Adolescent depression is increasingly recognized as a serious mental health disorder with distinct clinical and molecular features.Using single-nucleus RNA sequencing,we identified cell-specific transcriptomic changes...Adolescent depression is increasingly recognized as a serious mental health disorder with distinct clinical and molecular features.Using single-nucleus RNA sequencing,we identified cell-specific transcriptomic changes in the nucleus accumbens(NAc),particularly in astrocytes,of adolescent macaques exhibiting depressive-like behaviors.The level of diacylglycerol kinase beta was significantly reduced in neurons and glial cells of depressed macaques,while FKBP5 levels increased in glial cells.Disruption of GABAergic synapses and disruption of D-glutamine and D-glutamate metabolism were linked to depressive phenotypes in medium spiny neurons(MSNs)and subtypes of astrocytes.Communication pathways between astrocytes and D1/D2-MSNs were also disrupted,involving factors like bone morphogenetic protein-6 and Erb-B2 receptor tyrosine kinase-4.Bulk transcriptomic and proteomic analyses corroborated these findings,and FKBP5 upregulation was confirmed by qRT-PCR,western blotting,and immunofluorescence in the NAc of rats and macaques with chronic unpredictable mild stress.Our results highlight the specific roles of different cell types in adolescent depression in the NAc,offering potential targets for new antidepressant therapies.展开更多
Background Thermogenic adipose tissue,both beige and brown,experiences whitening as animals are exposed to warmth and age,but the potential mechanisms are not fully understood.In this study,we employed singlenucleus R...Background Thermogenic adipose tissue,both beige and brown,experiences whitening as animals are exposed to warmth and age,but the potential mechanisms are not fully understood.In this study,we employed singlenucleus RNA-seq to construct a cell atlas during whitening progression and identified the characteristics of thermogenic adipocytes.Results Our histological studies and bulk transcriptome gene expression analysis confirmed that both perirenal and omental adipose tissues(pAT and oAT)exhibited progressive whitening in goats.Compared to the classic brown adipocytes in mice,goat thermogenic adipocytes were more closely related in gene expression patterns to human beige adipocytes,which was also confirmed by adipocyte type-and lineage-specific marker expression analysis.Furthermore,trajectory analysis revealed beige-and white-like adipocytes deriving from a common origin,coexisting and undergoing the transdifferentiation.In addition,differences in gene expression profiles and cell communication patterns(e.g.,FGF and CALCR signaling)between oAT and pAT suggested a lower thermogenic capacity of oAT than that of pAT.Conclusions We constructed a cell atlas of goat pAT and oAT and descripted the characteristics of thermogenic adipocytes during whitening progression.Altogether,our results make a significant contribution to the molecular and cellular mechanisms behind the whitening of thermogenic adipocytes,and providing new insights into obesity prevention in humans and cold adaptation in animals.展开更多
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 functi...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.展开更多
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 ...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.展开更多
Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is esse...Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change.An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ developmentrelated genes and thereby help us to understand organ developmental processes.Here,we constructed a comprehensive,integrated transcriptomic atlas for soybeans,integrating bulk RNA sequencing(RNAseq)datasets from 314 samples across the soybean life cycle,along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs:root,nodule,shoot apex,leaf,and stem.Investigating genes related to organ specificity,blade development,and nodule formation,we demonstrate that the atlas has robust power for exploring key genes involved in organ formation.In addition,we developed a user-friendly panoramic database for the transcriptomic atlas,enabling easy access and queries,which will serve as a valuable resource to significantly advance future soybean functional studies.展开更多
Alzheimer’s disease(AD)is the leading cause of dementia worldwide.Traditionally,pathological studies have concentrated on the abnormal buildup of amyloid b(Ab)plaques and neurofibrillary tangles(NFTs),which arise fro...Alzheimer’s disease(AD)is the leading cause of dementia worldwide.Traditionally,pathological studies have concentrated on the abnormal buildup of amyloid b(Ab)plaques and neurofibrillary tangles(NFTs),which arise from the excessive phosphorylation of tau proteins in the brain1,2.Despite extensive research.展开更多
Spinal cord injury(SCI)triggers a complex cascade of cellular and molecular responses,yet the complex cellular communication remains incompletely understood.This study explored how intercellular communication contribu...Spinal cord injury(SCI)triggers a complex cascade of cellular and molecular responses,yet the complex cellular communication remains incompletely understood.This study explored how intercellular communication contributes to the activation of microglia and astrocytes after SCI.Here,we integrated four datasets using single-cell RNA sequencing(scRNA-seq)or single-nucleus RNA sequencing(snRNA-seq)and constructed a comprehensive cellular atlas of the injured spinal cord.Transcriptomic changes in microglia and astrocytes were analyzed.We identified CD44 as a key receptor in SPP1-mediated microglial activation,which represented a subpopulation involved in inflammatory response in microglia.We defined a gliogenesis subpopulation of astrocytes that emerged at 3 dpi,which became the predominant cell type in the injured spinal cord.These astrocytes highly expressed the Nucleolin(Ncl)gene and interacted via the Pleiotrophin(Ptn)signaling pathway,which is associated with astrocyte proliferation.To validate these findings,we utilized a crush injury model.Flow cytometry of isolated microglia and astrocytes confirmed the upregulation of CD44 in microglia and NCL in astrocytes in response to SCI.In vivo results confirmed that the CD44 positive microglia accumulated and PLA results further confirmed the combination of SPP1 with CD44.In parallel,the upregulated expression of NCL in astrocytes facilitated their proliferation,underscoring the role of the NCL receptor in gliogenesis after SCI.In vitro validation demonstrated that exogenous SPP1 upregulates CD44 expression by promoting the phosphorylation of p65 and activating the NF-κB pathways in BV2 microglia,and that high expression of IL-6 indicates the activation of inflammation.PTN may enhance NCL expression and thus facilitates astrocyte proliferation.Collectively,our study identified key receptors that regulated inflammation responses and gliogenesis.Targeting the CD44 and NCL receptors may provide promising therapeutic strategies to modulate inflammation and promote tissue repair after SCI.展开更多
Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission ...Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, we meticulously constructed a transcriptomic atlas through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole. We identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members of the cytokinin oxidase/dehydrogenase (CKX) gene family, was further characterized as a key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as “Pioneer” activator, and GhMYB108, acting as “Successor” activator, orchestrate a sequential modulation of GhWRKY70/GhMYB108–GhRLF1–CTK (cytokinin) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines that exhibit rapid leaf falling and require less defoliant but show unaffected cotton yield were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter, proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability.展开更多
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...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.展开更多
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 compri...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.展开更多
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 co...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.展开更多
基金supported by STI2030-Major Projects(2022ZD0212900)the Joint Project of Chongqing Municipal Science and Technology Bureau and Chongqing Health Commission(2023CCXM003)+4 种基金the National Key Research and Development Program of China(2017YFA0505700)the National Natural Science Foundation of China(82271565 and 82301714)the China Postdoctoral Science Foundation(2023TQ0398,GZB20230916,2023MD734124)the Natural Science Foundation of Chongqing,China(CSTB2023NSCQ-BHX0106)the Postdoctoral Innovation Talents Support Program of Chongqing,China(2208013341918508).
文摘Adolescent depression is increasingly recognized as a serious mental health disorder with distinct clinical and molecular features.Using single-nucleus RNA sequencing,we identified cell-specific transcriptomic changes in the nucleus accumbens(NAc),particularly in astrocytes,of adolescent macaques exhibiting depressive-like behaviors.The level of diacylglycerol kinase beta was significantly reduced in neurons and glial cells of depressed macaques,while FKBP5 levels increased in glial cells.Disruption of GABAergic synapses and disruption of D-glutamine and D-glutamate metabolism were linked to depressive phenotypes in medium spiny neurons(MSNs)and subtypes of astrocytes.Communication pathways between astrocytes and D1/D2-MSNs were also disrupted,involving factors like bone morphogenetic protein-6 and Erb-B2 receptor tyrosine kinase-4.Bulk transcriptomic and proteomic analyses corroborated these findings,and FKBP5 upregulation was confirmed by qRT-PCR,western blotting,and immunofluorescence in the NAc of rats and macaques with chronic unpredictable mild stress.Our results highlight the specific roles of different cell types in adolescent depression in the NAc,offering potential targets for new antidepressant therapies.
基金supported by the National Key Research and Development Programme of China(grant number 2021YFF1001000)the National Natural Science Foundation of China(grant number 32170627)+1 种基金the Postdoctoral Innovative Talents Support Program of China(grant number BX20200282)the Natural Science Foundation of Sichuan Province(grant number 23NSFSC1804).
文摘Background Thermogenic adipose tissue,both beige and brown,experiences whitening as animals are exposed to warmth and age,but the potential mechanisms are not fully understood.In this study,we employed singlenucleus RNA-seq to construct a cell atlas during whitening progression and identified the characteristics of thermogenic adipocytes.Results Our histological studies and bulk transcriptome gene expression analysis confirmed that both perirenal and omental adipose tissues(pAT and oAT)exhibited progressive whitening in goats.Compared to the classic brown adipocytes in mice,goat thermogenic adipocytes were more closely related in gene expression patterns to human beige adipocytes,which was also confirmed by adipocyte type-and lineage-specific marker expression analysis.Furthermore,trajectory analysis revealed beige-and white-like adipocytes deriving from a common origin,coexisting and undergoing the transdifferentiation.In addition,differences in gene expression profiles and cell communication patterns(e.g.,FGF and CALCR signaling)between oAT and pAT suggested a lower thermogenic capacity of oAT than that of pAT.Conclusions We constructed a cell atlas of goat pAT and oAT and descripted the characteristics of thermogenic adipocytes during whitening progression.Altogether,our results make a significant contribution to the molecular and cellular mechanisms behind the whitening of thermogenic adipocytes,and providing new insights into obesity prevention in humans and cold adaptation in animals.
基金the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medi-cine(Grant No.:ZYYCXTD-D-202207)the National Natural Science Foundation of China(Grant Nos.:82270304,81774050,and 81901526)+1 种基金the Tianjin Special Project of New Generation Artificial Intelligence Technology(Project No.:18ZXZNSY00260)the Ministry of Education of People's Republic of China“Program for Innovative Research Team in University”(Project No.:IRT_16R54).
文摘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.
基金supported by the National Key R&D Program of China (2020YFA0509500,2021YFD1301101 and 2021YFA0805903)the Sichuan Science and Technology Program+3 种基金(2023YFN0088 and 2021YFYZ0030)the National Center of Technology Innovation for Pigs (SCCXTD-2023-08)the National Natural Science Foundation of China (32272837 and 32225046)Tianfu Agricultural Master Project。
文摘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.
基金supported by the National Natural Science Foundation of China(grant no.32388201)the National Key Research and Development Program of China(2022YFF1003301,and 2023YFF1000101)+1 种基金the Taishan Scholars Programthe Xplorer Prize.
文摘Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change.An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ developmentrelated genes and thereby help us to understand organ developmental processes.Here,we constructed a comprehensive,integrated transcriptomic atlas for soybeans,integrating bulk RNA sequencing(RNAseq)datasets from 314 samples across the soybean life cycle,along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs:root,nodule,shoot apex,leaf,and stem.Investigating genes related to organ specificity,blade development,and nodule formation,we demonstrate that the atlas has robust power for exploring key genes involved in organ formation.In addition,we developed a user-friendly panoramic database for the transcriptomic atlas,enabling easy access and queries,which will serve as a valuable resource to significantly advance future soybean functional studies.
基金supported by the National Natural Science Foundation of China(Grant No.32271220).
文摘Alzheimer’s disease(AD)is the leading cause of dementia worldwide.Traditionally,pathological studies have concentrated on the abnormal buildup of amyloid b(Ab)plaques and neurofibrillary tangles(NFTs),which arise from the excessive phosphorylation of tau proteins in the brain1,2.Despite extensive research.
基金Basic and Applied Basic Research Fund of Guangdong Province(2023B1515120077)Basic Research Project of Shenzhen Science and Technology Innovation Commission(JCYJ20210324123001003,JCYJ20220530144801003,JCYJ20240813150406009)+2 种基金Natural Science Foundation of Guangdong Province[2024A1515012364,2025A1515010926]National Natural Science Foundation of China(Grant No.82272534,82071362)Shenzhen Key Laboratory of Bone Tissue Repair and Translational Research(NO.ZDSYS20230626091402006).
文摘Spinal cord injury(SCI)triggers a complex cascade of cellular and molecular responses,yet the complex cellular communication remains incompletely understood.This study explored how intercellular communication contributes to the activation of microglia and astrocytes after SCI.Here,we integrated four datasets using single-cell RNA sequencing(scRNA-seq)or single-nucleus RNA sequencing(snRNA-seq)and constructed a comprehensive cellular atlas of the injured spinal cord.Transcriptomic changes in microglia and astrocytes were analyzed.We identified CD44 as a key receptor in SPP1-mediated microglial activation,which represented a subpopulation involved in inflammatory response in microglia.We defined a gliogenesis subpopulation of astrocytes that emerged at 3 dpi,which became the predominant cell type in the injured spinal cord.These astrocytes highly expressed the Nucleolin(Ncl)gene and interacted via the Pleiotrophin(Ptn)signaling pathway,which is associated with astrocyte proliferation.To validate these findings,we utilized a crush injury model.Flow cytometry of isolated microglia and astrocytes confirmed the upregulation of CD44 in microglia and NCL in astrocytes in response to SCI.In vivo results confirmed that the CD44 positive microglia accumulated and PLA results further confirmed the combination of SPP1 with CD44.In parallel,the upregulated expression of NCL in astrocytes facilitated their proliferation,underscoring the role of the NCL receptor in gliogenesis after SCI.In vitro validation demonstrated that exogenous SPP1 upregulates CD44 expression by promoting the phosphorylation of p65 and activating the NF-κB pathways in BV2 microglia,and that high expression of IL-6 indicates the activation of inflammation.PTN may enhance NCL expression and thus facilitates astrocyte proliferation.Collectively,our study identified key receptors that regulated inflammation responses and gliogenesis.Targeting the CD44 and NCL receptors may provide promising therapeutic strategies to modulate inflammation and promote tissue repair after SCI.
基金supported by funding from the National Key Project of Research and the Development Plan of China(2021YFF1000103)the National Natural Science Foundation of China(32171942)The development fund for Xinjiang talents XL,and the Agricultural GG Project of Xinjiang Production and Construction Corps(NYHXGG,2023AA102).
文摘Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, we meticulously constructed a transcriptomic atlas through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole. We identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members of the cytokinin oxidase/dehydrogenase (CKX) gene family, was further characterized as a key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as “Pioneer” activator, and GhMYB108, acting as “Successor” activator, orchestrate a sequential modulation of GhWRKY70/GhMYB108–GhRLF1–CTK (cytokinin) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines that exhibit rapid leaf falling and require less defoliant but show unaffected cotton yield were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter, proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability.
基金supported by the CAS Project for Young Scientists in Basic Research(YSBR-011)National Key Research and Development Program of China(2021YFF1000103)。
文摘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.
基金This work was supported by the National Key Research and Development Program of China(2021YFC2700400,2018YFC1004303)the National Natural Science Foundation of China(31988101,82201798,82192874,82071606,82101707)+3 种基金CAMS Innovation Fund for Medical Sciences(2021-I2M-5-001)Shandong Provincial Key Research and Development Program(2020ZLYS02)the Taishan Scholars Program of Shandong Province(ts20190988)the Fundamental Research Funds of Shandong University.
文摘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.
基金This work was supported by the National Key R&D Program of China(2020YFA0803604)the National Natural Science Foundation of China,Key Program(82130024)for funding.
文摘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.
