Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macro...Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.展开更多
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
Background Hexafluoropropylene oxide dimer acid(GenX),a substitute for per-and polyfluoroalkyl substances,has been widely detected in various environmental matrices and foods recently,attracting great attention.Howeve...Background Hexafluoropropylene oxide dimer acid(GenX),a substitute for per-and polyfluoroalkyl substances,has been widely detected in various environmental matrices and foods recently,attracting great attention.However,a systematic characterization of its reproductive toxicity is still missing.This study aims to explore the male reproductive toxicity caused by GenX exposure and the potential cellular and molecular regulatory mechanisms behind it.Results Normally developing mice were exposed to GenX,and testicular tissue was subsequently analyzed and validated using single-cell RNA sequencing.Our results revealed that GenX induced severe testicular damage,disrupted the balance between undifferentiated and differentiated spermatogonial stem cells,and led to strong variation in the cellular dynamics of spermatogenesis.Furthermore,GenX exposure caused global upregulation of testicular somatic cellular inflammatory responses,increased abnormal macrophage differentiation,and attenuated fibroblast adhesion,disorganizing the somatic-germline interactions.Conclusions In conclusion,this study revealed complex cellular dynamics and transcriptome changes in mouse testis after GenX exposure,providing a valuable resource for understanding its reproductive toxicity.展开更多
Polystyrene nanoparticles pose significant toxicological risks to aquatic ecosystems,yet their impact on zebrafish(Danio rerio)embryonic development,particularly erythropoiesis,remains underexplored.This study used si...Polystyrene nanoparticles pose significant toxicological risks to aquatic ecosystems,yet their impact on zebrafish(Danio rerio)embryonic development,particularly erythropoiesis,remains underexplored.This study used single-cell RNA sequencing to comprehensively evaluate the effects of polystyrene nanoparticle exposure on erythropoiesis in zebrafish embryos.In vivo validation experiments corroborated the transcriptomic findings,revealing that polystyrene nanoparticle exposure disrupted erythrocyte differentiation,as evidenced by the decrease in mature erythrocytes and concomitant increase in immature erythrocytes.Additionally,impaired heme synthesis further contributed to the diminished erythrocyte population.These findings underscore the toxic effects of polystyrene nanoparticles on hematopoietic processes,highlighting their potential to compromise organismal health in aquatic environments.展开更多
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
Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technolo...Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.展开更多
Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditio...Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditional and exercise therapy.Methods:Four samples were analyzed:older control(OC),older exercise(OE),younger control(YC),and younger exercise(YE).Single-cell RNA sequencing was used to distinguish cellular subtypes through their biomarker profiles.Data visualization included violin and t-SNE plots to illustrate biomarker expression across cell clusters such as oligodendrocytes,microglia,and astrocytes.Additionally,BV2 cells were exposed to amyloid-beta fragments to simulate Alzheimer’s disease,assessing the impact of exercise-induced cellular responses.Results:Distinct cellular subtypes were identified:oligodendrocytes(MBP,St18),microglia(Dock8),and astrocytes(Aqp4,Gpc5).Sample OE was predominantly oligodendrocytes,while YE had more astrocytes,inhibitory neurons,and Canal-Retzius cells.YC showed a significant presence of Olfm3+ganglion neurons.ZEB1 gene knockout revealed changes in SMAD family gene expression,which regulate ferroptosis.Oxidative stress levels were also evaluated.Conclusion:This profiling enhances our understanding of brain cellular functions and interactions,potentially informing targeted therapies in neurological research.Exercise may influence brain cell immune responses and cell death pathways by regulating specific gene expressions,offering new insights for treating neuroinflammation and degeneration.展开更多
Drug resistance remains a major challenge in breast cancer chemotherapy,yet the metabolic alterations underlying this phenomenon are not fully understood.There is much evidence indicating the cellular heterogeneity am...Drug resistance remains a major challenge in breast cancer chemotherapy,yet the metabolic alterations underlying this phenomenon are not fully understood.There is much evidence indicating the cellular heterogeneity among cancer cells,which exhibit varying degrees of metabolic reprogramming and thus may result in differential contributions to drug resistance.A home-built single-cell quantitative mass spectrometry(MS)platform,which integrates micromanipulation and electro-osmotic sampling,was developed to quantitatively profile the tricarboxylic acid(TCA)cycle metabolites at the single-cell level.Using this platform,the metabolic profiles of drug-sensitive MCF-7 breast cancer cells and their drug-resistant derivative MCF-7/ADR cells were compared.This results revealed a selective upregulation of downstream TCA cycle metabolites includingα-ketoglutarate,succinate,fumarate,and malate in drug-resistant cancer cells,while early TCA metabolites remained largely unchanged.Furthermore,notable variations in the abundance of the metabolites were observed in individual cells.The comparative analysis also revealed that not all MCF-7/ADR cells exhibit the same degree of metabolic deviation from the parental line in the metabolites during resistance acquisition.The observed metabolic profiles indicate enhanced glutaminolysis,altered mitochondrial electron transport chain activity,and increased metabolic flexibility in drug-resistant cancer cells that support their survival under chemotherapeutic stress.The findings further suggest the potential for incorporating cellular metabolic heterogeneity into future drug resistance studies.展开更多
Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development o...Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development of cutting-edge therapies in orthopedics.We present a single-cell transcriptome atlas of the meniscus,consisting of cell clusters corresponding to four major cell types:chondrocytes,endothelial cells,smooth muscle cells,and immune cells.Five distinct chondrocyte subclusters(CH0–CH4)were annotated,of which only one was widespread in both the red and white zones,indicating a major difference in the cellular makeup of the zones.Subclusters distinct to the white zone appear responsible for cartilage-specific matrix deposition and protection against adverse microenvironmental factors,while those in the red zone exhibit characteristics of mesenchymal stem cells and are more likely to proliferate and migrate.Additionally,they induce remodeling actions in other chondrocyte subclusters and promote the proliferation and maturation of endothelial cells,inducing healing and vascularization processes.Considering that they have substantial remodeling capabilities,these subclusters should be of great interest for tissue engineering studies.We also show that the cellular makeup of the pig meniscus is comparable to that of humans,which supports the use of pigs as a model in orthopedic therapy development.展开更多
The kidney is essential for maintaining fluid,electrolyte,and metabolite homeostasis,and for regulating blood pressure.The pig serves as a valuable biomedical model for human renal physiology,offering insights across ...The kidney is essential for maintaining fluid,electrolyte,and metabolite homeostasis,and for regulating blood pressure.The pig serves as a valuable biomedical model for human renal physiology,offering insights across different physiological states.In this study,single-cell RNA sequencing was used to profile 138469 cells from 12 pig kidney samples collected during the embryonic(E),fattening(F),and pregnancy(P)periods,identifying 29 cell types.Proximal tubule(PT)cells exhibited elevated expression of metabolism-related transcription factors(TFs),including GPD1,ACAA1,and AGMAT,with validation across multiple individuals,periods,and species.Fluorescence homologous double-labeling of paraffin sections further confirmed the expression of ACAA1 and AGMAT in PT cells.Comparative analysis of pig and human kidneys revealed a high degree of similarity among corresponding cell types.Analysis of cell-type heterogeneity highlighted the diversity of thick ascending limb(TAL)cells,identifying a TAL subpopulation related to immune function.Additionally,the functional heterogeneity of kidney-resident macrophages(KRM)was explored across different anatomical sites.In the renal medulla,KRM were implicated in phagocytosis and leukocyte activation,whereas in the renal pelvis,they functioned as ligands,recruiting neutrophils with bactericidal activity to the renal pelvis to combat urinary tract infections.展开更多
Background:Medulloblastoma(MB)is one of the most common malignant brain tumors that mainly affect children.Various approaches have been used to model MB to facilitate investigating tumorigenesis.This study aims to com...Background:Medulloblastoma(MB)is one of the most common malignant brain tumors that mainly affect children.Various approaches have been used to model MB to facilitate investigating tumorigenesis.This study aims to compare the recapitulation of MB between subcutaneous patient-derived xenograft(sPDX),intracranial patient-derived xenograft(iPDX),and genetically engineered mouse models(GEMM)at the single-cell level.Methods:We obtained primary human sonic hedgehog(SHH)and group 3(G3)MB samples from six patients.For each patient specimen,we developed two sPDX and iPDX models,respectively.Three Patch+/-GEMM models were also included for sequencing.Single-cell RNA sequencing was performed to compare gene expression profiles,cellular composition,and functional pathway enrichment.Bulk RNA-seq deconvolution was performed to compare cellular composition across models and human samples.Results:Our results showed that the sPDX tumor model demonstrated the highest correlation to the overall transcriptomic profiles of primary human tumors at the single-cell level within the SHH and G3 subgroups,followed by the GEMM model and iPDX.The GEMM tumor model was able to recapitulate all subpopulations of tumor microenvironment(TME)cells that can be clustered in human SHH tumors,including a higher proportion of tumor-associated astrocytes and immune cells,and an additional cluster of vascular endothelia when compared to human SHH tumors.Conclusions:This study was the first to compare experimental models for MB at the single-cell level,providing value insights into model selection for different research purposes.sPDX and iPDX are suitable for drug testing and personalized therapy screenings,whereas GEMM models are valuable for investigating the interaction between tumor and TME cells.展开更多
BACKGROUND Hepatocellular carcinoma(HCC)is notorious for its aggressive progression and dismal prognosis,with chromatin accessibility dynamics emerging as pivotal yet poorly understood drivers.AIM To dissect how multi...BACKGROUND Hepatocellular carcinoma(HCC)is notorious for its aggressive progression and dismal prognosis,with chromatin accessibility dynamics emerging as pivotal yet poorly understood drivers.AIM To dissect how multilayered chromatin regulation sustains oncogenic transcription and tumor-stroma crosstalk in HCC,we combined multiomics single cell analysis.METHODS We integrated single-cell RNA sequencing and paired single-cell assay for transposase-accessible chromatin with sequencing data of HCC samples,complemented by bulk RNA sequencing validation across The Cancer Genome Atlas,Liver Cancer Institute,and GSE25907 cohorts.Cell type-specific chromatin architectures were resolved via ArchR,with regulatory hubs identified through peak-to-gene linkages and coaccessibility networks.Functional validation employed A485-mediated histone 3 lysine 27 acetylation suppression and small interfering RNA targeting DGAT1.RESULTS Malignant hepatocytes exhibited expanded chromatin accessibility profiles,characterized by increased numbers of accessible peaks and larger physical regions despite reduced peak intensity.Enhancer-like peaks enriched in malignant regulation,forming long-range hubs.Eighteen enhancer-like peak-related genes showed tumor-specific overexpression and diagnostic accuracy,correlating with poor prognosis.Intercellular coaccessibility analysis revealed tumor-stroma symbiosis via shared chromatin states.Pharmacological histone 3 lysine 27 acetylation inhibition paradoxically downregulated DGAT1,the hub gene most strongly regulated by chromatin accessibility.DGAT1 knockdown suppressed cell proliferation.CONCLUSION Multilayered chromatin reprogramming sustains HCC progression through tumor-stroma crosstalk and DGAT1-related oncogenic transcription,defining targetable epigenetic vulnerabilities.展开更多
As a common malignant tumor,the heterogeneity of colorectal cancer plays an important role in tumor progression and treatment response.In recent years,the rapid development of single-cell transcriptomics and spatial t...As a common malignant tumor,the heterogeneity of colorectal cancer plays an important role in tumor progression and treatment response.In recent years,the rapid development of single-cell transcriptomics and spatial transcriptomics technologies has provided new perspectives for resolving the heterogeneity of colorectal cancer.These techniques can reveal the complexity of cellular composition and their interactions in the tumor microenvironment,and thus facilitate a deeper understanding of tumor biology.However,in practical applications,researchers still face technical challenges such as data processing and result interpretation.The aim of this paper is to explore how to use artificial intelligence(AI)technology to enhance the research efficiency of single-cell and spatial transcriptomics,analyze the current research progress and its limitations,and explore how combining AI approaches can provide new ideas for decoding the heterogeneity of colorectal cancer,and ultimately provide theoretical basis and practical guidance for the clinical precision treatment.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
KanCell is a deep learning model based on Kolmogorov-Arnold networks(KAN)designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing and spatial transcriptomics(ST)data.ST technologie...KanCell is a deep learning model based on Kolmogorov-Arnold networks(KAN)designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing and spatial transcriptomics(ST)data.ST technologies provide insights into gene expression within tissue context,revealing cellular interactions and microenvironments.To fully leverage this potential,effective computational models are crucial.We evaluate KanCell on both simulated and real datasets from technologies such as STARmap,Slide-seq,Visium,and Spatial Transcriptomics.Our results demonstrate that KanCell outperforms existing methods across metrics like PCC,SSIM,COSSIM,RMSE,JSD,ARS,and ROC,with robust performance under varying cell numbers and background noise.Real-world applications on human lymph nodes,hearts,melanoma,breast cancer,dorsolateral prefrontal cortex,and mouse embryo brains confirmed its reliability.Compared with traditional approaches,KanCell effectively captures non-linear relationships and optimizes computational efficiency through KAN,providing an accurate and efficient tool for ST.By improving data accuracy and resolving cell type composition,KanCell reveals cellular heterogeneity,clarifies disease microenvironments,and identifies therapeutic targets,addressing complex biological challenges.展开更多
Colorectal cancer(CRC)is a common malignant tumor worldwide,and its tumor microenvironment(TME)plays a crucial role in tumor progression.Neutrophil extracellular traps(NETs),as an important component of the TME,have r...Colorectal cancer(CRC)is a common malignant tumor worldwide,and its tumor microenvironment(TME)plays a crucial role in tumor progression.Neutrophil extracellular traps(NETs),as an important component of the TME,have received widespread attention in recent years.This article explores the biological functions and molecular mechanisms of NETs in CRC and their impact on disease progression,while analyzing the application of single-cell sequencing technology(SCS)in this field.The development of SCS provides a new perspective for understanding the role of NETs in CRC.By combining SCS technology,targeting key regulatory nodes of NETs is expected to reverse the immunosuppressive microenvironment and provide a theoretical basis for developing novel diagnostic biomarkers and targeted therapeutic strategies,thereby promoting the development of precision medicine in CRC and helping enhance patient prognosis.Future research should further explore the integration of SCS technology with complementary methodologies to investigate NETs and develop specific detection methods and therapeutic strategies targeting NETs to enhance early diagnosis and treatment efficacy of tumors.展开更多
The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrat...The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrated with microfluidics,typically comprises barcode array,sample loading,and reaction unit array chips.Here,we present a review of microfluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and single cells,including protein biomarkers,microRNA(miRNA),circulating tumor DNA(ctDNA),single-cell secreted proteins,single-cell exosomes,and cell interactions.We begin with an overview of current high-throughput detection and analysis approaches.Following this,we outline recent improvements in microfluidic devices for biomolecule and single-cell detection,highlighting the benefits and limitations of these devices.This paper focuses on the research and development of microfluidic barcode biochips,covering their self-assembly substrate materials and their specific applications with biomolecules and single cells.Looking forward,we explore the prospects and challenges of this technology,with the aim of contributing toward the use of microfluidic barcode detection biochips in medical diagnostics and therapies,and their large-scale commercialization.展开更多
Objective:Prostate cancer(PCa)is a complex disease characterized by diverse cellular ecosystems within the tumor microenvironment(TME)and high tumor heterogeneity,which challenges clinically stratified management and ...Objective:Prostate cancer(PCa)is a complex disease characterized by diverse cellular ecosystems within the tumor microenvironment(TME)and high tumor heterogeneity,which challenges clinically stratified management and reinforces the need for novel strategies to fight against castration-resistant PCa(CRPC).Methods:We performed single-cell RNA sequencing(scRNA-seq)on 10 untreated primary PCa tissues and integrated public scRNA-seq resources from three normal prostate tissues,two untreated primary PCa tissues,and six CRPC tumors to portray a comprehensive cellular and molecular interaction atlas of PCa.We further integrated the single-cell and bulk transcriptomes of PCa to establish a molecular classification system.Results:scRNA-seq profiles revealed substantial inter-and intra-tumoral heterogeneity across different cell subpopulations in untreated PCa and CRPC tumors.In the malignant epithelial reservoir,cells evolved along decoupled paths in treatment-naive PCa and CRPC tumors,and distinct transcriptional reprogramming processes were activated,highlighting anti-androgen therapy-induced lineage plasticity.Based on the specifically expressed markers of the epithelial subpopulations,we conducted unsupervised clustering analysis in The Cancer Genome Atlas prostate adenocarcinoma(TCGA-PRAD)cohort and identified three molecularly and clinically distinct subtypes.The C1 subtype,characterized by high enrichment of CRPC-enriched epithelial cells,had a high risk of rapid development of anti-androgen resistance and might require active surveillance and additional promising intervention treatments,such as integrin A3(ITGA3)+integrin B1(ITGB1)inhibition.The C2 subtype resembled the immune-modulated subtype that was most likely to benefit from anti-LAG3 immunotherapy.The C3 subtype had a favorable prognosis.Conclusions:Our study provides a comprehensive and high-resolution landscape of the intricate architecture of the PCa TME,and our trichotomic molecular taxonomy could help facilitate precision oncology.展开更多
BACKGROUND Gastric cancer(GC)poses a substantial risk to human health due to its high prevalence and mortality rates.Nevertheless,current therapeutic strategies remain insufficient.Single-cell RNA sequencing(scRNA-seq...BACKGROUND Gastric cancer(GC)poses a substantial risk to human health due to its high prevalence and mortality rates.Nevertheless,current therapeutic strategies remain insufficient.Single-cell RNA sequencing(scRNA-seq)offers the potential to provide comprehensive insights into GC pathogenesis.AIM To explore the distribution and dynamic changes of cell populations in the GC tumor microenvironment using scRNA-seq techniques.METHODS Cancerous tissues and paracancerous tissues were obtained from patients diagnosed with GC at various stages(I,II,III,and IV).Single-cell suspensions were prepared and analyzed using scRNA-seq to examine transcriptome profiles and cell-cell interactions.Additionally,quantitative real-time polymerase chain reaction(qRT-PCR)and flow cytometry were applied for measuring the expression of cluster of differentiation(CD)2,CD3D,CD3E,cytokeratin 19,cytokeratin 8,and epithelial cell adhesion molecules.RESULTS Transcriptome data from 73645 single cells across eight tissues of four patients were categorized into 25 distinct cell clusters,representing 10 different cell types.Variations were observed in these cell type distribution.The adjacent epithelial cells in stages II and III exhibited a degenerative trend.Additionally,the quantity of CD4 T cells and CD8 T cells were evidently elevated in cancerous tissues.Interaction analysis displayed a remarkable increase in interaction between B cells and other mast cells in stages II,III,and IV of GC.These findings were further validated through qRT-PCR and flow cytometry,demonstrating elevated T cells and declined epithelial cells within the cancerous tissues.CONCLUSION This study provides a comprehensive analysis of cell dynamics across GC stages,highlighting key interactions within the tumor microenvironment.These findings offer valuable insights for developing novel therapeutic strategies.展开更多
Inflammation plays a crucial role in the regeneration of fish and avian retinas.However,how inflammation regulates Müller glia(MG)reprogramming remains unclear.Here,we used single-cell RNA sequencing to investiga...Inflammation plays a crucial role in the regeneration of fish and avian retinas.However,how inflammation regulates Müller glia(MG)reprogramming remains unclear.Here,we used single-cell RNA sequencing to investigate the cell heterogeneity and interactions of MG and immune cells in the regenerating zebrafish retina.We first showed that two types of quiescent MG(resting MG1 and MG2)reside in the uninjured retina.Following retinal injury,resting MG1 transitioned into an activated state expressing known reprogramming genes,while resting MG2 gave rise to rod progenitors.We further showed that retinal microglia can be categorized into three subtypes(microglia-1,microglia-2,and proliferative)and pseudotime analysis demonstrated dynamic changes in microglial status following retinal injury.Analysis of cell–cell interactions indicated extensive crosstalk between immune cells and MG,with many interactions shared among different immune cell types.Finally,we showed that inflammation activated Jak1–Stat3 signaling in MG,promoting their transition from a resting to an activated state.Our study reveals the cell heterogeneity and crosstalk of immune cells and MG in zebrafish retinal repair,and may provide valuable insights into future mammalian retina regeneration.展开更多
基金supported by Qingdao Key Medical and Health Discipline ProjectThe Intramural Research Program of the Affiliated Hospital of Qingdao University,No. 4910Qingdao West Coast New Area Science and Technology Project,No. 2020-55 (all to SW)。
文摘Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.
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 Guangdong Provincial Key Area Research and Development Program[grant number 2022B0202090002]China Postdoctoral Science Foundation[grant number 2024M760977].
文摘Background Hexafluoropropylene oxide dimer acid(GenX),a substitute for per-and polyfluoroalkyl substances,has been widely detected in various environmental matrices and foods recently,attracting great attention.However,a systematic characterization of its reproductive toxicity is still missing.This study aims to explore the male reproductive toxicity caused by GenX exposure and the potential cellular and molecular regulatory mechanisms behind it.Results Normally developing mice were exposed to GenX,and testicular tissue was subsequently analyzed and validated using single-cell RNA sequencing.Our results revealed that GenX induced severe testicular damage,disrupted the balance between undifferentiated and differentiated spermatogonial stem cells,and led to strong variation in the cellular dynamics of spermatogenesis.Furthermore,GenX exposure caused global upregulation of testicular somatic cellular inflammatory responses,increased abnormal macrophage differentiation,and attenuated fibroblast adhesion,disorganizing the somatic-germline interactions.Conclusions In conclusion,this study revealed complex cellular dynamics and transcriptome changes in mouse testis after GenX exposure,providing a valuable resource for understanding its reproductive toxicity.
基金supported by the Institute for Basic Science (IBS-R022-D1)Global Learning&Academic Research Institution for Master’s/Ph D students and Post-Doc Program of the National Research Foundation of Korea Grant funded by the Ministry of Education (RS-2023-00301938)+1 种基金National Research Foundation of Korea Grant funded by the Korean government (RS-2024-00406152,MSIT)Additional financial support was provided by the 2024 Post-Doc Development Program of Pusan National University,Korea Medical Institute,and KREONET。
文摘Polystyrene nanoparticles pose significant toxicological risks to aquatic ecosystems,yet their impact on zebrafish(Danio rerio)embryonic development,particularly erythropoiesis,remains underexplored.This study used single-cell RNA sequencing to comprehensively evaluate the effects of polystyrene nanoparticle exposure on erythropoiesis in zebrafish embryos.In vivo validation experiments corroborated the transcriptomic findings,revealing that polystyrene nanoparticle exposure disrupted erythrocyte differentiation,as evidenced by the decrease in mature erythrocytes and concomitant increase in immature erythrocytes.Additionally,impaired heme synthesis further contributed to the diminished erythrocyte population.These findings underscore the toxic effects of polystyrene nanoparticles on hematopoietic processes,highlighting their potential to compromise organismal health in aquatic environments.
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 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI)the Ministry of Health&Welfare,Republic of Korea (HR22C1734)+2 种基金the National Research Foundation (NRF) of Korea (2020R1A6A1A03043539,2020M3A9D8037604,2022R1C1C1004756)(to SBL)the NRF of Korea (2022R1C1C1005741 and RS-2023-00217595)the new faculty research fund of Ajou University School of Medicine (to EJL)。
文摘Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.
文摘Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditional and exercise therapy.Methods:Four samples were analyzed:older control(OC),older exercise(OE),younger control(YC),and younger exercise(YE).Single-cell RNA sequencing was used to distinguish cellular subtypes through their biomarker profiles.Data visualization included violin and t-SNE plots to illustrate biomarker expression across cell clusters such as oligodendrocytes,microglia,and astrocytes.Additionally,BV2 cells were exposed to amyloid-beta fragments to simulate Alzheimer’s disease,assessing the impact of exercise-induced cellular responses.Results:Distinct cellular subtypes were identified:oligodendrocytes(MBP,St18),microglia(Dock8),and astrocytes(Aqp4,Gpc5).Sample OE was predominantly oligodendrocytes,while YE had more astrocytes,inhibitory neurons,and Canal-Retzius cells.YC showed a significant presence of Olfm3+ganglion neurons.ZEB1 gene knockout revealed changes in SMAD family gene expression,which regulate ferroptosis.Oxidative stress levels were also evaluated.Conclusion:This profiling enhances our understanding of brain cellular functions and interactions,potentially informing targeted therapies in neurological research.Exercise may influence brain cell immune responses and cell death pathways by regulating specific gene expressions,offering new insights for treating neuroinflammation and degeneration.
基金supported by National Natural Science Foundation of China(22374080,22174068,21722504)Primary Research&Development Plan of Jiangsu Province(BK20221303,BE2022796)+1 种基金Open Foundation of State Key Laboratory of Reproductive Medicine(SKLRM-2022BP1,JX116GSP20240507)Science and Technology Development Fund of NJMU(NJMUQY2022003)。
文摘Drug resistance remains a major challenge in breast cancer chemotherapy,yet the metabolic alterations underlying this phenomenon are not fully understood.There is much evidence indicating the cellular heterogeneity among cancer cells,which exhibit varying degrees of metabolic reprogramming and thus may result in differential contributions to drug resistance.A home-built single-cell quantitative mass spectrometry(MS)platform,which integrates micromanipulation and electro-osmotic sampling,was developed to quantitatively profile the tricarboxylic acid(TCA)cycle metabolites at the single-cell level.Using this platform,the metabolic profiles of drug-sensitive MCF-7 breast cancer cells and their drug-resistant derivative MCF-7/ADR cells were compared.This results revealed a selective upregulation of downstream TCA cycle metabolites includingα-ketoglutarate,succinate,fumarate,and malate in drug-resistant cancer cells,while early TCA metabolites remained largely unchanged.Furthermore,notable variations in the abundance of the metabolites were observed in individual cells.The comparative analysis also revealed that not all MCF-7/ADR cells exhibit the same degree of metabolic deviation from the parental line in the metabolites during resistance acquisition.The observed metabolic profiles indicate enhanced glutaminolysis,altered mitochondrial electron transport chain activity,and increased metabolic flexibility in drug-resistant cancer cells that support their survival under chemotherapeutic stress.The findings further suggest the potential for incorporating cellular metabolic heterogeneity into future drug resistance studies.
基金supported by the National Centre for Research and Development TECHMATSTRATEG-Ⅲ/0027/2019,POWR.03.02.00-00-I006/17the IDUB UAM。
文摘Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development of cutting-edge therapies in orthopedics.We present a single-cell transcriptome atlas of the meniscus,consisting of cell clusters corresponding to four major cell types:chondrocytes,endothelial cells,smooth muscle cells,and immune cells.Five distinct chondrocyte subclusters(CH0–CH4)were annotated,of which only one was widespread in both the red and white zones,indicating a major difference in the cellular makeup of the zones.Subclusters distinct to the white zone appear responsible for cartilage-specific matrix deposition and protection against adverse microenvironmental factors,while those in the red zone exhibit characteristics of mesenchymal stem cells and are more likely to proliferate and migrate.Additionally,they induce remodeling actions in other chondrocyte subclusters and promote the proliferation and maturation of endothelial cells,inducing healing and vascularization processes.Considering that they have substantial remodeling capabilities,these subclusters should be of great interest for tissue engineering studies.We also show that the cellular makeup of the pig meniscus is comparable to that of humans,which supports the use of pigs as a model in orthopedic therapy development.
基金supported by the International Cooperation and Exchange Program of the National Natural Science Foundation of China(32261133531)。
文摘The kidney is essential for maintaining fluid,electrolyte,and metabolite homeostasis,and for regulating blood pressure.The pig serves as a valuable biomedical model for human renal physiology,offering insights across different physiological states.In this study,single-cell RNA sequencing was used to profile 138469 cells from 12 pig kidney samples collected during the embryonic(E),fattening(F),and pregnancy(P)periods,identifying 29 cell types.Proximal tubule(PT)cells exhibited elevated expression of metabolism-related transcription factors(TFs),including GPD1,ACAA1,and AGMAT,with validation across multiple individuals,periods,and species.Fluorescence homologous double-labeling of paraffin sections further confirmed the expression of ACAA1 and AGMAT in PT cells.Comparative analysis of pig and human kidneys revealed a high degree of similarity among corresponding cell types.Analysis of cell-type heterogeneity highlighted the diversity of thick ascending limb(TAL)cells,identifying a TAL subpopulation related to immune function.Additionally,the functional heterogeneity of kidney-resident macrophages(KRM)was explored across different anatomical sites.In the renal medulla,KRM were implicated in phagocytosis and leukocyte activation,whereas in the renal pelvis,they functioned as ligands,recruiting neutrophils with bactericidal activity to the renal pelvis to combat urinary tract infections.
基金National Key Research and Development Program of China,Grant/Award Number:2022ZD0210100Beijing Nova Star Program,Grant/Award Number:2022002+2 种基金Natural Science Foundation of Beijing and Haidian Collaboration Foundation,Grant/Award Number:L232079National Natural Science Foundation of China,Grant/Award Number:82172608,82273343,81902975 and 82101356Capital Medical University Fund for Excellent Young Scholars,Grant/Award Number:KCB2304。
文摘Background:Medulloblastoma(MB)is one of the most common malignant brain tumors that mainly affect children.Various approaches have been used to model MB to facilitate investigating tumorigenesis.This study aims to compare the recapitulation of MB between subcutaneous patient-derived xenograft(sPDX),intracranial patient-derived xenograft(iPDX),and genetically engineered mouse models(GEMM)at the single-cell level.Methods:We obtained primary human sonic hedgehog(SHH)and group 3(G3)MB samples from six patients.For each patient specimen,we developed two sPDX and iPDX models,respectively.Three Patch+/-GEMM models were also included for sequencing.Single-cell RNA sequencing was performed to compare gene expression profiles,cellular composition,and functional pathway enrichment.Bulk RNA-seq deconvolution was performed to compare cellular composition across models and human samples.Results:Our results showed that the sPDX tumor model demonstrated the highest correlation to the overall transcriptomic profiles of primary human tumors at the single-cell level within the SHH and G3 subgroups,followed by the GEMM model and iPDX.The GEMM tumor model was able to recapitulate all subpopulations of tumor microenvironment(TME)cells that can be clustered in human SHH tumors,including a higher proportion of tumor-associated astrocytes and immune cells,and an additional cluster of vascular endothelia when compared to human SHH tumors.Conclusions:This study was the first to compare experimental models for MB at the single-cell level,providing value insights into model selection for different research purposes.sPDX and iPDX are suitable for drug testing and personalized therapy screenings,whereas GEMM models are valuable for investigating the interaction between tumor and TME cells.
基金Supported by the Science and Technology Planning Project of Guangzhou,No.2024A03J0102the Natural Science Foundation of Guangdong Province for Distinguished Young Scholar,No.2022B1515020024+1 种基金National Natural Science Foundation of China,No.82070574the Key Research and Development Program of Guangzhou,No.2023B03J1298.
文摘BACKGROUND Hepatocellular carcinoma(HCC)is notorious for its aggressive progression and dismal prognosis,with chromatin accessibility dynamics emerging as pivotal yet poorly understood drivers.AIM To dissect how multilayered chromatin regulation sustains oncogenic transcription and tumor-stroma crosstalk in HCC,we combined multiomics single cell analysis.METHODS We integrated single-cell RNA sequencing and paired single-cell assay for transposase-accessible chromatin with sequencing data of HCC samples,complemented by bulk RNA sequencing validation across The Cancer Genome Atlas,Liver Cancer Institute,and GSE25907 cohorts.Cell type-specific chromatin architectures were resolved via ArchR,with regulatory hubs identified through peak-to-gene linkages and coaccessibility networks.Functional validation employed A485-mediated histone 3 lysine 27 acetylation suppression and small interfering RNA targeting DGAT1.RESULTS Malignant hepatocytes exhibited expanded chromatin accessibility profiles,characterized by increased numbers of accessible peaks and larger physical regions despite reduced peak intensity.Enhancer-like peaks enriched in malignant regulation,forming long-range hubs.Eighteen enhancer-like peak-related genes showed tumor-specific overexpression and diagnostic accuracy,correlating with poor prognosis.Intercellular coaccessibility analysis revealed tumor-stroma symbiosis via shared chromatin states.Pharmacological histone 3 lysine 27 acetylation inhibition paradoxically downregulated DGAT1,the hub gene most strongly regulated by chromatin accessibility.DGAT1 knockdown suppressed cell proliferation.CONCLUSION Multilayered chromatin reprogramming sustains HCC progression through tumor-stroma crosstalk and DGAT1-related oncogenic transcription,defining targetable epigenetic vulnerabilities.
基金Supported by the Shandong Province Medical and Health Science and Technology Development Plan Project,No.202203030713Yantai Science and Technology Program,No.2024YD005,No.2024YD007 and No.2024YD010and Science and Technology Program of Yantai Affiliated Hospital of Binzhou Medical University,No.YTFY2022KYQD06。
文摘As a common malignant tumor,the heterogeneity of colorectal cancer plays an important role in tumor progression and treatment response.In recent years,the rapid development of single-cell transcriptomics and spatial transcriptomics technologies has provided new perspectives for resolving the heterogeneity of colorectal cancer.These techniques can reveal the complexity of cellular composition and their interactions in the tumor microenvironment,and thus facilitate a deeper understanding of tumor biology.However,in practical applications,researchers still face technical challenges such as data processing and result interpretation.The aim of this paper is to explore how to use artificial intelligence(AI)technology to enhance the research efficiency of single-cell and spatial transcriptomics,analyze the current research progress and its limitations,and explore how combining AI approaches can provide new ideas for decoding the heterogeneity of colorectal cancer,and ultimately provide theoretical basis and practical guidance for the clinical precision treatment.
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 the National Natural Science Foundation of China(52361145714,21673252)the Beijing Municipal Education Commission(2019821001)+1 种基金Climbing Program Foundation from Beijing Institute of Petrochemical Technology(BIPTAAl-2021007)the ZhiYuan Fund key Project from Beijing Institute of Petrochemical Technology(2024003).
文摘KanCell is a deep learning model based on Kolmogorov-Arnold networks(KAN)designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing and spatial transcriptomics(ST)data.ST technologies provide insights into gene expression within tissue context,revealing cellular interactions and microenvironments.To fully leverage this potential,effective computational models are crucial.We evaluate KanCell on both simulated and real datasets from technologies such as STARmap,Slide-seq,Visium,and Spatial Transcriptomics.Our results demonstrate that KanCell outperforms existing methods across metrics like PCC,SSIM,COSSIM,RMSE,JSD,ARS,and ROC,with robust performance under varying cell numbers and background noise.Real-world applications on human lymph nodes,hearts,melanoma,breast cancer,dorsolateral prefrontal cortex,and mouse embryo brains confirmed its reliability.Compared with traditional approaches,KanCell effectively captures non-linear relationships and optimizes computational efficiency through KAN,providing an accurate and efficient tool for ST.By improving data accuracy and resolving cell type composition,KanCell reveals cellular heterogeneity,clarifies disease microenvironments,and identifies therapeutic targets,addressing complex biological challenges.
基金the Shandong Province Medical and Health Science and Technology Development Plan Project,No.202203030713Yantai Science and Technology Program,No.2024YD005,No.2024YD007 and No.2024YD010and Science and Technology Program of Yantai Affiliated Hospital of Binzhou Medical University,No.YTFY2022KYQD06.
文摘Colorectal cancer(CRC)is a common malignant tumor worldwide,and its tumor microenvironment(TME)plays a crucial role in tumor progression.Neutrophil extracellular traps(NETs),as an important component of the TME,have received widespread attention in recent years.This article explores the biological functions and molecular mechanisms of NETs in CRC and their impact on disease progression,while analyzing the application of single-cell sequencing technology(SCS)in this field.The development of SCS provides a new perspective for understanding the role of NETs in CRC.By combining SCS technology,targeting key regulatory nodes of NETs is expected to reverse the immunosuppressive microenvironment and provide a theoretical basis for developing novel diagnostic biomarkers and targeted therapeutic strategies,thereby promoting the development of precision medicine in CRC and helping enhance patient prognosis.Future research should further explore the integration of SCS technology with complementary methodologies to investigate NETs and develop specific detection methods and therapeutic strategies targeting NETs to enhance early diagnosis and treatment efficacy of tumors.
基金supported by the National Key Research and Development Plan of China(2023YFB3210400)the Natural Science Innovation Group Foundation of China(T2321004)+3 种基金the National Natural Science Foundation of China(62174101)Shandong University Integrated Research and Cultivation Project(2022JC001)Key Research and Development Plan of Shandong Province(Major Science and Technology Innovation Project2022CXGC020501).
文摘The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrated with microfluidics,typically comprises barcode array,sample loading,and reaction unit array chips.Here,we present a review of microfluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and single cells,including protein biomarkers,microRNA(miRNA),circulating tumor DNA(ctDNA),single-cell secreted proteins,single-cell exosomes,and cell interactions.We begin with an overview of current high-throughput detection and analysis approaches.Following this,we outline recent improvements in microfluidic devices for biomolecule and single-cell detection,highlighting the benefits and limitations of these devices.This paper focuses on the research and development of microfluidic barcode biochips,covering their self-assembly substrate materials and their specific applications with biomolecules and single cells.Looking forward,we explore the prospects and challenges of this technology,with the aim of contributing toward the use of microfluidic barcode detection biochips in medical diagnostics and therapies,and their large-scale commercialization.
基金supported by Shanghai Science and Technology Commission,China(No.21S11902100)Shanghai Municipal Health Commission Scientific Research Project(No.202140308)+3 种基金Clinical Research Project of Tongji Hospital of Tongji University[No.ITJ(ZD)2209]Shanghai Tongji Hospital National Natural Science Foundation Cultivation Project(No.GJPY2216)Shanghai Medical Innovation Research Special Foundation(No.23Y11908800)CSCO-Haosen Oncology Research Fund(No.Y-HS202301-0096).
文摘Objective:Prostate cancer(PCa)is a complex disease characterized by diverse cellular ecosystems within the tumor microenvironment(TME)and high tumor heterogeneity,which challenges clinically stratified management and reinforces the need for novel strategies to fight against castration-resistant PCa(CRPC).Methods:We performed single-cell RNA sequencing(scRNA-seq)on 10 untreated primary PCa tissues and integrated public scRNA-seq resources from three normal prostate tissues,two untreated primary PCa tissues,and six CRPC tumors to portray a comprehensive cellular and molecular interaction atlas of PCa.We further integrated the single-cell and bulk transcriptomes of PCa to establish a molecular classification system.Results:scRNA-seq profiles revealed substantial inter-and intra-tumoral heterogeneity across different cell subpopulations in untreated PCa and CRPC tumors.In the malignant epithelial reservoir,cells evolved along decoupled paths in treatment-naive PCa and CRPC tumors,and distinct transcriptional reprogramming processes were activated,highlighting anti-androgen therapy-induced lineage plasticity.Based on the specifically expressed markers of the epithelial subpopulations,we conducted unsupervised clustering analysis in The Cancer Genome Atlas prostate adenocarcinoma(TCGA-PRAD)cohort and identified three molecularly and clinically distinct subtypes.The C1 subtype,characterized by high enrichment of CRPC-enriched epithelial cells,had a high risk of rapid development of anti-androgen resistance and might require active surveillance and additional promising intervention treatments,such as integrin A3(ITGA3)+integrin B1(ITGB1)inhibition.The C2 subtype resembled the immune-modulated subtype that was most likely to benefit from anti-LAG3 immunotherapy.The C3 subtype had a favorable prognosis.Conclusions:Our study provides a comprehensive and high-resolution landscape of the intricate architecture of the PCa TME,and our trichotomic molecular taxonomy could help facilitate precision oncology.
基金Supported by Xinjiang Uygur Autonomous Region Natural Science Foundation,No.2020D01C199.
文摘BACKGROUND Gastric cancer(GC)poses a substantial risk to human health due to its high prevalence and mortality rates.Nevertheless,current therapeutic strategies remain insufficient.Single-cell RNA sequencing(scRNA-seq)offers the potential to provide comprehensive insights into GC pathogenesis.AIM To explore the distribution and dynamic changes of cell populations in the GC tumor microenvironment using scRNA-seq techniques.METHODS Cancerous tissues and paracancerous tissues were obtained from patients diagnosed with GC at various stages(I,II,III,and IV).Single-cell suspensions were prepared and analyzed using scRNA-seq to examine transcriptome profiles and cell-cell interactions.Additionally,quantitative real-time polymerase chain reaction(qRT-PCR)and flow cytometry were applied for measuring the expression of cluster of differentiation(CD)2,CD3D,CD3E,cytokeratin 19,cytokeratin 8,and epithelial cell adhesion molecules.RESULTS Transcriptome data from 73645 single cells across eight tissues of four patients were categorized into 25 distinct cell clusters,representing 10 different cell types.Variations were observed in these cell type distribution.The adjacent epithelial cells in stages II and III exhibited a degenerative trend.Additionally,the quantity of CD4 T cells and CD8 T cells were evidently elevated in cancerous tissues.Interaction analysis displayed a remarkable increase in interaction between B cells and other mast cells in stages II,III,and IV of GC.These findings were further validated through qRT-PCR and flow cytometry,demonstrating elevated T cells and declined epithelial cells within the cancerous tissues.CONCLUSION This study provides a comprehensive analysis of cell dynamics across GC stages,highlighting key interactions within the tumor microenvironment.These findings offer valuable insights for developing novel therapeutic strategies.
基金supported by the National Natural Science Foundation of China,Nos.81970820(to HX),31771644(to JL),31930068(to JL),82371176(to JL),81801331(to LC)National Key Research and Development Project of China.Nos.2017YFA0104100(to JL),2017YFA0701304(to HX)+1 种基金Shanghai Yangzhi Rehabilitation Hospital(Shanghai Sunshine Rehabilitation Center)Talent Introduction Plan,No.KYPT202204(to LC)the Fundamental Research Funds for the Central Universities,No.22120230292(to JL)。
文摘Inflammation plays a crucial role in the regeneration of fish and avian retinas.However,how inflammation regulates Müller glia(MG)reprogramming remains unclear.Here,we used single-cell RNA sequencing to investigate the cell heterogeneity and interactions of MG and immune cells in the regenerating zebrafish retina.We first showed that two types of quiescent MG(resting MG1 and MG2)reside in the uninjured retina.Following retinal injury,resting MG1 transitioned into an activated state expressing known reprogramming genes,while resting MG2 gave rise to rod progenitors.We further showed that retinal microglia can be categorized into three subtypes(microglia-1,microglia-2,and proliferative)and pseudotime analysis demonstrated dynamic changes in microglial status following retinal injury.Analysis of cell–cell interactions indicated extensive crosstalk between immune cells and MG,with many interactions shared among different immune cell types.Finally,we showed that inflammation activated Jak1–Stat3 signaling in MG,promoting their transition from a resting to an activated state.Our study reveals the cell heterogeneity and crosstalk of immune cells and MG in zebrafish retinal repair,and may provide valuable insights into future mammalian retina regeneration.
