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Single-cell transcriptomic atlas of goat ovarian aging 被引量:1
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作者 Dejun Xu Shuaifei Song +5 位作者 Fuguo Wang Yawen Li Ziyuan Li Hui Yao Yongju Zhao Zhongquan Zhao 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第1期146-161,共16页
Background The ovaries are one of the first organs that undergo degenerative changes earlier in the aging process,and ovarian aging is shown by a decrease in the number and quality of oocytes.However,little is known a... Background The ovaries are one of the first organs that undergo degenerative changes earlier in the aging process,and ovarian aging is shown by a decrease in the number and quality of oocytes.However,little is known about the molecular mechanisms of female age-related fertility decline in different types of ovarian cells during aging,especially in goats.Therefore,the aim of this study was to reveal the mechanisms driving ovarian aging in goats at single-cell resolution.Results For the first time,we surveyed the single-cell transcriptomic landscape of over 27,000 ovarian cells from newborn,young and aging goats,and identified nine ovarian cell types with distinct gene-expression signatures.Functional enrichment analysis showed that ovarian cell types were involved in their own unique biological processes,such as Wnt beta-catenin signalling was enriched in germ cells,whereas ovarian steroidogenesis was enriched in granulosa cells(GCs).Further analysis showed that ovarian aging was linked to GCs-specific changes in the antioxidant system,oxidative phosphorylation,and apoptosis.Subsequently,we identified a series of dynamic genes,such as AMH,CRABP2,THBS1 and TIMP1,which determined the fate of GCs.Additionally,FOXO1,SOX4,and HIF1A were identified as significant regulons that instructed the differentiation of GCs in a distinct manner during ovarian aging.Conclusions This study revealed a comprehensive aging-associated transcriptomic atlas characterizing the cell typespecific mechanisms during ovarian aging at the single-cell level and offers new diagnostic biomarkers and potential therapeutic targets for age-related goat ovarian diseases. 展开更多
关键词 GOAT Granulosa cells Ovarian aging single-cell transcriptomic
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Identification and validation of a pyroptosis-related prognostic model for colorectal cancer based on bulk and single-cell RNA sequencing data 被引量:2
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作者 Li-Hua Zhu Jun Yang +3 位作者 Yun-Fei Zhang Li Yan Wan-Rong Lin Wei-Qing Liu 《World Journal of Clinical Oncology》 2024年第2期329-355,共27页
BACKGROUND Pyroptosis impacts the development of malignant tumors,yet its role in colorectal cancer(CRC)prognosis remains uncertain.AIM To assess the prognostic significance of pyroptosis-related genes and their assoc... BACKGROUND Pyroptosis impacts the development of malignant tumors,yet its role in colorectal cancer(CRC)prognosis remains uncertain.AIM To assess the prognostic significance of pyroptosis-related genes and their association with CRC immune infiltration.METHODS Gene expression data were obtained from The Cancer Genome Atlas(TCGA)and single-cell RNA sequencing dataset GSE178341 from the Gene Expression Omnibus(GEO).Pyroptosis-related gene expression in cell clusters was analyzed,and enrichment analysis was conducted.A pyroptosis-related risk model was developed using the LASSO regression algorithm,with prediction accuracy assessed through K-M and receiver operating characteristic analyses.A nomo-gram predicting survival was created,and the correlation between the risk model and immune infiltration was analyzed using CIBERSORTx calculations.Finally,the differential expression of the 8 prognostic genes between CRC and normal samples was verified by analyzing TCGA-COADREAD data from the UCSC database.RESULTS An effective pyroptosis-related risk model was constructed using 8 genes-CHMP2B,SDHB,BST2,UBE2D2,GJA1,AIM2,PDCD6IP,and SEZ6L2(P<0.05).Seven of these genes exhibited differential expression between CRC and normal samples based on TCGA database analysis(P<0.05).Patients with higher risk scores demonstrated increased death risk and reduced overall survival(P<0.05).Significant differences in immune infiltration were observed between low-and high-risk groups,correlating with pyroptosis-related gene expression.CONCLUSION We developed a pyroptosis-related prognostic model for CRC,affirming its correlation with immune infiltration.This model may prove useful for CRC prognostic evaluation. 展开更多
关键词 Colorectal cancer PYROPTOSIS single-cell RNA sequencing Immune infiltration Prognostic model
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The early life immune dynamics and cellular drivers at single-cell resolution in lamb forestomachs and abomasum 被引量:1
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作者 Kailang Huang Bin Yang +2 位作者 Zebang Xu Hongwei Chen Jiakun Wang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第1期218-235,共18页
Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered ... Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered stomach is crucial for the health and well-being of young ruminants,especially the immune development.However,the dynamics of immune development are poorly understood.Results We investigated the early gene expression patterns across the four-chambered stomach in Hu sheep,at 5,10,15,and 25 days of age.We found that forestomachs share similar gene expression patterns,all four stomachs underwent widespread activation of both innate and adaptive immune responses from d 5 to 25,whereas the metabolic function were significantly downregulated with age.We constructed a cell landscape of the four-chambered stomach using single-cell sequencing.Integrating transcriptomic and single-cell transcriptomic analyses revealed that the immune-associated module hub genes were highly expressed in T cells,monocytes and macrophages,as well as the defense-associated module hub genes were highly expressed in endothelial cells in the four-stomach tissues.Moreover,the non-immune cells such as epithelial cells play key roles in immune maturation.Cell communication analysis predicted that in addition to immune cells,non-immune cells recruit immune cells through macrophage migration inhibitory factor signaling in the forestomachs.Conclusions Our results demonstrate that the immune and defense responses of four stomachs are quickly developing with age in lamb's early life.We also identified the gene expression patterns and functional cells associated with immune development.Additionally,we identified some key receptors and signaling involved in immune regulation.These results help to understand the early life immune development at single-cell resolution,which has implications to develop nutritional manipulation and health management strategies based on specific targets including key receptors and signaling pathways. 展开更多
关键词 Early life Forestomachs Four-chambered stomach Immune cells Immune system maturation MIF signaling RUMEN Ruminant development single-cell transcriptomic sequencing
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Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development
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作者 Mingdong Zhu Meng Zhang +8 位作者 Kunyong Huang Feifei Lu Hong Wang Shaolu Zhao Yinghong Yu Shaoqing Tang Haining Wu Peisong Hu Xiangjin Wei 《The Crop Journal》 SCIE CSCD 2024年第3期688-697,共10页
Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis.Here,the spatial expression of genes in developing rice seed plumules was characterized by single-cell tr... Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis.Here,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice cultivar.Of 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific genes.Marker genes of multiple cell types were expressed in several clusters,suggesting a complex developmental system.Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters.Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain clusters.Spatial expression patterns of genes involved in rapid seed germination,seedling growth,and development were identified.These findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop. 展开更多
关键词 RICE Plumule single-cell sequencing Regulatory network
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Single-cell and spatial omics:exploring hypothalamic heterogeneity
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作者 Muhammad Junaid Eun Jeong Lee Su Bin Lim 《Neural Regeneration Research》 SCIE CAS 2025年第6期1525-1540,共16页
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
关键词 cellular diversity HYPOTHALAMUS multi-omics single-cell transcriptomics spatial transcriptomics
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Single-cell transcriptomics reveals T-cell heterogeneity and immunomodulatory role of CD4^(+) T native cells in Candida albicans infection
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作者 KERAN JIA YANHAO ZHANG +8 位作者 MENGYU JIANG MENGGE CUI JIA WANG JIAJIA ZHANG HUIHAI ZHAO MENGYAN LI HUA WANG QUANMING ZOU HAO ZENG 《BIOCELL》 SCIE 2024年第9期1355-1368,共14页
Objective:Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms,including coordinated innate and adaptive immune responses,to neutralize invading fungi effectively.Exploring the im... Objective:Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms,including coordinated innate and adaptive immune responses,to neutralize invading fungi effectively.Exploring the immune microenvironment has the potential to inform the development of therapeutic strategies for fungal infections.Methods:The study analyzed individual immune cell profiles in peripheral blood mononuclear cells from Candida albicans-infected mice and healthy control mice using single-cell transcriptomics,fluorescence quantitative PCR,and Western blotting.We investigated intergroup differences in the dynamics of immune cell subpopulation infiltration,pathway enrichment,and differentiation during Candida albicans infection.Results:Our findings indicate that infiltration of CD4^(+)naive cells,regulatory T(Treg)cells,and Microtubules(MT)-associated cells increased after infection,along with impaired T cell activity.Notably,CD4^(+) T cells and plasma cells were enhanced after infection,suggesting that antibody production is dependent on T cells.In addition,we screened 6 hub genes,transcription factor forkhead box protein 3(Foxp3),cytotoxic T-lymphocyte associated protein 4(CTLA4),Interleukin 2 Receptor Subunit Beta(Il2rb),Cd28,C-C Motif Chemokine Ligand 5(Ccl5),and Cd27 for alterations associated with CD4^(+) T cell differentiation.Conclusions:These results provide a comprehensive immunological landscape of the mechanisms of Candida albicans infection and greatly advance our understanding of adaptive immunity in fungal infections. 展开更多
关键词 Candida albicans single-cell transcriptomics Immune microenvironment Fungal infections Hub gene
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Applications of single-cell RNA sequencing in spermatogenesis and molecular evolution
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作者 Wen-Bo Chen Meng-Fei Zhang +1 位作者 Fan Yang Jin-Lian Hua 《Zoological Research》 SCIE CSCD 2024年第3期575-585,共11页
Spermatogenic cell heterogeneity is determined by the complex process of spermatogenesis differentiation.However,effectively revealing the regulatory mechanisms underlying mammalian spermatogenic cell development and ... Spermatogenic cell heterogeneity is determined by the complex process of spermatogenesis differentiation.However,effectively revealing the regulatory mechanisms underlying mammalian spermatogenic cell development and differentiation via traditional methods is difficult.Advances in technology have led to the emergence of many single-cell transcriptome sequencing protocols,which have partially addressed these challenges.In this review,we detail the principles of 10x Genomics technology and summarize the methods for downstream analysis of single-cell transcriptome sequencing data.Furthermore,we explore the role of single-cell transcriptome sequencing in revealing the heterogeneity of testicular ecological niche cells,delineating the establishment and disruption of testicular immune homeostasis during human spermatogenesis,investigating abnormal spermatogenesis in humans,and,ultimately,elucidating the molecular evolution of mammalian spermatogenesis. 展开更多
关键词 single-cell RNA sequencing(scRNA-seq) SPERMATOGENESIS Molecular evolution Sertoli cell
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Single-cell profiling of the pig cecum at various developmental stages
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作者 Yan-Yuan Xiao Qing Zhang +9 位作者 Fei Huang Lin Rao Tian-Xiong Yao Si-Yu Yang Lei Xie Xiao-Xiao Zou Li-Ping Cai Jia-Wen Yang Bin Yang Lu-Sheng Huang 《Zoological Research》 SCIE CSCD 2024年第1期55-68,共14页
The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding... The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages. 展开更多
关键词 single-cell RNA-seq CECUM Bama Xiang pigs Various developmental stages Cellular heterogeneity
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A viscoelastic metamaterial beam for integrated vibration isolation and energy harvesting
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作者 Long ZHAO Zeqi LU +1 位作者 Hu DING Liqun CHEN 《Applied Mathematics and Mechanics(English Edition)》 SCIE EI CSCD 2024年第7期1243-1260,共18页
Locally resonant metamaterials have low-frequency band gaps and the capability of converging vibratory energy in the band gaps at resonant cells.It has been demonstrated by several researchers that the dissipatioin of... Locally resonant metamaterials have low-frequency band gaps and the capability of converging vibratory energy in the band gaps at resonant cells.It has been demonstrated by several researchers that the dissipatioin of vibratory energy within the band gap can be improved by using viscoelastic materials.This paper designs an integrated viscoelastic metamaterial for energy harvesting and vibration isolation.The viscoelastic metamaterial is achieved by a viscoelastic beam periodically arrayed with spatial ball-pendulum nonlinear energy harvesters.The nonlinear resonator with an energy harvesting function is achieved by placing a free-rolling magnetic ball in a spherical cavity with an additional induction coil.The dynamic equations of viscoelastic metamaterials under transverse excitation are established,and the energy harvesting and vibration isolation characteristics within the dispersion relation of viscoelastic metamaterials are analyzed.The results show that the vibrations of the main body of the viscoelastic metamaterial beam are significantly suppressed in the frequency range of the local resonance band gap.At the same time,the elastic waves are limited in the nonlinear resonator with an energy harvesting function,which improves the energy output.Finally,an experimental platform of viscoelastic metamaterial vibration is established for validation purposes. 展开更多
关键词 viscoelastic metamaterial nonlinear vibration vibration isolation energy harvesting
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Food nutrition and toxicology targeting on specific organs in the era of single-cell sequencing
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作者 Xiaofei Wang Xiaowen Cheng +2 位作者 Huiling Liu Xiaohuan Mu Hao Zheng 《Food Science and Human Wellness》 SCIE CSCD 2024年第1期75-89,共15页
Due to the complex natures of dietary food components,it is difficult to elucidate how the compounds affect host health.Dietary food often selectively presents its mechanism of action on different cell types,and parti... Due to the complex natures of dietary food components,it is difficult to elucidate how the compounds affect host health.Dietary food often selectively presents its mechanism of action on different cell types,and participates in the modulation of targeted cells and their microenvironments within organs.However,the limitations of traditional in vitro assays or in vivo animal experiments cannot comprehensively examine cellular heterogeneity and the tissue-biased influences.Single-cell RNA sequencing(sc RNA-seq)has emerged as an indispensable methodology to decompose tissues into different cell types for the demonstration of transcriptional profiles of individual cells.Sc RNA-seq applications has been summarized on three typical organs(brain,liver,kidney),and two representative immune-and tumor related health problems.The everincreasing role of sc RNA-seq in dietary food research with further improvement can provide sub-cellular information and the coupling between other cellular modalities.In this review,we propose utilizing sc RNAseq to more effectively capture the subtle and complex effects of food chemicals,and how they may lead to health problems at single-cell resolution.This novel technique will be valuable to elucidate the underlying mechanism of both the health benefits of food nutrients and the detrimental consequences food toxicants at the cellular level. 展开更多
关键词 Dietary food Cellular heterogeneity single-cell RNA sequencing Food nutrients Food toxicants
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Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer
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作者 Lu Tang Zhong-Pei Huang +1 位作者 Heng Mei Yu Hu 《Military Medical Research》 SCIE CAS CSCD 2024年第5期717-746,共30页
Advances in chimeric antigen receptor(CAR)-T cell therapy have significantly improved clinical outcomes of patients with relapsed or refractory hematologic malignancies.However,progress is still hindered as clinical b... Advances in chimeric antigen receptor(CAR)-T cell therapy have significantly improved clinical outcomes of patients with relapsed or refractory hematologic malignancies.However,progress is still hindered as clinical benefit is only available for a fraction of patients.A lack of understanding of CAR-T cell behaviors in vivo at the single-cell level impedes their more extensive application in clinical practice.Mounting evidence suggests that single-cell sequencing techniques can help perfect the receptor design,guide gene-based T cell modification,and optimize the CAR-T manufacturing conditions,and all of them are essential for long-term immunosurveillance and more favorable clinical outcomes.The information generated by employing these methods also potentially informs our understanding of the numerous complex factors that dictate therapeutic efficacy and toxicities.In this review,we discuss the reasons why CAR-T immunotherapy fails in clinical practice and what this field has learned since the milestone of single-cell sequencing technologies.We further outline recent advances in the application of single-cell analyses in CAR-T immunotherapy.Specifically,we provide an overview of single-cell studies focusing on target antigens,CAR-transgene integration,and preclinical research and clinical applications,and then discuss how it will affect the future of CAR-T cell therapy. 展开更多
关键词 single-cell sequencing Cancer immunotherapy CAR-T therapy Cell heterogeneity Trajectory inference Tumor microenvironment
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Dynamic analysis of a novel multilink-spring mechanism for vibration isolation and energy harvesting
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作者 谢佳衡 杨涛 唐介 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第5期366-379,共14页
Due to technical limitations,existing vibration isolation and energy harvesting(VIEH)devices have poor performance at low frequency.This paper proposes a new multilink-spring mechanism(MLSM)that can be used to solve t... Due to technical limitations,existing vibration isolation and energy harvesting(VIEH)devices have poor performance at low frequency.This paper proposes a new multilink-spring mechanism(MLSM)that can be used to solve this problem.The VIEH performance of the MLSM under harmonic excitation and Gaussian white noise was analyzed.It was found that the MLSM has good vibration isolation performance for low-frequency isolation and the frequency band can be widened by adjusting parameters to achieve a higher energy harvesting power.By comparison with two special cases,the results show that the MLSM is basically the same as the other two oscillators in terms of vibration isolation but has better energy harvesting performance under multistable characteristics.The MLSM is expected to reduce the impact of vibration on high-precision sensitive equipment in some special sites such as subways and mines,and at the same time supply power to structural health monitoring devices. 展开更多
关键词 multilink-spring mechanism nonlinear dynamics vibration isolation energy harvester
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Revolutionizing stem cell research:unbiased insights through single-cell sequencing
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作者 HAO WU NA HUO +3 位作者 SITUO WANG ZIWEI LIU YI JIANG QUAN SHI 《BIOCELL》 SCIE 2024年第11期1531-1542,共12页
Stem cells have shown great application potential in wound repair,tissue regeneration,and disease treatment.Therefore,a full understanding of stem cells and their related regulatory mechanisms in disease treatment is ... Stem cells have shown great application potential in wound repair,tissue regeneration,and disease treatment.Therefore,a full understanding of stem cells and their related regulatory mechanisms in disease treatment is conducive to improving the therapeutic effect of stem cells.However,thus far,there are still many unsolved mysteries in thefield of stem cells due to technical limitations,which hinder the in-depth exploration of stem cells and their wide clinical application.Single-cell sequencing(SCS)has provided very powerful and unbiased insights into cell gene expression profiles at the single-cell level,bringing exciting results to the stem cellfield.At present,SCS has been widely applied in thefield of stem cells,covering various aspects,including lineage tracing the development of stem cells,identifying new stem cell types,exploring cellular heterogeneity,and identifying internal functional subpopulations.In this paper,we focus on the latest research progress and discuss the application of SCS technology in stem cells. 展开更多
关键词 Stem cell single-cell sequencing Cellular heterogeneity SUBPOPULATIONS Functional analysis Lineage-tracing
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Multi-layer quasi-zero-stiffness meta-structure for high-efficiency vibration isolation at low frequency
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作者 Jiahao ZHOU Jiaxi ZHOU +3 位作者 Hongbin PAN Kai WANG Changqi CAI Guilin WEN 《Applied Mathematics and Mechanics(English Edition)》 SCIE EI CSCD 2024年第7期1189-1208,共20页
An easily stackable multi-layer quasi-zero-stiffness(ML-QZS)meta-structure is proposed to achieve highly efficient vibration isolation performance at low frequency.First,the distributed shape optimization method is us... An easily stackable multi-layer quasi-zero-stiffness(ML-QZS)meta-structure is proposed to achieve highly efficient vibration isolation performance at low frequency.First,the distributed shape optimization method is used to design the unit cel,i.e.,the single-layer QZS(SL-QZS)meta-structure.Second,the stiffness feature of the unit cell is investigated and verified through static experiments.Third,the unit cells are stacked one by one along the direction of vibration isolation,and thus the ML-QZS meta-structure is constructed.Fourth,the dynamic modeling of the ML-QZS vibration isolation metastructure is conducted,and the dynamic responses are obtained from the equations of motion,and verified by finite element(FE)simulations.Finally,a prototype of the ML-QZS vibration isolation meta-structure is fabricated by additive manufacturing,and the vibration isolation performance is evaluated experimentally.The results show that the vibration isolation performance substantially enhances when the number of unit cells increases.More importantly,the ML-QZS meta-structure can be easily extended in the direction of vibration isolation when the unit cells are properly stacked.Hence,the ML-FQZS vibration isolation meta-structure should be a fascinating solution for highly efficient vibration isolation performance at low frequency. 展开更多
关键词 quasi-zero stiffness(QZS) meta-structure high efficiency low frequency vibration isolation
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A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with Early Allograft Dysfunction
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作者 Xin Shao Zheng Wang +8 位作者 Kai Wang Xiaoyan Lu Ping Zhang Rongfang Guo Jie Liao Penghui Yang Shusen Zheng Xiao Xu Xiaohui Fan 《Engineering》 SCIE EI CAS CSCD 2024年第5期193-208,共16页
Liver transplantation(LT)is the standard therapy for individuals afflicted with end-stage liver disease.Despite notable advancements in LT technology,the incidence of early allograft dysfunction(EAD)remains a critical... Liver transplantation(LT)is the standard therapy for individuals afflicted with end-stage liver disease.Despite notable advancements in LT technology,the incidence of early allograft dysfunction(EAD)remains a critical concern,exacerbating the current organ shortage and detrimentally affecting the prognosis of recipients.Unfortunately,the perplexing hepatic heterogeneity has impeded characterization of the cellular traits and molecular events that contribute to EAD.Herein,we constructed a pioneering single-cell transcriptomic landscape of human transplanted livers derived from non-EAD and EAD patients,with 12 liver samples collected from 7 donors during the cold perfusion and portal reperfusion stages.Comparison of the 75231 cells of non-EAD and EAD patients revealed an EAD-associated immune niche comprising mucosal-associated invariant T cells,granzyme B^(+)(GZMB^(+))granzyme K^(+)(GZMK^(+))natural killer cells,and S100 calcium binding protein A12^(+)(S100A12^(+))neutrophils.Moreover,we verified this immune niche and its association with EAD occurrence in two independent cohorts.Our findings elucidate the cellular characteristics of transplanted livers and the EAD-associated pathogenic immune niche at the single-cell level,thus,offering valuable insights into EAD onset. 展开更多
关键词 Human liver transplantation Early allograft dysfunction Pathogenic immune niche single-cell analysis Cell-cell communication
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High throughput and rapid isolation of extracellular vesicles and exosomes with purity using size exclusion liquid chromatography
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作者 Kshipra S.Kapoor Kristen Harris +5 位作者 Kent A.Arian Lihua Ma Beatriz Schueng Zancanela Kaira A.Church Kathleen M.McAndrews Raghu Kalluri 《Bioactive Materials》 SCIE CSCD 2024年第10期683-695,共13页
Extracellular vesicles(EVs)have emerged as potential biomarkers for diagnosing a range of diseases without invasive procedures.Extracellular vesicles also offer advantages compared to synthetic vesicles for delivery o... Extracellular vesicles(EVs)have emerged as potential biomarkers for diagnosing a range of diseases without invasive procedures.Extracellular vesicles also offer advantages compared to synthetic vesicles for delivery of various drugs;however,limitations in segregating EVs from other particles and soluble proteins have led to inconsistent EV retrieval rates with low levels of purity.Here,we report a new high-yield(88.47%)and rapid(<20 min)EV isolation method termed size exclusion–fast protein liquid chromatography(SE-FPLC).We show SE-FPLC can effectively isolate EVs from multiple sources including EVs derived from human and mouse cells and serum samples.The results indicate that SE-FPLC can successfully remove highly abundant protein contaminants such as albumin and lipoprotein complexes,which can represent a major hurdle in large scale isolation of EVs.The high-yield nature of SE-FPLC allows for easy industrial scaling up of EV production for various clinical utilities.SE-FPLC also enables analysis of small volumes of blood for use in point-of-care diagnostics in the clinic.Collectively,SE-FPLC offers many advantages over current EV isolation methods and offers rapid clinical translation. 展开更多
关键词 Extracellular vesicles Size exclusion-fast performance liquid CHROMATOGRAPHY isolation methods
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Single-cell sequencing technology in diabetic wound healing:New insights into the progenitors-based repair strategies
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作者 Zhen Xiang Rui-Peng Cai +1 位作者 Yang Xiao Yong-Can Huang 《World Journal of Stem Cells》 SCIE 2024年第5期462-466,共5页
Diabetes mellitus(DM),an increasingly prevalent chronic metabolic disease,is characterised by prolonged hyperglycaemia,which leads to long-term health consequences.Although much effort has been put into understanding ... Diabetes mellitus(DM),an increasingly prevalent chronic metabolic disease,is characterised by prolonged hyperglycaemia,which leads to long-term health consequences.Although much effort has been put into understanding the pathogenesis of diabetic wounds,the underlying mechanisms remain unclear.The advent of single-cell RNA sequencing(scRNAseq)has revolutionised biological research by enabling the identification of novel cell types,the discovery of cellular markers,the analysis of gene expression patterns and the prediction of develop-mental trajectories.This powerful tool allows for an in-depth exploration of pathogenesis at the cellular and molecular levels.In this editorial,we focus on progenitor-based repair strategies for diabetic wound healing as revealed by scRNAseq and highlight the biological behaviour of various healing-related cells and the alteration of signalling pathways in the process of diabetic wound healing.ScRNAseq could not only deepen our understanding of the complex biology of diabetic wounds but also identify and validate new targets for inter-vention,offering hope for improved patient outcomes in the management of this challenging complication of DM. 展开更多
关键词 single-cell sequencing Diabetic wound healing Cell subpopulations Heterogeneity PATHOGENESIS Progenitor cells
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Action of circulating and infiltrating B cells in the immune microenvironment of colorectal cancer by single-cell sequencing analysis
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作者 Jing-Po Zhang Bing-Zheng Yan +1 位作者 Jie Liu Wei Wang 《World Journal of Gastrointestinal Oncology》 SCIE 2024年第6期2683-2696,共14页
BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer(CRC),one of the most prevalent malignancies worldwide.In this study,multi-omics and single-cell sequencing t... BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer(CRC),one of the most prevalent malignancies worldwide.In this study,multi-omics and single-cell sequencing techniques were used to investigate the mechanism of action of circulating and infiltrating B cells in CRC.By revealing the heterogeneity and functional differences of B cells in cancer immunity,we aim to deepen our understanding of immune regulation and provide a scientific basis for the development of more effective cancer treatment strategies.AIM To explore the role of circulating and infiltrating B cell subsets in the immune microenvironment of CRC,explore the potential driving mechanism of B cell development,analyze the interaction between B cells and other immune cells in the immune microenvironment and the functions of communication molecules,and search for possible regulatory pathways to promote the anti-tumor effects of B cells.METHODS A total of 69 paracancer(normal),tumor and peripheral blood samples were collected from 23 patients with CRC from The Cancer Genome Atlas database(https://portal.gdc.cancer.gov/).After the immune cells were sorted by multicolor flow cytometry,the single cell transcriptome and B cell receptor group library were sequenced using the 10X Genomics platform,and the data were analyzed using bioinformatics tools such as Seurat.The differences in the number and function of B cell infiltration between tumor and normal tissue,the interaction between B cell subsets and T cells and myeloid cell subsets,and the transcription factor regulatory network of B cell subsets were explored and analyzed.RESULTS Compared with normal tissue,the infiltrating number of CD20+B cell subsets in tumor tissue increased significantly.Among them,germinal center B cells(GCB)played the most prominent role,with positive clone expansion and heavy chain mutation level increasing,and the trend of differentiation into memory B cells increased.However,the number of plasma cells in the tumor microenvironment decreased significantly,and the plasma cells secreting IgA antibodies decreased most obviously.In addition,compared with the immune microenvironment of normal tissues,GCB cells in tumor tissues became more closely connected with other immune cells such as T cells,and communication molecules that positively regulate immune function were significantly enriched.CONCLUSION The role of GCB in CRC tumor microenvironment is greatly enhanced,and its affinity to tumor antigen is enhanced by its significantly increased heavy chain mutation level.Meanwhile,GCB has enhanced its association with immune cells in the microenvironment,which plays a positive anti-tumor effect. 展开更多
关键词 Colorectal cancer Multi-omics analysis single-cell sequencing analysis Immune microenvironment Infiltrating B cells
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Seismic control of multi-degrees-of-freedom structures by vertical mass isolation method using MR dampers
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作者 Mohamad Shahrokh Abdi Masoud Nekooei Mohammad-Ali Jafari 《Earthquake Engineering and Engineering Vibration》 SCIE EI CSCD 2024年第2期503-510,共8页
Vertical mass isolation(VMI)is one of the novel methods for the seismic control of structures.In this method,the entire structure is assumed to consist of two mass and stiffness subsystems,and an isolated layer is loc... Vertical mass isolation(VMI)is one of the novel methods for the seismic control of structures.In this method,the entire structure is assumed to consist of two mass and stiffness subsystems,and an isolated layer is located among them.In this study,the magnetorheological damper in three modes:passive-off,passive-on,and semi-active mode with variable voltage between zero and 9 volts was used as an isolated layer between two subsystems.Multi-degrees-of-freedom structures with 5,10,and 15 floors in two dimensions were examined under 11 pairs of near field earthquakes.On each level,the displacement of MR dampers was taken into account.The responses of maximum displacement,maximum inter-story drift,and maximum base shear in controlled and uncontrolled buildings were compared to assess the suggested approach for seismic control of the structures.According to the results,the semi-active control method can reduce the response by more than 12%compared to the uncontrolled mode in terms of maximum displacement of the mass subsystem of the structures.This method can reduce more than 16%and 20%of the responses compared to the uncontrolled mode in terms of maximum inter-story drift and base shear of the structure,respectively. 展开更多
关键词 seismic control vertical mass isolation base shear magnetorheological damper semi-active control
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Single-cell transcriptomic profiling reveals ZEB1-mediated regulation in microglial subtypes and the impact of exercise on neuroinflammatory responses
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作者 Jin-Fang Wu Yi-Sheng Chen Yu-Chun Xie 《Traditional Medicine Research》 2025年第2期55-64,共10页
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
关键词 single-cell transcriptomics brain tissue cellular subtypes biomarker expression neuronal diversity
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