Microwave thermochemotherapy(MTC)has been applied to treat lip squamous cell carcinoma(LSCC),but a deeper understanding of its therapeutic mechanisms and molecular biology is needed.To address this,we used single-cell...Microwave thermochemotherapy(MTC)has been applied to treat lip squamous cell carcinoma(LSCC),but a deeper understanding of its therapeutic mechanisms and molecular biology is needed.To address this,we used single-cell transcriptomics(scRNA-seq)and spatial transcriptomics(ST)to highlight the pivotal role of tumor-associated neutrophils(TANs)among tumor-infiltrating immune cells and their therapeutic response to MTC.MNDA+TANs with anti-tumor activity(N1-phenotype)are found to be abundantly infiltrated by MTC with benefit of increased blood perfusion,and these TANs are characterized by enhanced cytotoxicity,ameliorated hypoxia,and upregulated IL1B,activating T&NK cells and fibroblasts via IL1B-IL1R.In this highly anti-tumor immunogenic and hypoxia-reversed microenvironment under MTC,fibroblasts accumulated in the tumor front(TF)can recruit N1-TANs via CXCL2-CXCR2 and clear N2-TANs(pro-tumor phenotype)via CXCL12-CXCR4,which results in the aggregation of N1-TANs and extracellular matrix(ECM)deposition.In addition,we construct an N1-TANs marker,MX2,which positively correlates with better prognosis in LSCC patients,and employ deep learning techniques to predict expression of MX2 from hematoxylin-eosin(H&E)-stained images so as to conveniently guide decision making in clinical practice.Collectively,our findings demonstrate that the N1-TANs/fibroblasts defense wall formed in response to MTC effectively combat LSCC.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
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
Aging is one of the causes of cognitive dysfunction,which seriously affects people's quality of life.Unsaponifiable matter(USM)has antioxidant potential,but the molecular mechanisms that ameliorate aging and cogni...Aging is one of the causes of cognitive dysfunction,which seriously affects people's quality of life.Unsaponifiable matter(USM)has antioxidant potential,but the molecular mechanisms that ameliorate aging and cognitive dysfunction are unknown.In this study,we used a galactose-induced brain aging mouse model and systematically analyzed the mechanism of USM in delaying aging in mice by detecting changes in serum and brain by metabolomics and transcriptomics.USM was compared with the model group,and non-targeted metabolomics identified 68(15 up-regulated,53 down-regulated)differentially metabolites,and transcriptomics identified 303 differentially expressed genes(228 up-regulated,75 down-regulated).Combined multi-omics analyses showed that USM maintains normal brain function by regulating glycolytic processes,the tricarboxylic acid cycle(TCA),tryptophan metabolism,pyrimidine metabolism,the alanine,aspartate,and glutamate metabolism,and p38 mitogen-activated protein kinase(p38 MAPK)pathway.Meanwhile,USM increased neurotransmitter release from GABAergic synapses and cholinergic synapses by regulating synaptic vesicle cycling.In summary,USM increased energy metabolism and enhanced brain nerve signaling in the mouse brain,thereby delaying brain aging.This investigation offers novel perspectives into the molecular mechanism of USM to mitigate brain aging.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
Gastric cancer(GC)remains a major global health challenge,because of its poor prognosis and limited treatment options in advanced stages1,2.Recent advancements in immunotherapy,highlighted by the findings of the CHECK...Gastric cancer(GC)remains a major global health challenge,because of its poor prognosis and limited treatment options in advanced stages1,2.Recent advancements in immunotherapy,highlighted by the findings of the CHECKMATE-649,ORIENT-16,and KEYNOTE-859 trials,have markedly transformed the treatment paradigm for advanced gastric cancer(AGC)3-5.展开更多
Background:In this research,we explored the operational principles of Huangqin Shegan decoction(HQSGD)for addressing acute pneumonia utilizing network pharmacology(NP)and transcriptomic analysis.Methods:Methods:A rat ...Background:In this research,we explored the operational principles of Huangqin Shegan decoction(HQSGD)for addressing acute pneumonia utilizing network pharmacology(NP)and transcriptomic analysis.Methods:Methods:A rat model of acute pneumonia was developed by treating rats with lipopolysaccharide(LPS)through a non-exposed tracheal drip.The pharmacological effects of HQSGD were evaluated via histopathological analysis of rat lung tissues,histological scoring of lung injury,assessment of lung index,serum inflammatory factors,oxidative stress levels,western blotting,and qRT-PCR.The active compounds of HQSGD were detected utilizing ultra-performance liquid chromatography coupled with tandem mass spectrometry(UPLC-MS/MS).NP and transcriptomic analysis were integrated to determine signaling pathways implicated in the pharmacological activity of HQSGD.The expression levels of mRNA and protein for factors implicated in these pathways were evaluated in rat lung tissues via qRT-PCR and western blotting,respectively.Results:HQSGD alleviated acute pneumonia in rats by reducing the lung index and the levels of TNF-α,IL-1β,CRP,and MDA while increasing the levels of SOD.The UPLC-MS/MS and NP techniques facilitated the identification of 28 bioactive constituents present in HQSGD.The principal 20 KEGG pathways were identified by intersecting the targets of HQSGD with pneumonia-related targets.These pathways were screened by comparing the transcriptomic data of the blank and model cohorts and those of the model and drug administration cohorts.GO and KEGG analyses indicated that the PI3K/AKT/NF-κB pathway was a potentially effective target of HQSGD.Conclusion:This investigation revealed the overall multi-component,multi-target,and multi-pathway interactions of HQSGD in the treatment of acute pneumonia.展开更多
While bulk RNA sequencing and single-cell RNA sequencing have shed light on cellular heterogeneity and potential molecular mechanisms in the musculoskeletal system in both physiological and various pathological states...While bulk RNA sequencing and single-cell RNA sequencing have shed light on cellular heterogeneity and potential molecular mechanisms in the musculoskeletal system in both physiological and various pathological states,the spatial localization of cells and molecules and intercellular interactions within the tissue context require further elucidation.Spatial transcriptomics has revolutionized biological research by simultaneously capturing gene expression profiles and in situ spatial information of tissues,gradually finding applications in musculoskeletal research.This review provides a summary of recent advances in spatial transcriptomics and its application to the musculoskeletal system.The classification and characteristics of data acquisition techniques in spatial transcriptomics are briefly outlined,with an emphasis on widely-adopted representative technologies and the latest technological breakthroughs,accompanied by a concise workflow for incorporating spatial transcriptomics into musculoskeletal system research.The role of spatial transcriptomics in revealing physiological mechanisms of the musculoskeletal system,particularly during developmental processes,is thoroughly summarized.Furthermore,recent discoveries and achievements of this emerging omics tool in addressing inflammatory,traumatic,degenerative,and tumorous diseases of the musculoskeletal system are compiled.Finally,challenges and potential future directions for spatial transcriptomics,both as a field and in its applications in the musculoskeletal system,are discussed.展开更多
The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the...The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the relationships among pallial subregions in different species remain poorly characterized,particularly regarding the identification of homologous neurons and their transcriptional signatures.In this study,we utilized singlenucleus RNA sequencing to examine over 130?000 nuclei from the macaque(Macaca fascicularis)neocortex,complemented by datasets from humans(Homo sapiens),mice(Mus musculus),zebra finches(Taeniopygia guttata),turtles(Chrysemys picta bellii),and lizards(Pogona vitticeps),enablingcomprehensivecross-species comparison.Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium.Notable similarities were observed among cell subtypes,particularly within PVALB+inhibitory neurons,which exhibited species-preferred subtypes.Furthermore,correlations between pallial subregions and several transcription factor candidates were identified,including RARB,DLX2,STAT6,NR3C1,and THRB,with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts.These results highlight the conserved nature of inhibitory neurons,remarkable regional divergence of excitatory neurons,and species-specific gene expression and regulation in amniote pallial neurons.Collectively,these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.展开更多
A comprehensive understanding of the molecular details at spatial levels within heterogeneous cardiac tissue in heart failure(HF)is paramount for enhancing our knowledge of the pathophysiology of HF and pinpointing po...A comprehensive understanding of the molecular details at spatial levels within heterogeneous cardiac tissue in heart failure(HF)is paramount for enhancing our knowledge of the pathophysiology of HF and pinpointing potential therapeutic targets.Here,we present an analytical strategy for the deep discovery of heterogeneous metabolism and drug response in the heart tissue of rats with HF using airflow-assisted desorption electrospray ionization mass spectrometry imaging(AFADESI-MSI)coupled with bulk RNAsequencing.Spatial metabolomics illustrated pronounced metabolic heterogeneity between the infarct(I),infarct margin(IM),and non-infarct(NI)areas of heart tissue in HF.Integrated transcriptomics showed that increased mRNA expression of ATP citrate lyase disrupted the tricarboxylic acid(TCA)cycle in the NI area.Impairment of the carnitine shuttle system led to a significant accumulation of carnitines,suggesting potential abnormalities in fatty acid(FA)oxidation.Coupling on-tissue chemical derivatization with AFADESI-MSI enabled us to confirm the occurrence of incomplete oxidation of FAs in the NI area.Additionally,we observed a heterogeneous drug response between the anti-HF medications valsartan and Qishen Yiqi Dripping Pills(QDP).Valsartan exhibited a more pronounced effect on metabolic regulation in the I area,whereas QDP exerted stronger regulatory effects on metabolism in the NI area.Utilizing this method,four potential therapeutic targets were identified in HF:CPT1A,PDHB,ACLY,and BCAT2,which were preliminarily validated by western blotting.Overall,integrating spatial metabolomics with transcriptomics facilitates comprehensive analyses that link differential metabolites and genes,enabling a more precise characterization of metabolic changes in heart injury microareas and providing effective methods for elucidating molecular mechanisms and identifying potential therapeutic targets for HF.展开更多
Diabetic kidney disease(DKD),a primary cause of end-stage renal disease,results from progressive tissue remodeling and loss of kidney function.While single-cell RNA sequencing has significantly accelerated our underst...Diabetic kidney disease(DKD),a primary cause of end-stage renal disease,results from progressive tissue remodeling and loss of kidney function.While single-cell RNA sequencing has significantly accelerated our understanding of cellular diversity and dynamics in DKD,its lack of spatial resolution limits insights into tissue-specific dysregulation and the microenvironment.Spatial transcriptomics(ST)is an innovative technology that combines gene expression with spatial localization,offering a powerful approach to dissect the molecular mechanisms of DKD.This mini-review introduces how ST has transformed DKD research by enabling spatially resolved analysis of cell interactions and identifying localized molecular alterations in glomeruli and tubules.ST has revealed dynamic intercellular communication within the renal microenvironment,lesion-specific gene expression patterns,and immune infiltration profiles.For example,SlideseqV2 has highlighted disease-specific cellular neighborhoods and associated signaling networks.Furthermore,ST has pinpointed key genes implicated in disease progression,such as fibrosis-related proteins and transcription factors in tubular damage.By integration of ST with computational tools such as machine learning and network-based analysis can help uncover gene regulatory mechanisms and potential therapeutic targets.However,challenges remain in limited spatial resolution,high data complexity,and computational demands.Addressing these limitations is essential for advancing precision medicine in DKD.展开更多
Spatial transcriptomics technology provides novel insights into the spatial organization of gene expression during embryonic development.In this study,we propose a method that integrates analysis across both temporal ...Spatial transcriptomics technology provides novel insights into the spatial organization of gene expression during embryonic development.In this study,we propose a method that integrates analysis across both temporal and spatial dimensions to investigate spatial transcriptomics data from mouse embryos at different developmental stages.We quantified the spatial expression pattern of each gene at various stages by calculating its Moran’s I.Furthermore,by employing time-series clustering to identify dynamic co-expression modules,we identified several developmentally stage-specific regulatory gene modules.A key finding was the presence of distinct,stage-specific gene network modules across different developmental periods:Early modules focused on morphogenesis,mid-stage on organ development,and late-stage on neural and tissue maturation.Functional enrichment analysis further confirmed the core biological functions of each module.The dynamic,spatially-resolved gene expression model constructed in this study not only provides new biological insights into the programmed spatiotemporal reorganization of gene regulatory networks during embryonic development but also presents an effective approach for analyzing complex spatiotemporal omics data.This work provides a new perspective for understanding developmental biology,regenerative medicine,and related fields.展开更多
Periodontal bone defects,primarily caused by periodontitis,are highly prevalent in clinical settings and manifest as bone fenestration,dehiscence,or attachment loss,presenting a significant challenge to oral health.In...Periodontal bone defects,primarily caused by periodontitis,are highly prevalent in clinical settings and manifest as bone fenestration,dehiscence,or attachment loss,presenting a significant challenge to oral health.In regenerative medicine,harnessing developmental principles for tissue repair offers promising therapeutic potential.Of particular interest is the condensation of progenitor cells,an essential event in organogenesis that has inspired clinically effective cell aggregation approaches in dental regeneration.However,the precise cellular coordination mechanisms during condensation and regeneration remain elusive.Here,taking the tooth as a model organ,we employed single-cell RNA sequencing to dissect the cellular composition and heterogeneity of human dental follicle and dental papilla,revealing a distinct Platelet-derived growth factor receptor alpha(PDGFRA)mesenchymal stem/stromal cell(MSC)population with remarkable odontogenic potential.Interestingly,a reciprocal paracrine interaction between PDGFRA^(+)dental follicle stem cells(DFSCs)and CD31^(+)Endomucin^(+)endothelial cells(ECs)was mediated by Vascular endothelial growth factor A(VEGFA)and Platelet-derived growth factor subunit BB(PDGFBB).This crosstalk not only maintains the functionality of PDGFRA^(+)DFSCs but also drives specialized angiogenesis.In vivo periodontal bone regeneration experiments further reveal that communication between PDGFRA+DFSC aggregates and recipient ECs is essential for effective angiogenic-osteogenic coupling and rapid tissue repair.Collectively,our results unravel the importance of MSC-EC crosstalk mediated by the VEGFA and PDGFBB-PDGFRA reciprocal signaling in orchestrating angiogenesis and osteogenesis.These findings not only establish a framework for deciphering and promoting periodontal bone regeneration in potential clinical applications but also offer insights for future therapeutic strategies in dental or broader regenerative medicine.展开更多
Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various tissues.Graph-based geometric deep learning has gained widespread adoption for...Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various tissues.Graph-based geometric deep learning has gained widespread adoption for spatial domain identification tasks.Currently,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain identification.To tackle this challenge,we propose a novel method,SpaGRA(https://github.com/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph augmentation.SpaGRA uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive learning.Additionally,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random selection.Experimental results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different protocols.Using SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD data.Overall,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.展开更多
The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic an...The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.展开更多
[Objectives]To further explore the mechanism of quercetin regulating the activity of Sune-1 cells.[Methods]High-throughput mRNA-miRNA transcriptome sequencing technology was used to screen miRNA in Sune-1 cells treate...[Objectives]To further explore the mechanism of quercetin regulating the activity of Sune-1 cells.[Methods]High-throughput mRNA-miRNA transcriptome sequencing technology was used to screen miRNA in Sune-1 cells treated with quercetin.[Results]Statistical analysis showed that 1264 miRNAs were differentially expressed in Sune-1 cells treated with quercetin,of which 716 were significantly up-regulated and 548 were significantly down-regulated;191 miRNAs were differentially expressed in Sune-1 cells treated with quercetin,of which 129 were significantly up-regulated and 62 were significantly down-regulated.By comparing the expression differences of these mRNAs and miRNAs in different samples,six different expression patterns were clustered.The expression of the above miRNAs was verified by real-time quantitative PCR(qPCR),and the results were highly consistent with the transcriptome sequencing data.In addition,Gene Ontology annotation and functional enrichment analysis of miRNA target genes showed that CTGF,VHL and H19,which are related to the regulation of cell proliferation signal transduction,were predicted to be new targets of differential miRNAs such as miR494-3p and miR675-3p and may play an important regulatory role in the process of Quercetin inhibiting the proliferation of Sune-1 cells.[Conclusions]This study provides a basis for the rational use of anti-tumor functional components of traditional Chinese medicine,and also provides a theoretical basis for the targeted therapy of nasopharyngeal carcinoma.展开更多
Waterlogging stress significantly impairs plant growth and reduces crop yields.Spermidine(Spd),functioning as a second messenger,demonstrates positive effects on plant growth under waterlogging stress conditions.Howev...Waterlogging stress significantly impairs plant growth and reduces crop yields.Spermidine(Spd),functioning as a second messenger,demonstrates positive effects on plant growth under waterlogging stress conditions.However,the molecular mechanisms by which exogenous Spd application alleviates waterlogging stress remain unclear.This study employed physiological analysis and multi-omics approaches to investigate the effect of Spd application on waterlogging stress.The application of Spd enhanced the expression of genes related to light-harvesting complex(LHC),photosynthesis,and starch-related pathways,while inhibiting chlorophyll degradation and maintaining higher photosynthetic rates,thereby increasing biomass accumulation under waterlogging stress.The activation of genes associated with trehalose and Spd biosynthesis resulted in elevated accumulation of trehalose and endogenous Spd.The inhibition of 1-aminocyclopropane-1-carboxylic acid(ACC)oxidase(ACO)expression contributed to reduced ethylene emission,enhancing maize resistance to waterlogging.Following Spd application,auxin-related genes were up-regulated and indole acetic acid(IAA)content increased,promoting cell elongation in maize and maintaining normal growth under waterlogging stress.Additionally,the upregulation of lipid-related genes led to increased lipid content,protecting cell membranes under waterlogging conditions.These molecular and physiological modifications collectively enhanced resistance to waterlogging stress.These findings advance our understanding of Spd's regulatory roles in mitigating waterlogging damage and provide valuable insights for breeding waterlogging-tolerant maize varieties.展开更多
Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains...Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains very high levels of Vc. However, the Vc content of R. roxburghii varies considerably during plant development and ripening. To better understand the molecular mechanisms that underlie fluctuations in Vc content of R. roxburghii fruit at different developmental stages, we performed transcriptomic and metabolomic analyses and identified two significant gene networks/modules and 168 transcription factors directly involved in Vc synthesis. Promoter analysis of two core genes involved in Vc synthesis, RrGGP and RrGalUR, revealed the presence of a retroviral long terminal repeat(LTR) insert in the RrGalUR promoter. Using yeast one-hybrid and dual-luciferase assays, we demonstrated that the transcription factors RrHY5H and RrZIP9 bind to the promoter of RrGGP to promote its expression. RrZIP6 and RrWRKY4 bind to the LTR in the RrGalUR promoter to promote its expression. Our results reveal a molecular mechanism that controls Vc synthesis and accumulation in R. roxburghii fruit.展开更多
BACKGROUND Diabetic neuropathy(DN)is a progressive disorder with limited effective treatment options.AIM To identify potential therapeutic targets for DN by integrating plasma proteomic and transcriptomic data.METHODS...BACKGROUND Diabetic neuropathy(DN)is a progressive disorder with limited effective treatment options.AIM To identify potential therapeutic targets for DN by integrating plasma proteomic and transcriptomic data.METHODS A comprehensive analytical framework was developed to identify multi-omics biomarkers of DN.Protein-protein interaction network and Gene Ontology analyses were performed to explore the biological functions of biomarkers.Tier 1 target proteins were further analyzed.Candidate drug prediction and molecular docking studies were conducted to identify potential treatments while assessing the side effects of key target proteins.The mediation of immune cells in the association between proteins and DN was examined through two-step network Mendelian randomization(MR)analysis.RESULTS Nine DN-associated proteins were identified by analyzing protein quantitative trait loci from extensive genome-wide association study data.BTN3A1 and MICB were confirmed using MR,summary data-based MR,and colocalization analyses.Of the nine,HSPA1B,PSMB9,BTN3A1,SCGN,NOTUM,and MICB showed negative associations with DN,whereas WARS,BRD2,and CSNK2B were positive.Gene Ontology analysis indicated enrichment in inflammatory response and neuronal injury pathways.BTN3A1 and MICB were identified as Tier 1 targets.Drug prediction and molecular docking analyses indicated cyclosporin A as a potential therapeutic candidate.Two-step network MR analysis showed that MICB mediated DN through human leukocyte antigen-DR++monocytes.These integrated findings point to an immune-mediated mechanism with translational potential and nominate BTN3A1 and MICB for focused functional validation.CONCLUSION Our integrated multi-omics approach identified two promising therapeutic targets for DN,laying the groundwork for new treatment strategies and enhancing our understanding of MICB’s role in DN.展开更多
Background Clostridium perfringens is a pathogen that secretes multiple toxins,impacting humans and animals.It can cause intestinal diseases such as necrotic enteritis.Although tannins inhibit C.perfringens proliferat...Background Clostridium perfringens is a pathogen that secretes multiple toxins,impacting humans and animals.It can cause intestinal diseases such as necrotic enteritis.Although tannins inhibit C.perfringens proliferation,the precise underlying mechanisms are unclear.Objective This study integrated transcriptomics and metabolomics to systematically investigate the mechanism by which tannins,specifically pentagalloylglucose(PGG)and tannic acid(TA),inhibit C.perfringens and potential pathways to alleviate infection in vivo.Results Ion concentration measurements,flow cytometric analysis,and transmission electron microscopy revealed that PGG and TA damaged the cell membrane structure of C.perfringens,triggering cytoplasmic content leakage.Additionally,PGG and TA significantly affected C.perfringens at the transcriptional and metabolic levels.Bioinformatics analysis revealed that PGG and TA induced amino acid restriction,disrupted energy metabolism,and impeded the ability of C.perfringens to sense and respond to the external environment.In an in vitro C.perfringens-infected intestinal cell model,PGG and TA boundαtoxin,significantly reduced the mRNA expression of inflammatory factors,and improved intestinal barrier function and cell viability.Compared to PGG,TA exhibited stronger inhibitory activity against C.perfringens and binding toαtoxin.In vivo,PGG and TA alleviated C.perfringens-induced weight loss in mice,improved intestinal villi morphology,and reduced intestinal inflammation and tight junction gene dysregulation.Conclusion These findings indicate that tannins inhibit C.perfringens,improve gut tissue integrity and reduce inflammation,demonstrating their multi-target effects of resisting intestinal diseases caused by harmful bacteria.This offers new insights for plant polyphenol-based strategies against necrotic enteritis.展开更多
基金supported by National Natural Science Foundation of China grants(Nos.82173326 and 82473058)Key Research and Development Project of Sichuan Province(Nos.2024YFFK0374 and 2024YFFK0198)Interdisciplinary Innovation Project of West China College of Stomatology,Sichuan University(RD-03-202004).
文摘Microwave thermochemotherapy(MTC)has been applied to treat lip squamous cell carcinoma(LSCC),but a deeper understanding of its therapeutic mechanisms and molecular biology is needed.To address this,we used single-cell transcriptomics(scRNA-seq)and spatial transcriptomics(ST)to highlight the pivotal role of tumor-associated neutrophils(TANs)among tumor-infiltrating immune cells and their therapeutic response to MTC.MNDA+TANs with anti-tumor activity(N1-phenotype)are found to be abundantly infiltrated by MTC with benefit of increased blood perfusion,and these TANs are characterized by enhanced cytotoxicity,ameliorated hypoxia,and upregulated IL1B,activating T&NK cells and fibroblasts via IL1B-IL1R.In this highly anti-tumor immunogenic and hypoxia-reversed microenvironment under MTC,fibroblasts accumulated in the tumor front(TF)can recruit N1-TANs via CXCL2-CXCR2 and clear N2-TANs(pro-tumor phenotype)via CXCL12-CXCR4,which results in the aggregation of N1-TANs and extracellular matrix(ECM)deposition.In addition,we construct an N1-TANs marker,MX2,which positively correlates with better prognosis in LSCC patients,and employ deep learning techniques to predict expression of MX2 from hematoxylin-eosin(H&E)-stained images so as to conveniently guide decision making in clinical practice.Collectively,our findings demonstrate that the N1-TANs/fibroblasts defense wall formed in response to MTC effectively combat LSCC.
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 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 Key Research and Development Program(2022YFD1600402).
文摘Aging is one of the causes of cognitive dysfunction,which seriously affects people's quality of life.Unsaponifiable matter(USM)has antioxidant potential,but the molecular mechanisms that ameliorate aging and cognitive dysfunction are unknown.In this study,we used a galactose-induced brain aging mouse model and systematically analyzed the mechanism of USM in delaying aging in mice by detecting changes in serum and brain by metabolomics and transcriptomics.USM was compared with the model group,and non-targeted metabolomics identified 68(15 up-regulated,53 down-regulated)differentially metabolites,and transcriptomics identified 303 differentially expressed genes(228 up-regulated,75 down-regulated).Combined multi-omics analyses showed that USM maintains normal brain function by regulating glycolytic processes,the tricarboxylic acid cycle(TCA),tryptophan metabolism,pyrimidine metabolism,the alanine,aspartate,and glutamate metabolism,and p38 mitogen-activated protein kinase(p38 MAPK)pathway.Meanwhile,USM increased neurotransmitter release from GABAergic synapses and cholinergic synapses by regulating synaptic vesicle cycling.In summary,USM increased energy metabolism and enhanced brain nerve signaling in the mouse brain,thereby delaying brain aging.This investigation offers novel perspectives into the molecular mechanism of USM to mitigate brain aging.
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supported by The National Key Research and Development Program of China(Grant no.2021YFA0910100)Healthy Zhejiang One Million People Cohort(Grant no.K-20230085)+5 种基金Post-doctoral Innovative Talent Support Program(Grant no.BX2023375)Lingyan Project of Zhejiang Provincial Department of Science and Technology(Grant no.2025C02059)the National Natural Science Foundation of China(Grant nos.82304946,82473489,and 82403546)Natural Science Foundation of Zhejiang Province(Grant nos.LR21H280001,LGF22H160056,ZCLQN25H1602,and LMS25H160006)Medicine and Health Science Fund of Zhejiang Province Health Commission(Grant nos.2025KY047 and 2022KY658)Traditional Chinese Medicine Science and Technology Project of Zhejiang Provincial Health Commission(Grant no.2022ZA023).
文摘Gastric cancer(GC)remains a major global health challenge,because of its poor prognosis and limited treatment options in advanced stages1,2.Recent advancements in immunotherapy,highlighted by the findings of the CHECKMATE-649,ORIENT-16,and KEYNOTE-859 trials,have markedly transformed the treatment paradigm for advanced gastric cancer(AGC)3-5.
基金the"Qin Medicine"Quality Evaluation and Resource Development Discipline Innovation Team Project of Shaanxi University of Traditional Chinese Medicine(2019-QN01)Shaanxi University of Traditional Chinese Medicine School of Pharmacy/Shaanxi Engineering Research Centre for the Application and Development of Qinling Herbal Medicine,"Qin Medicine"Research and Development Key Laboratory(2019-QYPT-002)+2 种基金Shaanxi Provincial Administration of Traditional Chinese Medicine Province,Research and Development Key Laboratory(2019-QYPT-002)Shaanxi Provincial Administration of Traditional Chinese Medicine Province Chinese medicine province-wide earmarked special project:"Qin medicine planting and breeding guide research"(2021-QYZL-02)Shaanxi Provincial Science and Technology Department project:Chinese medicine Scutellaria baicalensis germplasm selection,seedling breeding and planting key technology research(2016KTTSSF01-01-01)and other projects.
文摘Background:In this research,we explored the operational principles of Huangqin Shegan decoction(HQSGD)for addressing acute pneumonia utilizing network pharmacology(NP)and transcriptomic analysis.Methods:Methods:A rat model of acute pneumonia was developed by treating rats with lipopolysaccharide(LPS)through a non-exposed tracheal drip.The pharmacological effects of HQSGD were evaluated via histopathological analysis of rat lung tissues,histological scoring of lung injury,assessment of lung index,serum inflammatory factors,oxidative stress levels,western blotting,and qRT-PCR.The active compounds of HQSGD were detected utilizing ultra-performance liquid chromatography coupled with tandem mass spectrometry(UPLC-MS/MS).NP and transcriptomic analysis were integrated to determine signaling pathways implicated in the pharmacological activity of HQSGD.The expression levels of mRNA and protein for factors implicated in these pathways were evaluated in rat lung tissues via qRT-PCR and western blotting,respectively.Results:HQSGD alleviated acute pneumonia in rats by reducing the lung index and the levels of TNF-α,IL-1β,CRP,and MDA while increasing the levels of SOD.The UPLC-MS/MS and NP techniques facilitated the identification of 28 bioactive constituents present in HQSGD.The principal 20 KEGG pathways were identified by intersecting the targets of HQSGD with pneumonia-related targets.These pathways were screened by comparing the transcriptomic data of the blank and model cohorts and those of the model and drug administration cohorts.GO and KEGG analyses indicated that the PI3K/AKT/NF-κB pathway was a potentially effective target of HQSGD.Conclusion:This investigation revealed the overall multi-component,multi-target,and multi-pathway interactions of HQSGD in the treatment of acute pneumonia.
基金supported by The National Natural Science Youth Foundation of China(Grant No.82102584).
文摘While bulk RNA sequencing and single-cell RNA sequencing have shed light on cellular heterogeneity and potential molecular mechanisms in the musculoskeletal system in both physiological and various pathological states,the spatial localization of cells and molecules and intercellular interactions within the tissue context require further elucidation.Spatial transcriptomics has revolutionized biological research by simultaneously capturing gene expression profiles and in situ spatial information of tissues,gradually finding applications in musculoskeletal research.This review provides a summary of recent advances in spatial transcriptomics and its application to the musculoskeletal system.The classification and characteristics of data acquisition techniques in spatial transcriptomics are briefly outlined,with an emphasis on widely-adopted representative technologies and the latest technological breakthroughs,accompanied by a concise workflow for incorporating spatial transcriptomics into musculoskeletal system research.The role of spatial transcriptomics in revealing physiological mechanisms of the musculoskeletal system,particularly during developmental processes,is thoroughly summarized.Furthermore,recent discoveries and achievements of this emerging omics tool in addressing inflammatory,traumatic,degenerative,and tumorous diseases of the musculoskeletal system are compiled.Finally,challenges and potential future directions for spatial transcriptomics,both as a field and in its applications in the musculoskeletal system,are discussed.
基金supported by the National Key Research and Development Program (2022YEF0203200)National Science and Technology Innovation 2030 Major Program (STI2030-2021ZD0200100)National Key Research and Development Program (2018YFA0801400,2021YFA0805100)。
文摘The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the relationships among pallial subregions in different species remain poorly characterized,particularly regarding the identification of homologous neurons and their transcriptional signatures.In this study,we utilized singlenucleus RNA sequencing to examine over 130?000 nuclei from the macaque(Macaca fascicularis)neocortex,complemented by datasets from humans(Homo sapiens),mice(Mus musculus),zebra finches(Taeniopygia guttata),turtles(Chrysemys picta bellii),and lizards(Pogona vitticeps),enablingcomprehensivecross-species comparison.Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium.Notable similarities were observed among cell subtypes,particularly within PVALB+inhibitory neurons,which exhibited species-preferred subtypes.Furthermore,correlations between pallial subregions and several transcription factor candidates were identified,including RARB,DLX2,STAT6,NR3C1,and THRB,with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts.These results highlight the conserved nature of inhibitory neurons,remarkable regional divergence of excitatory neurons,and species-specific gene expression and regulation in amniote pallial neurons.Collectively,these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.
基金supported by the National Natural Science Foundation of China(No.82374158)National Science and Technology Major Project(No.2018ZX09711001-002-004)+1 种基金the Jiangxi University of Chinese Medicine Science and Technology Innovation Team Development Program(No.CXTD22007)the Medical and Health Technology Innovation Project(No.2022-I2M-1-020).
文摘A comprehensive understanding of the molecular details at spatial levels within heterogeneous cardiac tissue in heart failure(HF)is paramount for enhancing our knowledge of the pathophysiology of HF and pinpointing potential therapeutic targets.Here,we present an analytical strategy for the deep discovery of heterogeneous metabolism and drug response in the heart tissue of rats with HF using airflow-assisted desorption electrospray ionization mass spectrometry imaging(AFADESI-MSI)coupled with bulk RNAsequencing.Spatial metabolomics illustrated pronounced metabolic heterogeneity between the infarct(I),infarct margin(IM),and non-infarct(NI)areas of heart tissue in HF.Integrated transcriptomics showed that increased mRNA expression of ATP citrate lyase disrupted the tricarboxylic acid(TCA)cycle in the NI area.Impairment of the carnitine shuttle system led to a significant accumulation of carnitines,suggesting potential abnormalities in fatty acid(FA)oxidation.Coupling on-tissue chemical derivatization with AFADESI-MSI enabled us to confirm the occurrence of incomplete oxidation of FAs in the NI area.Additionally,we observed a heterogeneous drug response between the anti-HF medications valsartan and Qishen Yiqi Dripping Pills(QDP).Valsartan exhibited a more pronounced effect on metabolic regulation in the I area,whereas QDP exerted stronger regulatory effects on metabolism in the NI area.Utilizing this method,four potential therapeutic targets were identified in HF:CPT1A,PDHB,ACLY,and BCAT2,which were preliminarily validated by western blotting.Overall,integrating spatial metabolomics with transcriptomics facilitates comprehensive analyses that link differential metabolites and genes,enabling a more precise characterization of metabolic changes in heart injury microareas and providing effective methods for elucidating molecular mechanisms and identifying potential therapeutic targets for HF.
基金Supported by Science and Technology Research Program of Chongqing Municipal Education Commission,No.KJQN202100538Talent Innovation Project in Life Sciences of Chongqing Normal University,No.CSSK2023-04.
文摘Diabetic kidney disease(DKD),a primary cause of end-stage renal disease,results from progressive tissue remodeling and loss of kidney function.While single-cell RNA sequencing has significantly accelerated our understanding of cellular diversity and dynamics in DKD,its lack of spatial resolution limits insights into tissue-specific dysregulation and the microenvironment.Spatial transcriptomics(ST)is an innovative technology that combines gene expression with spatial localization,offering a powerful approach to dissect the molecular mechanisms of DKD.This mini-review introduces how ST has transformed DKD research by enabling spatially resolved analysis of cell interactions and identifying localized molecular alterations in glomeruli and tubules.ST has revealed dynamic intercellular communication within the renal microenvironment,lesion-specific gene expression patterns,and immune infiltration profiles.For example,SlideseqV2 has highlighted disease-specific cellular neighborhoods and associated signaling networks.Furthermore,ST has pinpointed key genes implicated in disease progression,such as fibrosis-related proteins and transcription factors in tubular damage.By integration of ST with computational tools such as machine learning and network-based analysis can help uncover gene regulatory mechanisms and potential therapeutic targets.However,challenges remain in limited spatial resolution,high data complexity,and computational demands.Addressing these limitations is essential for advancing precision medicine in DKD.
基金supported by the National Natural Science Foundation of China(Grant Nos.12090052,U24A2014,and 12325405).
文摘Spatial transcriptomics technology provides novel insights into the spatial organization of gene expression during embryonic development.In this study,we propose a method that integrates analysis across both temporal and spatial dimensions to investigate spatial transcriptomics data from mouse embryos at different developmental stages.We quantified the spatial expression pattern of each gene at various stages by calculating its Moran’s I.Furthermore,by employing time-series clustering to identify dynamic co-expression modules,we identified several developmentally stage-specific regulatory gene modules.A key finding was the presence of distinct,stage-specific gene network modules across different developmental periods:Early modules focused on morphogenesis,mid-stage on organ development,and late-stage on neural and tissue maturation.Functional enrichment analysis further confirmed the core biological functions of each module.The dynamic,spatially-resolved gene expression model constructed in this study not only provides new biological insights into the programmed spatiotemporal reorganization of gene regulatory networks during embryonic development but also presents an effective approach for analyzing complex spatiotemporal omics data.This work provides a new perspective for understanding developmental biology,regenerative medicine,and related fields.
基金supported by grants from the National Key Research and Development Program of China(2022YFA1104400)the National Natural Science Foundation of China(82170988,82371020,82301028,82401201,82471011)+5 种基金the Young Science and Technology Rising Star Project of Shaanxi Province(2024ZC-KJXX-122)the China Postdoctoral Science Foundation(BX20230485)the Project of State Key Laboratory of Oral&Maxillofacial Reconstruction and Regeneration(2024MS04)the Shaanxi Provincial Health Research and Innovation Platform Construction Plan(2024PT-04)the“Rapid Response”Research projects(2023KXKT017 and 2023KXKT090)the Intramural Research Program project founded by Fourth Military Medical University(2024QMJJ008).
文摘Periodontal bone defects,primarily caused by periodontitis,are highly prevalent in clinical settings and manifest as bone fenestration,dehiscence,or attachment loss,presenting a significant challenge to oral health.In regenerative medicine,harnessing developmental principles for tissue repair offers promising therapeutic potential.Of particular interest is the condensation of progenitor cells,an essential event in organogenesis that has inspired clinically effective cell aggregation approaches in dental regeneration.However,the precise cellular coordination mechanisms during condensation and regeneration remain elusive.Here,taking the tooth as a model organ,we employed single-cell RNA sequencing to dissect the cellular composition and heterogeneity of human dental follicle and dental papilla,revealing a distinct Platelet-derived growth factor receptor alpha(PDGFRA)mesenchymal stem/stromal cell(MSC)population with remarkable odontogenic potential.Interestingly,a reciprocal paracrine interaction between PDGFRA^(+)dental follicle stem cells(DFSCs)and CD31^(+)Endomucin^(+)endothelial cells(ECs)was mediated by Vascular endothelial growth factor A(VEGFA)and Platelet-derived growth factor subunit BB(PDGFBB).This crosstalk not only maintains the functionality of PDGFRA^(+)DFSCs but also drives specialized angiogenesis.In vivo periodontal bone regeneration experiments further reveal that communication between PDGFRA+DFSC aggregates and recipient ECs is essential for effective angiogenic-osteogenic coupling and rapid tissue repair.Collectively,our results unravel the importance of MSC-EC crosstalk mediated by the VEGFA and PDGFBB-PDGFRA reciprocal signaling in orchestrating angiogenesis and osteogenesis.These findings not only establish a framework for deciphering and promoting periodontal bone regeneration in potential clinical applications but also offer insights for future therapeutic strategies in dental or broader regenerative medicine.
基金supported by the National Natural Science Foundation of China(Nos.62303271,U1806202,62103397)the Natural Science Foundation of Shandong Province(ZR2023QF081)Funding for open access charge:the National Natural Science Foundation of China(Nos.62303271,U1806202).
文摘Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various tissues.Graph-based geometric deep learning has gained widespread adoption for spatial domain identification tasks.Currently,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain identification.To tackle this challenge,we propose a novel method,SpaGRA(https://github.com/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph augmentation.SpaGRA uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive learning.Additionally,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random selection.Experimental results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different protocols.Using SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD data.Overall,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.
文摘The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.
基金Supported by Educational Research Project for Young and Middle-aged Teachers in Fujian Province(Science and Technology Category,JAT210477)。
文摘[Objectives]To further explore the mechanism of quercetin regulating the activity of Sune-1 cells.[Methods]High-throughput mRNA-miRNA transcriptome sequencing technology was used to screen miRNA in Sune-1 cells treated with quercetin.[Results]Statistical analysis showed that 1264 miRNAs were differentially expressed in Sune-1 cells treated with quercetin,of which 716 were significantly up-regulated and 548 were significantly down-regulated;191 miRNAs were differentially expressed in Sune-1 cells treated with quercetin,of which 129 were significantly up-regulated and 62 were significantly down-regulated.By comparing the expression differences of these mRNAs and miRNAs in different samples,six different expression patterns were clustered.The expression of the above miRNAs was verified by real-time quantitative PCR(qPCR),and the results were highly consistent with the transcriptome sequencing data.In addition,Gene Ontology annotation and functional enrichment analysis of miRNA target genes showed that CTGF,VHL and H19,which are related to the regulation of cell proliferation signal transduction,were predicted to be new targets of differential miRNAs such as miR494-3p and miR675-3p and may play an important regulatory role in the process of Quercetin inhibiting the proliferation of Sune-1 cells.[Conclusions]This study provides a basis for the rational use of anti-tumor functional components of traditional Chinese medicine,and also provides a theoretical basis for the targeted therapy of nasopharyngeal carcinoma.
基金supported by the China Agriculture Research System(CARS-02-20)the Henan Province Agro-ecosystem Field Observation and Research Station,China(30602535)。
文摘Waterlogging stress significantly impairs plant growth and reduces crop yields.Spermidine(Spd),functioning as a second messenger,demonstrates positive effects on plant growth under waterlogging stress conditions.However,the molecular mechanisms by which exogenous Spd application alleviates waterlogging stress remain unclear.This study employed physiological analysis and multi-omics approaches to investigate the effect of Spd application on waterlogging stress.The application of Spd enhanced the expression of genes related to light-harvesting complex(LHC),photosynthesis,and starch-related pathways,while inhibiting chlorophyll degradation and maintaining higher photosynthetic rates,thereby increasing biomass accumulation under waterlogging stress.The activation of genes associated with trehalose and Spd biosynthesis resulted in elevated accumulation of trehalose and endogenous Spd.The inhibition of 1-aminocyclopropane-1-carboxylic acid(ACC)oxidase(ACO)expression contributed to reduced ethylene emission,enhancing maize resistance to waterlogging.Following Spd application,auxin-related genes were up-regulated and indole acetic acid(IAA)content increased,promoting cell elongation in maize and maintaining normal growth under waterlogging stress.Additionally,the upregulation of lipid-related genes led to increased lipid content,protecting cell membranes under waterlogging conditions.These molecular and physiological modifications collectively enhanced resistance to waterlogging stress.These findings advance our understanding of Spd's regulatory roles in mitigating waterlogging damage and provide valuable insights for breeding waterlogging-tolerant maize varieties.
基金supported in part by the Priority Academic Program Development of Jiangsu Higher Education Institutions and the State Key Laboratory of Crop Genetics and Germplasm Enhancement (Grant No. ZW201813)supported by the high-performance computing platform at the Bioinformatics Center of Nanjing Agricultural University。
文摘Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains very high levels of Vc. However, the Vc content of R. roxburghii varies considerably during plant development and ripening. To better understand the molecular mechanisms that underlie fluctuations in Vc content of R. roxburghii fruit at different developmental stages, we performed transcriptomic and metabolomic analyses and identified two significant gene networks/modules and 168 transcription factors directly involved in Vc synthesis. Promoter analysis of two core genes involved in Vc synthesis, RrGGP and RrGalUR, revealed the presence of a retroviral long terminal repeat(LTR) insert in the RrGalUR promoter. Using yeast one-hybrid and dual-luciferase assays, we demonstrated that the transcription factors RrHY5H and RrZIP9 bind to the promoter of RrGGP to promote its expression. RrZIP6 and RrWRKY4 bind to the LTR in the RrGalUR promoter to promote its expression. Our results reveal a molecular mechanism that controls Vc synthesis and accumulation in R. roxburghii fruit.
基金Supported by the Key Project of the Affiliated Hospital of North Sichuan Medical College,No.2023ZD008the Project of the Doctoral Initiation Fund,No.2023GC002+3 种基金Scientific Research and Development Program Project,No.2024PTZK008Sichuan Province Clinical Key Specialty Construction Project,No.2023GZZKP002Science and Technology Project of Nanchong,No.22SXQT0364Research Development Plan Project of Affiliated Hospital of North Sichuan Medical College,No.2024MPZK003.
文摘BACKGROUND Diabetic neuropathy(DN)is a progressive disorder with limited effective treatment options.AIM To identify potential therapeutic targets for DN by integrating plasma proteomic and transcriptomic data.METHODS A comprehensive analytical framework was developed to identify multi-omics biomarkers of DN.Protein-protein interaction network and Gene Ontology analyses were performed to explore the biological functions of biomarkers.Tier 1 target proteins were further analyzed.Candidate drug prediction and molecular docking studies were conducted to identify potential treatments while assessing the side effects of key target proteins.The mediation of immune cells in the association between proteins and DN was examined through two-step network Mendelian randomization(MR)analysis.RESULTS Nine DN-associated proteins were identified by analyzing protein quantitative trait loci from extensive genome-wide association study data.BTN3A1 and MICB were confirmed using MR,summary data-based MR,and colocalization analyses.Of the nine,HSPA1B,PSMB9,BTN3A1,SCGN,NOTUM,and MICB showed negative associations with DN,whereas WARS,BRD2,and CSNK2B were positive.Gene Ontology analysis indicated enrichment in inflammatory response and neuronal injury pathways.BTN3A1 and MICB were identified as Tier 1 targets.Drug prediction and molecular docking analyses indicated cyclosporin A as a potential therapeutic candidate.Two-step network MR analysis showed that MICB mediated DN through human leukocyte antigen-DR++monocytes.These integrated findings point to an immune-mediated mechanism with translational potential and nominate BTN3A1 and MICB for focused functional validation.CONCLUSION Our integrated multi-omics approach identified two promising therapeutic targets for DN,laying the groundwork for new treatment strategies and enhancing our understanding of MICB’s role in DN.
基金The China Agriculture Research System Program(Project No.CARS-41-G04)Shenyang Governmental Science and Technology Program(Project No.22316-2-02)supported this work.
文摘Background Clostridium perfringens is a pathogen that secretes multiple toxins,impacting humans and animals.It can cause intestinal diseases such as necrotic enteritis.Although tannins inhibit C.perfringens proliferation,the precise underlying mechanisms are unclear.Objective This study integrated transcriptomics and metabolomics to systematically investigate the mechanism by which tannins,specifically pentagalloylglucose(PGG)and tannic acid(TA),inhibit C.perfringens and potential pathways to alleviate infection in vivo.Results Ion concentration measurements,flow cytometric analysis,and transmission electron microscopy revealed that PGG and TA damaged the cell membrane structure of C.perfringens,triggering cytoplasmic content leakage.Additionally,PGG and TA significantly affected C.perfringens at the transcriptional and metabolic levels.Bioinformatics analysis revealed that PGG and TA induced amino acid restriction,disrupted energy metabolism,and impeded the ability of C.perfringens to sense and respond to the external environment.In an in vitro C.perfringens-infected intestinal cell model,PGG and TA boundαtoxin,significantly reduced the mRNA expression of inflammatory factors,and improved intestinal barrier function and cell viability.Compared to PGG,TA exhibited stronger inhibitory activity against C.perfringens and binding toαtoxin.In vivo,PGG and TA alleviated C.perfringens-induced weight loss in mice,improved intestinal villi morphology,and reduced intestinal inflammation and tight junction gene dysregulation.Conclusion These findings indicate that tannins inhibit C.perfringens,improve gut tissue integrity and reduce inflammation,demonstrating their multi-target effects of resisting intestinal diseases caused by harmful bacteria.This offers new insights for plant polyphenol-based strategies against necrotic enteritis.
