Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mecha...Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies.Previous studies primarily focused on neuronal death,potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury.To address these gaps,we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations,altered cell communication networks,and novel molecular mechanisms involved in post-cardiac arrest brain injury.In this study,we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation,and from sham control pigs.Sequencing results revealed changes in the proportions of different cell types,suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils.These results were validated through western blotting,quantitative reverse transcription-polymerase chain reaction,and immunofluorescence staining.We also identified and validated a unique subcluster of activated microglia with high expression of S100A8,which increased over time following cardiac arrest.This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins.Additionally,we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes.Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin,driving pro-inflammatory microglial polarization.Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus,offering potential novel targets for neuroprotection and repair following cardiac arrest.展开更多
The triple transgenic mouse model of Alzheimer’s disease(3×Tg-AD)is a widely used model that exhibits region-dependent patterns of progressive amyloid-βand tau pathology.Although structural brain abnormalities ...The triple transgenic mouse model of Alzheimer’s disease(3×Tg-AD)is a widely used model that exhibits region-dependent patterns of progressive amyloid-βand tau pathology.Although structural brain abnormalities on magnetic resonance imaging have been observed in 3×Tg-AD mice at later disease stages(>12 months)and as early as 2 months,few studies have investigated changes in these mice during the stage with extensive amyloid-βdeposition and onset of tau pathology(around 9 months).This study aimed to assess brain morphometry and microstructure alterations in 9 month-old 3×Tg-AD mice to better understand the neural mechanisms underlying these specific pathological features.Voxel-based analyses were employed on T2-weighted and diffusion tensor imaging to identify differences between 3×Tg-AD and control mice.Compared with controls,3×Tg-AD mice exhibited lower gray matter volume in several regions including both hippocampal regions,the right thalamus,the left caudoputamen,and the cortex.Reduced white matter volume was observed in fiber tracts including the corpus callosum,internal capsule,stria terminalis,and olfactory tract.Whole-brain diffusion tensor imaging analysis revealed a significant decrease in fractional anisotropy and an increase in both radial and mean diffusivity within the left dentate gyrus of the hippocampal region and right striatum-like amygdala nuclei,with no significant difference in axial diffusivity.Correlation analyses demonstrated significant associations between behavioral performance measures,with both gray and white matter volumes within regions showing significant morphometric differences.Notably,behavioral performance also exhibited significant correlations with diffusion tensor imaging measures particularly within the left dentate gyrus of the hippocampal region and right striatum-like amygdala nuclei.Immunofluorescence analysis confirmed increased amyloid-βplaques and p-Tau protein expression in the hippocampal regions of 3×Tg-AD mice,which corroborated the magnetic resonance imaging findings.Transcriptome analysis in hippocampus tissue identified 1389 differentially expressed genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that numerous differentially expressed genes were enriched in biological processes relevant to synapse structure,cognition,learning,and memory,with particular emphasis on Wnt and mitogen-activated protein kinase signaling pathways.Collectively,these findings suggest that intricate anatomical and microstructural alterations occur in 3×Tg-AD model mice at the onset of pathology around 9 months,potentially driven by gene expression alterations.Moreover,our results support the potential utility of brain volume and diffusion metrics as biomarkers for Alzheimer’s disease pathology,which could have significant implications for clinical diagnosis of Alzheimer’s disease patients.展开更多
Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA...Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers of spinal cord injury.展开更多
Objective:Leucine-rich alpha-2 glycoprotein 1(Lrg1)could regulate diverse cells in cerebral ischemiareperfusion.Our study seeks to uncover Lrg1’s impact on endothelial cell heterogeneity via differentiation pathways ...Objective:Leucine-rich alpha-2 glycoprotein 1(Lrg1)could regulate diverse cells in cerebral ischemiareperfusion.Our study seeks to uncover Lrg1’s impact on endothelial cell heterogeneity via differentiation pathways and transcription factors.Method:The CSOmap model measured cell-to-brain-center distances using single-cell RNA sequencing(scRNA-seq)data in middle cerebral artery occlusion reperfusion(MCAO/R).Monocle2 mapped endothelial differentiation paths.Gene set enrichment analysis(GSEA)analyzed endothelial subcluster variations.Database searches revealed a zinc finger MIZ-type containing 1 protein-frizzled 3(Zmiz1-Fzd3)promoter interaction.Endothelial cells were transfected with a Fzd3 promoter-luciferase plasmid.Polymerase chain reaction(PCR)and western blotting assessed MCAO/R or Zmiz1 overexpression effects on Fzd3-related mRNA and proteins.A retroviral vector carrying Zmiz1 was injected into the brains of mice to study its effect on Fzd3.Result:Lrg1−/−mice exhibited elevated cell adhesion proteins and decreased microvascular leakage after MCAO/R.CSOmap showed widened astrocyte spacing in thesemice.RSS revealed Zmiz1 overexpression inMCAO/R+Lrg1−/−mice.MCAO/R and pcDNA3-Zmiz1 transfection both enhanced luciferase activity with Fzd3,indicating Zmiz1 binding to Fzd3.Retroviral Zmiz1 injection or knockdown disrupted ischemic brain tight junctions,highlighting Zmiz1’s key role in blood-brain barrier protection,likely through Fzd3 pathway modulation.Conclusion:The findings indicate Lrg1 knockout induces endothelial differentiation by activating Zmiz1,which is crucial for maintaining blood-brain barrier function,possibly via modulating the Fzd3 pathway.展开更多
Objective Adaptive immune responses play a critical role in the pathogenesis of amyotrophic lateral sclerosis(ALS).In this study,we investigated the functional mechanisms of T cell subtypes and assessed the causal lin...Objective Adaptive immune responses play a critical role in the pathogenesis of amyotrophic lateral sclerosis(ALS).In this study,we investigated the functional mechanisms of T cell subtypes and assessed the causal links between CD4+cytotoxic T cell-related genes and ALS risk.Methods Single-cell RNA sequencing(scRNA-seq)of peripheral blood mononuclear cells(PBMCs)from patients with ALS and healthy controls(HC)was used to identify differentially expressed genes(DEGs)in CD4+cytotoxic T cells.Comprehensive analyses of CD4+cytotoxic T cells,including pseudotemporal trajectory,intercellular communication,and metabolic pathway analysis,were performed.Mendelian randomization(MR)analysis evaluated the causal effects of DEGs on ALS risk,with validation using independent genome-wide association study(GWAS)data.Expression patterns of the causal genes were further verified using scRNA-seq,bulk-seq,and clinical samples.Results CD4+cytotoxic T cells were significantly expanded in patients with ALS.The upregulated genes S100A6,SERPINB6,SMAD7,and TPST2 were positively correlated with ALS susceptibility,whereas DIP2A showed a protective association.Conclusion S100A6,SERPINB6,SMAD7,TPST2,and DIP2A were identified as causal genes and potential therapeutic targets in ALS,implicating CD4+cytotoxic T cells in the disease mechanisms.Further studies targeting these genes and neuroinflammatory pathways are warranted.展开更多
OBJECTIVE:To investigate Acupuncture-herb therapy modulates gut microbiota in abdominal obesity.METHODS:A randomized controlled trial was designed in accordance with standard protocols.Abdominally obese subjects were ...OBJECTIVE:To investigate Acupuncture-herb therapy modulates gut microbiota in abdominal obesity.METHODS:A randomized controlled trial was designed in accordance with standard protocols.Abdominally obese subjects were randomized into four groups:A2(Control):double placebo,A1(Needle):press needle+placebo herb,A3(herb):herbal medicine(Huatan Lishi Fang化痰利湿方)+placebo needle,A4(Combination):press needle+herbal medicine.After 12 weeks of treatment,groups were relabeled B1-B4.Weight,waist circumference,and body mass index were measured monthly.Gut microbiota was analyzed via 16S rRNA sequencing for diversity and abundance.RESULTS:Combined needle-herb therapy significantly reduced waist circumference(P<0.05).All treatments altered gut microbiota composition.The combination group showed significant changes in diversity(Chao1,Shannon,Simpson;P<0.05).Needle therapy increased Bacteroidia;herbs reduced Lachnospiraceae and Megamonas.All results were significant(P<0.05).CONCLUSION:Combined needle-herb treatment modulated 25 key gut flora across multiple taxonomic levels in abdominal obesity.It reduced Firmicutes and Bacteroidota.Bacteroidota,Actinobacteriota,and Prevotellaceae may suppress obesity,whereas Proteobacteria,Lachnospiraceae,and Megamonas may promote it.The combination specifically altered Bacteroidaceae,Lachnospiraceae,Bacteroidia,and Megamonas.展开更多
sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search.Here,we b...sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search.Here,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than RNAcentral.The new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques.It also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam.The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on MSAs.MARS is accessible at https://ngdc.cncb.ac.cn/omix/release/OMIX003037,and RNAcmap3 is accessible at http://zhouyq-lab.szbl.ac.cn/download/.展开更多
Objective:Osteoarthritis(OA) is a progressive joint disease characterized by degeneration and de struction of articular cartilage.Arctiin(ARC) has been shown in many studies to have potential anti-inflammatory,anti-ap...Objective:Osteoarthritis(OA) is a progressive joint disease characterized by degeneration and de struction of articular cartilage.Arctiin(ARC) has been shown in many studies to have potential anti-inflammatory,anti-apoptotic,and antioxidant effects in various diseases.However,the mechanism by which ARC exerts its protective effects in OA is not fully understood.Here,we explore the mechanism by which ARC plays its protective role in OA.Materials and Methods:Mouse chondrocytes were isolated and characterized through toluidine blue staining and collagen Ⅱ immunofluorescence labeling.A mouse-based experimental model was developed to induce chondrocyte inflammation through Interleukin-1β(IL-1β).Sub sequently,ARC was administe red in various doses to mitigate this inflammation.Techniques such as biochemical assay s,Enzyme-linked immunosorbent assay,quantitative real-time polymerase chain re action(qRT-PCR),Western blotting,and immunofluorescence labeling were employed to detect changes in nitric oxide(NO),lactate dehydrogenase(LDH),inflammatory markers,and components of the cartilage matrix in chondrocytes.RNA-sequencing(RNA-seq) was utilized to explore variations in gene expression among chondrocyte s acro ss different groups.The genes and signaling pathways that were identified underwe nt analysis through Gene Ontology and Kyoto Encyclope dia of Genes and Genomes enrichment studies.Validation of gene and protein e xpression was carried out using qRT-PCR,Western blotting,and cellular flow cytometry,based on the results from sequencing,Furthermore,Safranin-O fast green staining and immunohistochemistry staining were performed on slices of the mice knee joint to evaluate the OA Research Society International score,alterations in the cartilage matrix,and levels of apopto sis-related proteins at sites of knee cartilage damage in an arthritis model induced by mono sodium iodo acetate(MIA) and phy sical activity.Results:It was found that ARC effectively inhibits the production of IL-1β-induced chondrocytes' inducible NO synthase,cyclooxygenase-2,NO,LDH,IL-6,and tumor necrosis factor-α.ARC exhibited a dose-dependent effect on chondrocytes by reducing IL-1β-induced matrix metalloproteinase-3(MMP-3) and a disintegrin and metalloproteinase with thrombo spondin motifs-5 levels while increasing Aggrecan levels.RNA-seq and bioinformatics analysis revealed that ARC's therapeutic effects involve apoptotic signaling pathways through the downregulation of Bcl-2-associated X protein(B ax) and caspase-3 expre ssion and the upregulation of B-cell lymphoma-2(Bcl-2) expression in IL-1β-induced chondrocytes.ARC significantly raised the levels of aggrecan and Bcl-2 and decreased the levels of MMP-3,B ax,and caspase-3 in an arthritis model induced by MIA and movement.Conclusions:Through RNA-seq,in vitro cell assays,and in vivo experiments,this research established the link between apoptosis and inflammation in the progression of OA and confirmed the protective effects of ARC on chondrocytes and its key targets.This highlights ARC's therapeutic potential and its role in the development of treatments for OA.展开更多
The involvement of small RNAs in cotton fiber development is under explored.The objective of this work was to directly clone,annotate,and analyze small RNAs of developing ovules to reveal
In recent years,advancements in single-cell and spatial transcriptomics,which are highly regarded developments in the current era,particularly the emerging integration of single-cell and spatiotemporal transcriptomics...In recent years,advancements in single-cell and spatial transcriptomics,which are highly regarded developments in the current era,particularly the emerging integration of single-cell and spatiotemporal transcriptomics,have enabled a detailed molecular comprehension of the complex regulation of cell fate.The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine.Currently,single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors.Start-ing from the perspective of RNA sequencing technology,this review outlined the signifcance of single-cell RNA sequencing(scRNA-seq)in prostate cancer research,encompassing preclinical medicine and clinical applications.We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies,as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis,treatment,and drug resistance characteristics of prostate cancer.These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer.Furthermore,we explore the potential clinical applications stemming from other single-cell technologies in this review,paving the way for future research in precision medicine.展开更多
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
AIM:To explore the immune cell infiltration and molecular mechanisms of retinal ischemia-reperfusion injury(RIRI)to identify potential therapeutic targets.METHODS:In the bulk RNA-seq analysis,This study performed diff...AIM:To explore the immune cell infiltration and molecular mechanisms of retinal ischemia-reperfusion injury(RIRI)to identify potential therapeutic targets.METHODS:In the bulk RNA-seq analysis,This study performed differential gene expression analysis,weighted gene co-expression network analysis,and protein-protein interaction network analysis to identify hub genes.QuanTIseq was used to determine the composition of infiltrating immune cells.Following the identification of hub genes,single-cell RNA-seq analysis was employed to pinpoint the specific immune cell types expressing these hub genes.Cell-cell communication analysis to explore signaling pathways and interactions between immune cells was further performed.Finally,the expression of these key immune regulators in vivo using quantitative real-time polymerase chain reaction(qRT-PCR)was validated.RESULTS:Bulk RNA-seq analysis identified Stat2,Irf7,Irgm1,Igtp,Parp9,Irgm2,Nlrc5,and Tap1 as hub genes,with strong correlations to immune cell infiltration.Single-cell RNA-seq analysis further revealed six immune cell clusters,showing Irf7 predominantly in microglia and Tap1 in dendritic cells(DCs).And cell-cell communication analysis showed that microglia and DCs play central roles in coordinating immune activity.qRT-PCR validated the upregulation of these genes.CONCLUSION:In the acute phase of RIRI,Irf7 and Tap1 may be the potential therapeutic targets to reduce inflammation and promote neurological function recovery.展开更多
Pigeons and certain other avian species produce a milklike secretion in their crop sacs to nourish offspring,yet the detailed processes involved are not fully elucidated.This study investigated the crop sacs of 225-da...Pigeons and certain other avian species produce a milklike secretion in their crop sacs to nourish offspring,yet the detailed processes involved are not fully elucidated.This study investigated the crop sacs of 225-day-old unpaired non-lactating male pigeons(MN)and males initiating lactation on the first day after incubation(ML).Using RNA sequencing,ribosomeprofiling,andsingle-cell transcriptome sequencing(scRNA-seq),we identified a significant up-regulation of genes associated with ribosome assembly and protein synthesis in ML compared to MN.Results from scRNA-seq analysis identified 12distinct cell types and 22 clusters,with secretory epithelial cells(SECs)exhibiting marked expression of plasma cell markers,including IGLL1 and MZB1.RNA fluorescence in situ hybridization(RNA FISH)and IgY quantification confirmed the critical role of SECs in producing endogenous IgY during lactation.We propose that fibroblast-derived BAFF signals activate SECs,mimicking B cell transformation and enhancing protein production through the unfolded protein response(UPR).These findings shed light on the cellular dynamics of pigeon milk production and contribute to a broader understanding of avian biology.展开更多
Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be...Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.展开更多
Wei et al reported a comprehensive single-cell transcriptomic analysis of the small intestine during early acute pancreatitis(AP)and identified activated mast cells and their secretion of CCL5 as pivotal factors drivi...Wei et al reported a comprehensive single-cell transcriptomic analysis of the small intestine during early acute pancreatitis(AP)and identified activated mast cells and their secretion of CCL5 as pivotal factors driving gut barrier dysfunction.By integrating scRNA-seq with in vitro and in vivo functional assays,this study advances our understanding of the cellular and molecular events underlying AP-associated intestinal injury.In this commentary,I highlight the methodological innovations employed in the study,contextualize its findings in the literature,and propose directions for future research.As an avid researcher in single-cell sequen-cing,I approached this letter with a spirit of academic inquiry and welcome any further discussion or corrections that may enhance my understanding.展开更多
Orthopedic conditions have emerged as global health concerns,impacting approximately 1.7 billion individuals worldwide.However,the limited understanding of the underlying pathological processes at the cellular and mol...Orthopedic conditions have emerged as global health concerns,impacting approximately 1.7 billion individuals worldwide.However,the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders.The advent of single-cell RNA sequencing(scRNA-seq)technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity.Nevertheless,investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges.In this comprehensive review,we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines.By utilizing these methodologies,crucial insights into the developmental dynamics,maintenance of homeostasis,and pathological processes involved in spine,joint,bone,muscle,and tendon disorders have been uncovered.Specifically focusing on the joint diseases of degenerative disc disease,osteoarthritis,and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension.These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.展开更多
BACKGROUND Intestinal barrier dysfunction is a prevalent and varied manifestation of acute pancreatitis(AP).Molecular mechanisms underlying the early intestinal barrier in AP remain poorly understood.AIM To explore th...BACKGROUND Intestinal barrier dysfunction is a prevalent and varied manifestation of acute pancreatitis(AP).Molecular mechanisms underlying the early intestinal barrier in AP remain poorly understood.AIM To explore the biological processes and mechanisms of intestinal injury associated with AP,and to find potential targets for early prevention or treatment of intestinal barrier injury.METHODS This study utilized single-cell RNA sequencing of the small intestine,alongside in vitro and in vivo experiments,to examine intestinal barrier function homeostasis during the early stages of AP and explore involved biological processes and potential mechanisms.RESULTS Seventeen major cell types and 33232 cells were identified across all samples,including normal,AP1(4x caerulein injections,animals sacrificed 2 h after the last injection),and AP2(8x caerulein injections,animals sacrificed 4 h after the last injection).An average of 980 genes per cell was found in the normal intestine,compared to 927 in the AP1 intestine and 1382 in the AP2 intestine.B cells,dendritic cells,mast cells(MCs),and monocytes in AP1 and AP2 showed reduced numbers compared to the normal intestine.Enterocytes,brush cells,enteroendocrine cells,and goblet cells maintained numbers similar to the normal intestine,while cytotoxic T cells and natural killer(NK)cells increased.Enterocytes in early AP exhibited elevated programmed cell death and intestinal barrier dysfunction but retained absorption capabilities.Cytotoxic T cells and NK cells showed enhanced pathogen-fighting abilities.Activated MCs,secreted chemokine(C-C motif)ligand 5(CCL5),promoted neutrophil and macrophage infiltration and contributed to barrier dysfunction.CONCLUSION These findings enrich our understanding of biological processes and mechanisms in AP-associated intestinal injury,suggesting that CCL5 from MCs is a potential target for addressing dysfunction.展开更多
The study of Tang et al investigated the distribution and dynamic changes of cell populations in the tumor microenvironment of gastric cancer(GC)patients using single-cell RNA sequencing(scRNA-seq).This comprehensive ...The study of Tang et al investigated the distribution and dynamic changes of cell populations in the tumor microenvironment of gastric cancer(GC)patients using single-cell RNA sequencing(scRNA-seq).This comprehensive analysis highlights key interactions within the tumor microenvironment across different GC stages.Discussing applications of scRNA-seq data in clinical settings could pave the way for developing promising and personalized therapeutic strategies for GC patients.Therefore,further exploration of selecting anticancer drug candidates through gene screening derived from scRNA-seq will provide deeper insights into GC care.展开更多
Germ-free mice exhibit profound immunological immaturity.Despite recent studies emphasizing the role of specific bacterium-derived metabolites in immune cell development and differentiation,the mechanisms linking micr...Germ-free mice exhibit profound immunological immaturity.Despite recent studies emphasizing the role of specific bacterium-derived metabolites in immune cell development and differentiation,the mechanisms linking microbiota absence to systemic immune deficits remain incompletely defined.Here,droplet-based single-cell RNA sequencing of bone marrow and peripheral blood from both germ-free and specific pathogen-free mice was performed,identifying 25 transcriptionally distinct cell types.Neutrophil apoptosis was elevated in germ-free mice,potentially due to the absence of niacin dehydrogenase,a metabolite primarily produced by Pseudomonas.In addition,germ-free mice exhibited increased excretion of 5’-methylthioadenosine,enhanced ERK activation driven by reactive oxygen species,and disruption of bone marrow stromal antigen 2 signaling.Monocytes and CD8^(+)T cells from germ-free mice showed diminished responses to interferon-β and interferon-γ,consistent with heightened viral susceptibility.These findings establish a microbiota-dependent regulatory pathway linking immunodeficiency to microbial absence in germ-free mice,confirmed through complementary validation techniques.展开更多
Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and...Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.展开更多
基金supported by the National Science Foundation of China,Nos.82325031(to FX),82030059(to YC),82102290(to YG),U23A20485(to YC)Noncommunicable Chronic Diseases-National Science and Technology Major Project,No.2023ZD0505504(to FX),2023ZD0505500(to YC)the Key R&D Program of Shandong Province,No.2022ZLGX03(to YC).
文摘Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies.Previous studies primarily focused on neuronal death,potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury.To address these gaps,we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations,altered cell communication networks,and novel molecular mechanisms involved in post-cardiac arrest brain injury.In this study,we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation,and from sham control pigs.Sequencing results revealed changes in the proportions of different cell types,suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils.These results were validated through western blotting,quantitative reverse transcription-polymerase chain reaction,and immunofluorescence staining.We also identified and validated a unique subcluster of activated microglia with high expression of S100A8,which increased over time following cardiac arrest.This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins.Additionally,we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes.Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin,driving pro-inflammatory microglial polarization.Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus,offering potential novel targets for neuroprotection and repair following cardiac arrest.
基金supported by the National Key R&D Program of China,No.2023YFE0209500(to ZQ)the Natural Science Foundation of Guangdong Province,China,Nos.2023A1515010772(to YL),2025A1515011720(to YL)+1 种基金the Medical Science and Technology Research Foundation of Guangdong Province,No.A2024120(to YL)the National Natural Science Foundation of China,No.U22A20371(to ZQ).
文摘The triple transgenic mouse model of Alzheimer’s disease(3×Tg-AD)is a widely used model that exhibits region-dependent patterns of progressive amyloid-βand tau pathology.Although structural brain abnormalities on magnetic resonance imaging have been observed in 3×Tg-AD mice at later disease stages(>12 months)and as early as 2 months,few studies have investigated changes in these mice during the stage with extensive amyloid-βdeposition and onset of tau pathology(around 9 months).This study aimed to assess brain morphometry and microstructure alterations in 9 month-old 3×Tg-AD mice to better understand the neural mechanisms underlying these specific pathological features.Voxel-based analyses were employed on T2-weighted and diffusion tensor imaging to identify differences between 3×Tg-AD and control mice.Compared with controls,3×Tg-AD mice exhibited lower gray matter volume in several regions including both hippocampal regions,the right thalamus,the left caudoputamen,and the cortex.Reduced white matter volume was observed in fiber tracts including the corpus callosum,internal capsule,stria terminalis,and olfactory tract.Whole-brain diffusion tensor imaging analysis revealed a significant decrease in fractional anisotropy and an increase in both radial and mean diffusivity within the left dentate gyrus of the hippocampal region and right striatum-like amygdala nuclei,with no significant difference in axial diffusivity.Correlation analyses demonstrated significant associations between behavioral performance measures,with both gray and white matter volumes within regions showing significant morphometric differences.Notably,behavioral performance also exhibited significant correlations with diffusion tensor imaging measures particularly within the left dentate gyrus of the hippocampal region and right striatum-like amygdala nuclei.Immunofluorescence analysis confirmed increased amyloid-βplaques and p-Tau protein expression in the hippocampal regions of 3×Tg-AD mice,which corroborated the magnetic resonance imaging findings.Transcriptome analysis in hippocampus tissue identified 1389 differentially expressed genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that numerous differentially expressed genes were enriched in biological processes relevant to synapse structure,cognition,learning,and memory,with particular emphasis on Wnt and mitogen-activated protein kinase signaling pathways.Collectively,these findings suggest that intricate anatomical and microstructural alterations occur in 3×Tg-AD model mice at the onset of pathology around 9 months,potentially driven by gene expression alterations.Moreover,our results support the potential utility of brain volume and diffusion metrics as biomarkers for Alzheimer’s disease pathology,which could have significant implications for clinical diagnosis of Alzheimer’s disease patients.
文摘Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers of spinal cord injury.
基金supported by the Foundation Project:National Natural Science.Foundation of China(Nos.:82460249,82100417,81760094)The Foundation of Jiangxi Provincial Department of Science and Technology Outstanding Youth Fund Project(20212BAB206022,20242BAB23080).
文摘Objective:Leucine-rich alpha-2 glycoprotein 1(Lrg1)could regulate diverse cells in cerebral ischemiareperfusion.Our study seeks to uncover Lrg1’s impact on endothelial cell heterogeneity via differentiation pathways and transcription factors.Method:The CSOmap model measured cell-to-brain-center distances using single-cell RNA sequencing(scRNA-seq)data in middle cerebral artery occlusion reperfusion(MCAO/R).Monocle2 mapped endothelial differentiation paths.Gene set enrichment analysis(GSEA)analyzed endothelial subcluster variations.Database searches revealed a zinc finger MIZ-type containing 1 protein-frizzled 3(Zmiz1-Fzd3)promoter interaction.Endothelial cells were transfected with a Fzd3 promoter-luciferase plasmid.Polymerase chain reaction(PCR)and western blotting assessed MCAO/R or Zmiz1 overexpression effects on Fzd3-related mRNA and proteins.A retroviral vector carrying Zmiz1 was injected into the brains of mice to study its effect on Fzd3.Result:Lrg1−/−mice exhibited elevated cell adhesion proteins and decreased microvascular leakage after MCAO/R.CSOmap showed widened astrocyte spacing in thesemice.RSS revealed Zmiz1 overexpression inMCAO/R+Lrg1−/−mice.MCAO/R and pcDNA3-Zmiz1 transfection both enhanced luciferase activity with Fzd3,indicating Zmiz1 binding to Fzd3.Retroviral Zmiz1 injection or knockdown disrupted ischemic brain tight junctions,highlighting Zmiz1’s key role in blood-brain barrier protection,likely through Fzd3 pathway modulation.Conclusion:The findings indicate Lrg1 knockout induces endothelial differentiation by activating Zmiz1,which is crucial for maintaining blood-brain barrier function,possibly via modulating the Fzd3 pathway.
文摘Objective Adaptive immune responses play a critical role in the pathogenesis of amyotrophic lateral sclerosis(ALS).In this study,we investigated the functional mechanisms of T cell subtypes and assessed the causal links between CD4+cytotoxic T cell-related genes and ALS risk.Methods Single-cell RNA sequencing(scRNA-seq)of peripheral blood mononuclear cells(PBMCs)from patients with ALS and healthy controls(HC)was used to identify differentially expressed genes(DEGs)in CD4+cytotoxic T cells.Comprehensive analyses of CD4+cytotoxic T cells,including pseudotemporal trajectory,intercellular communication,and metabolic pathway analysis,were performed.Mendelian randomization(MR)analysis evaluated the causal effects of DEGs on ALS risk,with validation using independent genome-wide association study(GWAS)data.Expression patterns of the causal genes were further verified using scRNA-seq,bulk-seq,and clinical samples.Results CD4+cytotoxic T cells were significantly expanded in patients with ALS.The upregulated genes S100A6,SERPINB6,SMAD7,and TPST2 were positively correlated with ALS susceptibility,whereas DIP2A showed a protective association.Conclusion S100A6,SERPINB6,SMAD7,TPST2,and DIP2A were identified as causal genes and potential therapeutic targets in ALS,implicating CD4+cytotoxic T cells in the disease mechanisms.Further studies targeting these genes and neuroinflammatory pathways are warranted.
基金Supported by National Key R&D Program of China:Clinical Evaluation Research on Intervention Technologies for Abdominal Obesitythe Role of Gut Microbiota in the Effects of Combined Acupuncture and Medication on Abdominal Obesity:an Exploration with 16S rRNA Technology(Project Code:2019YFC1710102)。
文摘OBJECTIVE:To investigate Acupuncture-herb therapy modulates gut microbiota in abdominal obesity.METHODS:A randomized controlled trial was designed in accordance with standard protocols.Abdominally obese subjects were randomized into four groups:A2(Control):double placebo,A1(Needle):press needle+placebo herb,A3(herb):herbal medicine(Huatan Lishi Fang化痰利湿方)+placebo needle,A4(Combination):press needle+herbal medicine.After 12 weeks of treatment,groups were relabeled B1-B4.Weight,waist circumference,and body mass index were measured monthly.Gut microbiota was analyzed via 16S rRNA sequencing for diversity and abundance.RESULTS:Combined needle-herb therapy significantly reduced waist circumference(P<0.05).All treatments altered gut microbiota composition.The combination group showed significant changes in diversity(Chao1,Shannon,Simpson;P<0.05).Needle therapy increased Bacteroidia;herbs reduced Lachnospiraceae and Megamonas.All results were significant(P<0.05).CONCLUSION:Combined needle-herb treatment modulated 25 key gut flora across multiple taxonomic levels in abdominal obesity.It reduced Firmicutes and Bacteroidota.Bacteroidota,Actinobacteriota,and Prevotellaceae may suppress obesity,whereas Proteobacteria,Lachnospiraceae,and Megamonas may promote it.The combination specifically altered Bacteroidaceae,Lachnospiraceae,Bacteroidia,and Megamonas.
基金supported by grants from the National Key R&D Program of China(Grant No.2021YFF1200400)the Major Program of Shenzhen Bay Laboratory,China(Grant No.S201101001)+1 种基金the Shenzhen Science and Technology Innovation Program,China(Grant No.KQTD20170330155106581)the Griffith University Postgraduate Fellowship,Australia.
文摘sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search.Here,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than RNAcentral.The new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques.It also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam.The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on MSAs.MARS is accessible at https://ngdc.cncb.ac.cn/omix/release/OMIX003037,and RNAcmap3 is accessible at http://zhouyq-lab.szbl.ac.cn/download/.
基金supported by the National Natural Science Foundation of China (81873328)
文摘Objective:Osteoarthritis(OA) is a progressive joint disease characterized by degeneration and de struction of articular cartilage.Arctiin(ARC) has been shown in many studies to have potential anti-inflammatory,anti-apoptotic,and antioxidant effects in various diseases.However,the mechanism by which ARC exerts its protective effects in OA is not fully understood.Here,we explore the mechanism by which ARC plays its protective role in OA.Materials and Methods:Mouse chondrocytes were isolated and characterized through toluidine blue staining and collagen Ⅱ immunofluorescence labeling.A mouse-based experimental model was developed to induce chondrocyte inflammation through Interleukin-1β(IL-1β).Sub sequently,ARC was administe red in various doses to mitigate this inflammation.Techniques such as biochemical assay s,Enzyme-linked immunosorbent assay,quantitative real-time polymerase chain re action(qRT-PCR),Western blotting,and immunofluorescence labeling were employed to detect changes in nitric oxide(NO),lactate dehydrogenase(LDH),inflammatory markers,and components of the cartilage matrix in chondrocytes.RNA-sequencing(RNA-seq) was utilized to explore variations in gene expression among chondrocyte s acro ss different groups.The genes and signaling pathways that were identified underwe nt analysis through Gene Ontology and Kyoto Encyclope dia of Genes and Genomes enrichment studies.Validation of gene and protein e xpression was carried out using qRT-PCR,Western blotting,and cellular flow cytometry,based on the results from sequencing,Furthermore,Safranin-O fast green staining and immunohistochemistry staining were performed on slices of the mice knee joint to evaluate the OA Research Society International score,alterations in the cartilage matrix,and levels of apopto sis-related proteins at sites of knee cartilage damage in an arthritis model induced by mono sodium iodo acetate(MIA) and phy sical activity.Results:It was found that ARC effectively inhibits the production of IL-1β-induced chondrocytes' inducible NO synthase,cyclooxygenase-2,NO,LDH,IL-6,and tumor necrosis factor-α.ARC exhibited a dose-dependent effect on chondrocytes by reducing IL-1β-induced matrix metalloproteinase-3(MMP-3) and a disintegrin and metalloproteinase with thrombo spondin motifs-5 levels while increasing Aggrecan levels.RNA-seq and bioinformatics analysis revealed that ARC's therapeutic effects involve apoptotic signaling pathways through the downregulation of Bcl-2-associated X protein(B ax) and caspase-3 expre ssion and the upregulation of B-cell lymphoma-2(Bcl-2) expression in IL-1β-induced chondrocytes.ARC significantly raised the levels of aggrecan and Bcl-2 and decreased the levels of MMP-3,B ax,and caspase-3 in an arthritis model induced by MIA and movement.Conclusions:Through RNA-seq,in vitro cell assays,and in vivo experiments,this research established the link between apoptosis and inflammation in the progression of OA and confirmed the protective effects of ARC on chondrocytes and its key targets.This highlights ARC's therapeutic potential and its role in the development of treatments for OA.
文摘The involvement of small RNAs in cotton fiber development is under explored.The objective of this work was to directly clone,annotate,and analyze small RNAs of developing ovules to reveal
基金Chinese Scholarship Council(202206240086)National Natural Science Foundation of China(81974099,82170785,81974098,82170784)+4 种基金National Key Research and Development Program of China(2021YFC2009303)programs from Science and Technology Department of Sichuan Province(2021YFH0172)Young Investigator Award of Sichuan University 2017(2017SCU04A17)Technology Innovation Research and Development Project of Chengdu Science and Technology Bureau(2019-YF05-00296-SN)Sichuan University-Panzhihua science and technology cooperation special fund(2020CDPZH-4).
文摘In recent years,advancements in single-cell and spatial transcriptomics,which are highly regarded developments in the current era,particularly the emerging integration of single-cell and spatiotemporal transcriptomics,have enabled a detailed molecular comprehension of the complex regulation of cell fate.The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine.Currently,single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors.Start-ing from the perspective of RNA sequencing technology,this review outlined the signifcance of single-cell RNA sequencing(scRNA-seq)in prostate cancer research,encompassing preclinical medicine and clinical applications.We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies,as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis,treatment,and drug resistance characteristics of prostate cancer.These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer.Furthermore,we explore the potential clinical applications stemming from other single-cell technologies in this review,paving the way for future research in precision medicine.
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 National Natural Science Foundation of China(No.82071312).
文摘AIM:To explore the immune cell infiltration and molecular mechanisms of retinal ischemia-reperfusion injury(RIRI)to identify potential therapeutic targets.METHODS:In the bulk RNA-seq analysis,This study performed differential gene expression analysis,weighted gene co-expression network analysis,and protein-protein interaction network analysis to identify hub genes.QuanTIseq was used to determine the composition of infiltrating immune cells.Following the identification of hub genes,single-cell RNA-seq analysis was employed to pinpoint the specific immune cell types expressing these hub genes.Cell-cell communication analysis to explore signaling pathways and interactions between immune cells was further performed.Finally,the expression of these key immune regulators in vivo using quantitative real-time polymerase chain reaction(qRT-PCR)was validated.RESULTS:Bulk RNA-seq analysis identified Stat2,Irf7,Irgm1,Igtp,Parp9,Irgm2,Nlrc5,and Tap1 as hub genes,with strong correlations to immune cell infiltration.Single-cell RNA-seq analysis further revealed six immune cell clusters,showing Irf7 predominantly in microglia and Tap1 in dendritic cells(DCs).And cell-cell communication analysis showed that microglia and DCs play central roles in coordinating immune activity.qRT-PCR validated the upregulation of these genes.CONCLUSION:In the acute phase of RIRI,Irf7 and Tap1 may be the potential therapeutic targets to reduce inflammation and promote neurological function recovery.
基金supported by the Department of Agriculture and Rural Affairs of Jiangxi Province,China (JXARS-09)Science and Technology Program of Guangdong Province,China (2020B1212060060)。
文摘Pigeons and certain other avian species produce a milklike secretion in their crop sacs to nourish offspring,yet the detailed processes involved are not fully elucidated.This study investigated the crop sacs of 225-day-old unpaired non-lactating male pigeons(MN)and males initiating lactation on the first day after incubation(ML).Using RNA sequencing,ribosomeprofiling,andsingle-cell transcriptome sequencing(scRNA-seq),we identified a significant up-regulation of genes associated with ribosome assembly and protein synthesis in ML compared to MN.Results from scRNA-seq analysis identified 12distinct cell types and 22 clusters,with secretory epithelial cells(SECs)exhibiting marked expression of plasma cell markers,including IGLL1 and MZB1.RNA fluorescence in situ hybridization(RNA FISH)and IgY quantification confirmed the critical role of SECs in producing endogenous IgY during lactation.We propose that fibroblast-derived BAFF signals activate SECs,mimicking B cell transformation and enhancing protein production through the unfolded protein response(UPR).These findings shed light on the cellular dynamics of pigeon milk production and contribute to a broader understanding of avian biology.
基金Supported by Scientific Research Project of Putian University,No.2022059Special Project for Outstanding Young Talents of Putian University,No.2024072Natural Science Foundation of Fujian Province,No.2023J01160.
文摘Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.
基金Supported by the Top-level Talents Support Program of Yangzhou University“Lv Yang Jin Feng”Outstanding Doctor of YangzhouNatural Science Foundation of Jiangsu Province,No.BK20240907。
文摘Wei et al reported a comprehensive single-cell transcriptomic analysis of the small intestine during early acute pancreatitis(AP)and identified activated mast cells and their secretion of CCL5 as pivotal factors driving gut barrier dysfunction.By integrating scRNA-seq with in vitro and in vivo functional assays,this study advances our understanding of the cellular and molecular events underlying AP-associated intestinal injury.In this commentary,I highlight the methodological innovations employed in the study,contextualize its findings in the literature,and propose directions for future research.As an avid researcher in single-cell sequen-cing,I approached this letter with a spirit of academic inquiry and welcome any further discussion or corrections that may enhance my understanding.
基金National Key Research and Development Program of China(2022YFA1103202)National Natural Science Foundation of China(82272507,32270887,and 32200654)+6 种基金Natural Science Foundation of Chongqing(CSTB2023NSCQ-ZDJO008)Postdoctoral Innovative Talent Support Program(BX20220397)Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning(SFLKF202201)Project for Enhancing Innovation of Army Medical University(2023X1839)Talent Innovation Training Program at the Army Medical Center(ZXZYTSYS09)General Hospital of Western Theater Command Research Project(2021-XZYG-B10)University Grants Committee,Research Grants Council of Hong Kong,China(14113723,N_CUHK472/22,C7030-18G,T13-402/17-N,and AoE/M-402/20)。
文摘Orthopedic conditions have emerged as global health concerns,impacting approximately 1.7 billion individuals worldwide.However,the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders.The advent of single-cell RNA sequencing(scRNA-seq)technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity.Nevertheless,investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges.In this comprehensive review,we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines.By utilizing these methodologies,crucial insights into the developmental dynamics,maintenance of homeostasis,and pathological processes involved in spine,joint,bone,muscle,and tendon disorders have been uncovered.Specifically focusing on the joint diseases of degenerative disc disease,osteoarthritis,and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension.These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
基金Supported by National Natural Science Foundation of China,No.82300739Hunan Provincial Natural Science Foundation,No.2023JJ40821Changsha Natural Science Foundation,No.kq2208308.
文摘BACKGROUND Intestinal barrier dysfunction is a prevalent and varied manifestation of acute pancreatitis(AP).Molecular mechanisms underlying the early intestinal barrier in AP remain poorly understood.AIM To explore the biological processes and mechanisms of intestinal injury associated with AP,and to find potential targets for early prevention or treatment of intestinal barrier injury.METHODS This study utilized single-cell RNA sequencing of the small intestine,alongside in vitro and in vivo experiments,to examine intestinal barrier function homeostasis during the early stages of AP and explore involved biological processes and potential mechanisms.RESULTS Seventeen major cell types and 33232 cells were identified across all samples,including normal,AP1(4x caerulein injections,animals sacrificed 2 h after the last injection),and AP2(8x caerulein injections,animals sacrificed 4 h after the last injection).An average of 980 genes per cell was found in the normal intestine,compared to 927 in the AP1 intestine and 1382 in the AP2 intestine.B cells,dendritic cells,mast cells(MCs),and monocytes in AP1 and AP2 showed reduced numbers compared to the normal intestine.Enterocytes,brush cells,enteroendocrine cells,and goblet cells maintained numbers similar to the normal intestine,while cytotoxic T cells and natural killer(NK)cells increased.Enterocytes in early AP exhibited elevated programmed cell death and intestinal barrier dysfunction but retained absorption capabilities.Cytotoxic T cells and NK cells showed enhanced pathogen-fighting abilities.Activated MCs,secreted chemokine(C-C motif)ligand 5(CCL5),promoted neutrophil and macrophage infiltration and contributed to barrier dysfunction.CONCLUSION These findings enrich our understanding of biological processes and mechanisms in AP-associated intestinal injury,suggesting that CCL5 from MCs is a potential target for addressing dysfunction.
文摘The study of Tang et al investigated the distribution and dynamic changes of cell populations in the tumor microenvironment of gastric cancer(GC)patients using single-cell RNA sequencing(scRNA-seq).This comprehensive analysis highlights key interactions within the tumor microenvironment across different GC stages.Discussing applications of scRNA-seq data in clinical settings could pave the way for developing promising and personalized therapeutic strategies for GC patients.Therefore,further exploration of selecting anticancer drug candidates through gene screening derived from scRNA-seq will provide deeper insights into GC care.
基金supported by the Science Technology and Innovation Commission of Shenzhen Municipality,China(SGCX20190919142801722)。
文摘Germ-free mice exhibit profound immunological immaturity.Despite recent studies emphasizing the role of specific bacterium-derived metabolites in immune cell development and differentiation,the mechanisms linking microbiota absence to systemic immune deficits remain incompletely defined.Here,droplet-based single-cell RNA sequencing of bone marrow and peripheral blood from both germ-free and specific pathogen-free mice was performed,identifying 25 transcriptionally distinct cell types.Neutrophil apoptosis was elevated in germ-free mice,potentially due to the absence of niacin dehydrogenase,a metabolite primarily produced by Pseudomonas.In addition,germ-free mice exhibited increased excretion of 5’-methylthioadenosine,enhanced ERK activation driven by reactive oxygen species,and disruption of bone marrow stromal antigen 2 signaling.Monocytes and CD8^(+)T cells from germ-free mice showed diminished responses to interferon-β and interferon-γ,consistent with heightened viral susceptibility.These findings establish a microbiota-dependent regulatory pathway linking immunodeficiency to microbial absence in germ-free mice,confirmed through complementary validation techniques.
文摘Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.
