijing Natural Science Foundation(No.Z190019)K.C.Wong Education Foundation(Nos.GJTD-2019-06,GJTD-2019-08)Beijing Medical Research(2021-8)the Pilot Project for Public Welfare Development and Reform of Beijing-affliated Medical Research Institutes(No.11000022T000000461062)Young Elite Scientists Sponsorship Program by CAST(Nos.YESS20200012,YESS20210002)CAS Project for Young Scientists in Basic Research(No.YSBR-076,YSBR-012,YSBR-036)Youth Innovation Promotion Association of CAS(Nos.E1CAZW0401,2020085,2022083)the Informatization Plan of Chinese Academy of Sciences(Nos.CAS-WX2022SDC-XK14,CASWX2021SF-0301,CAS-WX2021SF-0101)the Tencent Foundation(No.2021-1045),CAMS Innovation Fund for Medical Sciences(No.2021-12M-1-050)the Fellowship of China Postdoctoral Science Foundation(2022M712216).
文摘Age-dependent loss of skeletal muscle mass and function is a feature of sarcopenia,and increases the risk of many aging-related metabolic diseases.Here,we report phenotypic and single-nucleus transcriptomic analyses of non-human primate skeletal muscle aging.A higher transcriptional fluctuation was observed in myonuclei relative to other interstitial cell types,indicating a higher susceptibility of skeletal muscle fiber to aging.We found a downregulation of Foxo3 in aged primate skeletal muscle,and identi-fied FOxo3 as a hub transcription factor maintaining skeletal muscle homeostasis.Through the establishment of a complementary experimental pipeline based on a human pluripotent stem cell-derived myotube model,we revealed that silence of Foxo3 accelerates human myotube senescence,whereas genetic activation of endogenous FOxO3 alleviates human myotube aging.Altogether,based on a combination of monkey skeletal muscle and human myotube aging research models,we unraveled the pivotal role of the FOxO3 in safeguarding primate skeletal muscle from aging,providing a comprehensive resource for the development of clinical diagnosis and targeted therapeutic interventions against human skeletal muscle aging and the onset of sarcopenia along with aging-relateddisorders.
基金supported by the National Key Research-and Development Program of China(2022YFA1103700)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA160000c0)+9 种基金the National Key Research and Development Program of China(2020YFAOB04000,2020YFA0112200,2021YFF1201005,2022YFA1103B00),the STI2030-Major Projects(20212D0202400)the National Natural Science Foundation af China(Grant Nos 81921006,82125011,92149301,9216820191949209,92049304,92049116,32121001,82192863,82122024.82071588,32000500,31900523,82201714,82271600,82201727)CAS Project for Young Scientists in Basic Research(YSBR-076,YSBR-012)the Program of the Beijing Natural Science Foundation(Z190019)China Postdoctoral Science Foundation(2022M712216)кC.Wong Education Foundation(GJTD-2019-06 GTD-2019-08)the lot Proje for Publie Welfare Development and Reform of Beijing-affiliated Medical Restarch Institutes(11000022T000000461062)Young Elte Scientists Sponsorship Progran by CAST YESS20000012,YES520210002)Yout Innovation Promotion Association of CAS(E1CAZWO-401,2022083)the Tencent Foundation(2021-1045)the Plan of Chinese Academy of Sciences(CAS-WX2021SF-0301,CAS-WX2021SF-0101,CAS-WX2022SDC-XK14)Strategic Collaborative Research Program of the Ferring Institute of ReproductiveMedicine,Grant No.FIRMC180305。
文摘The testis is pivotal for male reproduction,and its progressive functional decline in aging is associated with infertility.However,the regulatory mechanism underlying primate testicular aging remains largely elusive.Here,we resolve the aging-related cellular and molecular alterations of primate testicular aging by establishing a single-nucleus transcriptomic atlas.Gene-expression patterns along the spermatogenesis trajectory revealed molecular programs associated with attrition of spermatogonial stem cell reservoir,disturbed meiosis and impaired spermiogenesis along the sequential continuum.Remarkably,Sertoli cell was identified as the cell type most susceptible to aging,given its deeply perturbed age-associated transcriptional profiles.Concomitantly,downregulation of the transcription factor Wilms'Tumor 1(WTi),essential for Sertoli cell homeostasis,was associated with accelerated cellular senescence,disrupted tight junctions,and a compromised cell identity signature,which altogether may help create a hostile microenvironment for spermatogenesis.Collectively,our study depicts in-depth transcriptomic traits of non-human primate(NHP)testicular aging at single-cell resolution,providing potential diagnostic biomarkers and targets for therapeutic interventions against testicular aging and age-related male reproductive diseases.
基金supported by the National Key Research and Development Program of China(2018YFC2000100)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16000000)+6 种基金the National Natural Science Foundation of China(81921006,92149301,92168201,82125011,91949209,92049304,92049116,32121001,82192863,82122024,82071588,81901432,32000510,81861168034,32000500,81901433,81870228,81922027)the National Key Research and Development Program of China(2020YFA0804000,2020YFA0113400,2018YFA0107203,2020YFA0112200,2021YFF1201005,2021ZD0202401)the Program of the Beijing Natural Science Foundation(Z190019,JQ20031)K.C.Wong Education Foundation(GJTD-2019-06,GJTD-2019-08),Young Elite Scientists Sponsorship Program by CAST(YESS20200012,YESS20210002)The Pilot Project for Public Welfare Development and Reform of Beijing-affliated Medical Research Institutes(11000022T000000461062)CAS Project for Young Scientists in Basic Research(YSBR-012),Youth Innovation Promotion Association of CAS(E1CAZW0401,2022083)the Informatization Plan of Chinese Academy of Sciences(CAS-WX2021SF-0301,CASWX2022SDC-XK14),the Tencent Foundation(2021-1045).
文摘Aging poses a major risk factor for cardiovascular diseases,the leading cause of death in the aged population.However,the cell type-specific changes underlying cardiac aging are far from being clear.Here,we performed single-nucleus RNA-sequencing analysis of left ventricles from young and aged cynomolgus monkeys to define cell composition changes and transcriptomic alterations across different cell types associated with age.We found that aged cardiomyocytes underwent a dramatic loss in cell numbers and profound fluctuations in transcriptional profles.Via transcription regulatory network analysis,we identified FOxP1,a core transcription factor in organ development,as a key downregulated factor in aged cardiomyocytes,concomitant with the dysregulation of FoxP1 target genes associated with heart function and cardiac diseases.Consistently,the deficiency of FOxP1 led to hypertrophic and senescent phenotypes in human embryonic stem cell-derived cardiomyocytes.Altogether,our findings depict the celiular and molecular landscape of ventricular aging at the single-cell resolution,and identify drivers for primate cardiac aging and potential targets for intervention against cardiac aging and associated diseases.
文摘Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis,a worldwide prevalent inflammatory disease.However,a systematic characterization and comprehensive understanding of the regulatory mechanism underlying gingival aging is still lacking.Here,we systematically dissected the phenotypic characteristics of gingiva during aging in primates and constructed the first single-nucleus transcriptomic landscape of gingival aging,by which a panel of cell type-specific signatures were elucidated.Epithelial cells were identified as the most affected cell types by aging in the gingiva.Further analyses pinpointed the crucial role of YAP in epithelial self-renew and homeostasis,which declined during aging in epithelial cells,especially in basal cells.The decline of YAP activity during aging was confrmed in the human gingival tissues,and downregulation of YAP in human primary gingival keratinocytes recapitulated the major phenotypic defects observed in the aged primate gingiva while overexpression of YAP showed rejuvenation effects.Our work provides an in-depth understanding of gingival aging and serves as a rich resource for developing novel strategies to combat aging-associated gingival diseases,with the ultimate goal of advancing periodontal health and promoting healthy aging.
基金supported by the Shenzhen Fundamental Research Program,China(No.JCYJ20180306173518936)Sanming Project of Medicine in Shenzhen,China(No.SZSM201612055)+1 种基金HKU-SZH Fund for Shenzhen Key Medical Discipline(China)(No.SZXK2020084)China National GeneBank(CNGB).
文摘To uncover the role of satellite cells(SCs)in paravertebral muscle development and aging,we constructed a single-nucleus transcriptomic atlas of mouse paravertebral muscle across seven timepoints spanning the embryo(day 16.5)to old(month 24)stages.Eight cell types,including SCs,fast muscle cells,and slow muscle cells,were identified.An energy metabolism-related gene set,TCA CYCLE IN SENESCENCE,was enriched in SCs.Forty-two skeletal muscle disease-related genes were highly expressed in SCs and exhibited similar expression patterns.Among them,Pdha1 was the core gene in the TCA CYCLE IN SENESCENCE;Pgam2,Sod1,and Suclg1 are transcription factors closely associated with skeletal muscle energy metabolism.Transcription factor enrichment analysis of the 42 genes revealed that Myod1 and Mef2a were also highly expressed in SCs,which regulated Pdha1 expression and were associated with skeletal muscle development.These findings hint that energy metabolism may be pivotal in SCs development and aging.Three ligand-receptor pairs of extracellular matrix(ECM)-receptor interactions,Lamc1-Dag1,Lama2-Dag1,and Hspg2-Dag1,may play a vital role in SCs interactions with slow/fast muscle cells and SCs self-renewal.Finally,we built the first database of a skeletal muscle single-cell transcriptome,the Musculoskeletal Cell Atlas(http://www.mskca.tech),which lists 630,040 skeletal muscle cells and provides interactive visualization,a useful resource for revealing skeletal muscle cellular heterogeneity during development and aging.Our study could provide new targets and ideas for developing drugs to inhibit skeletal muscle aging and treat skeletal muscle diseases.
