Colorectal tumors often create an immunosuppressive microenvironment that prevents them from responding to immunotherapy.Cannabidiol(CBD)is a non-psychoactive natural active ingredient from the cannabis plant that has...Colorectal tumors often create an immunosuppressive microenvironment that prevents them from responding to immunotherapy.Cannabidiol(CBD)is a non-psychoactive natural active ingredient from the cannabis plant that has various pharmacological effects,including neuroprotective,antiemetic,anti-inflammatory,and antineoplastic activities.This study aimed to elucidate the specific anticancer mechanism of CBD by single-cell RNA sequencing(scRNA-seq)and single-cell ATAC sequencing(scATAC-seq)technologies.Here,we report that CBD inhibits colorectal cancer progression by modulating the suppressive tumor microenvironment(TME).Our single-cell transcriptome and ATAC sequencing results showed that CBD suppressed M2-like macrophages and promoted M1-like macrophages in tumors both in strength and quantity.Furthermore,CBD significantly enhanced the interaction between M1-like macrophages and tumor cells and restored the intrinsic anti-tumor properties of macrophages,thereby preventing tumor progression.Mechanistically,CBD altered the metabolic pattern of macrophages and related anti-tumor signaling pathways.We found that CBD inhibited the alternative activation of macrophages and shifted the metabolic process from oxidative phosphorylation and fatty acid oxidation to glycolysis by inhibiting the phosphatidylinositol 3-kinase-protein kinase B signaling pathway and related downstream target genes.Furthermore,CBD-mediated macrophage plasticity enhanced the response to anti-programmed cell death protein-1(PD-1)immunotherapy in xenografted mice.Taken together,we provide new insights into the anti-tumor effects of CBD.展开更多
单细胞染色质转座酶可及性的高通量测序(single-cell assay for transposase-accessible chromatin with high-throughput sequencing,scATAC-seq)是利用转座酶研究单细胞染色质开放性的高通量测序技术,对于研究全基因组的表观遗传调控...单细胞染色质转座酶可及性的高通量测序(single-cell assay for transposase-accessible chromatin with high-throughput sequencing,scATAC-seq)是利用转座酶研究单细胞染色质开放性的高通量测序技术,对于研究全基因组的表观遗传调控具有重要的意义。可从多个维度揭示有关染色质“组装”的重要信息,从而映射出细胞中的转录因子调控蛋白的结合区域和核小体定位等信息。目前,scATAC-seq技术已在生物和医学领域得到广泛应用,主要用于开放染色质图谱的绘制、细胞分化和发育、疾病致病机制以及肿瘤微环境的研究。本文阐述了scATAC-seq技术研究单细胞染色质开放区域的发展概况、数据分析和相关应用,期望对单细胞全基因组水平的染色质开放区域研究、顺式调控元件鉴定以及遗传调控网络的解析等提供借鉴,以期为今后更好的在生命科学研究中起到推动作用。展开更多
Olfaction,the sense of smell,is a fundamental trait crucial to many species.The olfactory bulb(OB)plays pivotal roles in processing and transmitting odor information from the environment to the brain.The cellular hete...Olfaction,the sense of smell,is a fundamental trait crucial to many species.The olfactory bulb(OB)plays pivotal roles in processing and transmitting odor information from the environment to the brain.The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing.However,the epigenetic landscape of the m OB remains mostly unexplored.Herein,we apply single-cell assay for transposaseaccessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the m OB.Based on single-cell epigenetic signatures,m OB cells are classified into 21 clusters corresponding to 11 cell types.We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred.In addition,the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage.Our study provides a valuable epigenetic data set for the m OB at single-cell resolution,and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.展开更多
The distinct characteristics ofγδT cells determine their vital roles in the formation of local immune responses and contribute to tissue homeostasis.However,the heterogeneity ofγδT cells across tissues remains unc...The distinct characteristics ofγδT cells determine their vital roles in the formation of local immune responses and contribute to tissue homeostasis.However,the heterogeneity ofγδT cells across tissues remains unclear.By combining transcriptional and chromatin analyses with a truly unbiased fashion,we constructed a single-cell transcriptome and chromatin accessibility landscape of mouseγδT cells in the lymph,spleen,and thymus.We also revealed the heterogeneity ofγδT1 andγδT17 cells across these tissues and inferred their potential regulatory mechanisms.In the thymus,we reconstructed the developmental trajectory and gained further insights into the signature genes from the mature stage,intermediate stage,and immature stage ofγδT cells on the basis of single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing data.Notably,a novel Gzma^(+)γδT cell subset was identified with immature properties and only localized to the thymus.Finally,NR1 D1,a circadian transcription factor(TF),was validated as a key and negative regulator ofγδT17 cell differentiation by performing a combined analysis of TF motif enrichment,regulon enrichment,and Nr1 d1 knockout mice.In summary,our data represent a comprehensive mapping on the transcriptome and chromatin accessibility dynamics of mouseγδT cells,providing a valuable resource and reference for future studies onγδT cells.展开更多
Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility landscapes.With the rapid development of single-cell tech...Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility landscapes.With the rapid development of single-cell technology,open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches.The application of scATAC-seq has become as popular as that of scRNA-seq.However,owing to the nature of scATAC-seq data,which are sparse and noisy,processing the data requires different methodologies and empirical experience.This review presents a practical guide for processing scATAC-seq data,from quality evaluation to downstream analysis,for various applications.In addition to the epigenomic profiling from scATAC-seq,we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage.We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.展开更多
Cellular immune responses as well as generalized and periarticular bone loss are the key pathogenic features of rheumatoid arthritis(RA).Under the pathological conditions of RA,dysregulated inflammation and immune pro...Cellular immune responses as well as generalized and periarticular bone loss are the key pathogenic features of rheumatoid arthritis(RA).Under the pathological conditions of RA,dysregulated inflammation and immune processes tightly interact with skeletal system,resulting in pathological bone damage via inhibition of bone formation or induction of bone resorption.Singlecell omics technologies are revolutionary tools in the field of modern biological research.They enable the display of the state and function of cells in various environments from a single-cell resolution,thus making it conducive to identify the dysregulated molecular mechanisms of bone destruction in RA as well as the discovery of potential therapeutic targets and biomarkers.Here,we summarize the latest findings of single-cell omics technologies in osteoimmunology research in RA.These results suggest that single-cell omics have made significant contributions to transcriptomics and dynamics of specific cells involved in bone remodeling,providing a new direction for our understanding of cellular heterogeneity in the study of osteoimmunology in RA.展开更多
基金supported by the National Key Research and Development Plan,China(Grant No.:2022YFC3500202)the Natural Science Foundation of China(Grant Nos.:82172558,and 82205024)+4 种基金the Scientific and Technological Innovation Action Plan of Natural Science Foundation Project of Shanghai,China(Grant No.:22ZR1447400)the Scientific and Technological Innovation Action Plan,China(Grant No.:22ZR1447400)the Fundamental Research Funds for the Central Universities,China(Grant Nos.:020814380179,020814380174)the Distinguished Young Scholars of Nanjing,China(Grant No.:JQX20008)the School of Life Science(NJU)-Sipimo Joint Funds and Mountain Climbing Talents Project of Nanjing University,China(Grant No.:2015018).
文摘Colorectal tumors often create an immunosuppressive microenvironment that prevents them from responding to immunotherapy.Cannabidiol(CBD)is a non-psychoactive natural active ingredient from the cannabis plant that has various pharmacological effects,including neuroprotective,antiemetic,anti-inflammatory,and antineoplastic activities.This study aimed to elucidate the specific anticancer mechanism of CBD by single-cell RNA sequencing(scRNA-seq)and single-cell ATAC sequencing(scATAC-seq)technologies.Here,we report that CBD inhibits colorectal cancer progression by modulating the suppressive tumor microenvironment(TME).Our single-cell transcriptome and ATAC sequencing results showed that CBD suppressed M2-like macrophages and promoted M1-like macrophages in tumors both in strength and quantity.Furthermore,CBD significantly enhanced the interaction between M1-like macrophages and tumor cells and restored the intrinsic anti-tumor properties of macrophages,thereby preventing tumor progression.Mechanistically,CBD altered the metabolic pattern of macrophages and related anti-tumor signaling pathways.We found that CBD inhibited the alternative activation of macrophages and shifted the metabolic process from oxidative phosphorylation and fatty acid oxidation to glycolysis by inhibiting the phosphatidylinositol 3-kinase-protein kinase B signaling pathway and related downstream target genes.Furthermore,CBD-mediated macrophage plasticity enhanced the response to anti-programmed cell death protein-1(PD-1)immunotherapy in xenografted mice.Taken together,we provide new insights into the anti-tumor effects of CBD.
文摘单细胞染色质转座酶可及性的高通量测序(single-cell assay for transposase-accessible chromatin with high-throughput sequencing,scATAC-seq)是利用转座酶研究单细胞染色质开放性的高通量测序技术,对于研究全基因组的表观遗传调控具有重要的意义。可从多个维度揭示有关染色质“组装”的重要信息,从而映射出细胞中的转录因子调控蛋白的结合区域和核小体定位等信息。目前,scATAC-seq技术已在生物和医学领域得到广泛应用,主要用于开放染色质图谱的绘制、细胞分化和发育、疾病致病机制以及肿瘤微环境的研究。本文阐述了scATAC-seq技术研究单细胞染色质开放区域的发展概况、数据分析和相关应用,期望对单细胞全基因组水平的染色质开放区域研究、顺式调控元件鉴定以及遗传调控网络的解析等提供借鉴,以期为今后更好的在生命科学研究中起到推动作用。
基金supported by Shenzhen Sanming Engineering Project(SZSM202011012)Shenzhen Innovation Science and Technology Committee(JCYJ20180228175358223)National Natural Science Foundation of China(31670742)。
文摘Olfaction,the sense of smell,is a fundamental trait crucial to many species.The olfactory bulb(OB)plays pivotal roles in processing and transmitting odor information from the environment to the brain.The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing.However,the epigenetic landscape of the m OB remains mostly unexplored.Herein,we apply single-cell assay for transposaseaccessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the m OB.Based on single-cell epigenetic signatures,m OB cells are classified into 21 clusters corresponding to 11 cell types.We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred.In addition,the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage.Our study provides a valuable epigenetic data set for the m OB at single-cell resolution,and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.
基金supported by the National Natural Science Foundation of China(31830021,32030036,32000615,and 32100695)the National Key Research and Development Program of China(2020YFA0803502)+2 种基金the 111 Project(B16021)China Postdoctoral Science Foundation(2020M683180,2019M663374,and 2020T130251)Guangdong Basic and Applied Basic Research Foundation(2020A1515111045 and 2020A1515111081)。
文摘The distinct characteristics ofγδT cells determine their vital roles in the formation of local immune responses and contribute to tissue homeostasis.However,the heterogeneity ofγδT cells across tissues remains unclear.By combining transcriptional and chromatin analyses with a truly unbiased fashion,we constructed a single-cell transcriptome and chromatin accessibility landscape of mouseγδT cells in the lymph,spleen,and thymus.We also revealed the heterogeneity ofγδT1 andγδT17 cells across these tissues and inferred their potential regulatory mechanisms.In the thymus,we reconstructed the developmental trajectory and gained further insights into the signature genes from the mature stage,intermediate stage,and immature stage ofγδT cells on the basis of single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing data.Notably,a novel Gzma^(+)γδT cell subset was identified with immature properties and only localized to the thymus.Finally,NR1 D1,a circadian transcription factor(TF),was validated as a key and negative regulator ofγδT17 cell differentiation by performing a combined analysis of TF motif enrichment,regulon enrichment,and Nr1 d1 knockout mice.In summary,our data represent a comprehensive mapping on the transcriptome and chromatin accessibility dynamics of mouseγδT cells,providing a valuable resource and reference for future studies onγδT cells.
基金supported by the National Key R&D Program of China(2021YFA1102100 to J.X.)the National Natural Science Foundation of China(32070644)to J.X.,the Guangdong Basic and Applied Basic Research Foundation(2019A1515110387,2019B1515130004 to J.X.)the Fundamental Research Funds for the Central Universities,Sun Yat-sen University(No.22lgqb30 to JX).
文摘Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility landscapes.With the rapid development of single-cell technology,open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches.The application of scATAC-seq has become as popular as that of scRNA-seq.However,owing to the nature of scATAC-seq data,which are sparse and noisy,processing the data requires different methodologies and empirical experience.This review presents a practical guide for processing scATAC-seq data,from quality evaluation to downstream analysis,for various applications.In addition to the epigenomic profiling from scATAC-seq,we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage.We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.
文摘Cellular immune responses as well as generalized and periarticular bone loss are the key pathogenic features of rheumatoid arthritis(RA).Under the pathological conditions of RA,dysregulated inflammation and immune processes tightly interact with skeletal system,resulting in pathological bone damage via inhibition of bone formation or induction of bone resorption.Singlecell omics technologies are revolutionary tools in the field of modern biological research.They enable the display of the state and function of cells in various environments from a single-cell resolution,thus making it conducive to identify the dysregulated molecular mechanisms of bone destruction in RA as well as the discovery of potential therapeutic targets and biomarkers.Here,we summarize the latest findings of single-cell omics technologies in osteoimmunology research in RA.These results suggest that single-cell omics have made significant contributions to transcriptomics and dynamics of specific cells involved in bone remodeling,providing a new direction for our understanding of cellular heterogeneity in the study of osteoimmunology in RA.
