Applications of single cell RNA sequencing to research of stem cells

Stem cells(SCs)with their self-renewal and pluripotent differentiation potential,show great promise for therapeutic applications to some refractory diseases such as stroke,Parkinsonism,myocardial infarction,and diabetes.Furthermore,as seed cells in tissue engineering,SCs have been applied widely to tissue and organ regeneration.However,previous studies have shown that SCs are heterogeneous and consist of many cell subpopulations.Owing to this heterogeneity of cell states,gene expression is highly diverse between cells even within a single tissue,making precise identification and analysis of biological properties difficult,which hinders their further research and applications.Therefore,a defined understanding of the heterogeneity is a key to research of SCs.Traditional ensemble-based sequencing approaches,such as microarrays,reflect an average of expression levels across a large population,which overlook unique biological behaviors of individual cells,conceal cell-to-cell variations,and cannot understand the heterogeneity of SCs radically.The development of high throughput single cell RNA sequencing(scRNA-seq)has provided a new research tool in biology,ranging from identification of novel cell types and exploration of cell markers to the analysis of gene expression and predicating developmental trajectories.scRNA-seq has profoundly changed our understanding of a series of biological phenomena.Currently,it has been used in research of SCs in many fields,particularly for the research of heterogeneity and cell subpopulations in early embryonic development.In this review,we focus on the scRNA-seq technique and its applications to research of SCs.

Single-cell RNA sequencing in cornea research:Insights into limbal stem cells and their niche regulation

The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye,which acts as a protective barrier and is critical for clear and stable vision.Its continuous renewal or wound healing depends on the proliferation and differentiation of limbal stem cells(LSCs),a cell population that resides at the limbus in a highly regulated niche.Dysfunction of LSCs or their niche can cause limbal stem cell deficiency,a disease that is manifested by failed epithelial wound healing or even blindness.Nevertheless,compared to stem cells in other tissues,little is known about the LSCs and their niche.With the advent of single-cell RNA sequencing,our understanding of LSC characteristics and their microenvironment has grown considerably.In this review,we summarized the current findings from single-cell studies in the field of cornea research and focused on important advancements driven by this technology,including the heterogeneity of the LSC population,novel LSC markers and regulation of the LSC niche,which will provide a reference for clinical issues such as corneal epithelial wound healing,ocular surface reconstruction and interventions for related diseases.

Progress in Single Cell Sequencing Technology

Cells are the basic unit of life structure and life activities.Because of the complex micro-environment of cells,the content of components that play a key role is relatively small,so single-cell analysis is extremely challenging.In recent years,single-cell sequencing technology has been developed and matured.Single-cell sequencing can reveal the composition and physiological diversity of cells,and the existing single-cell separation technology,single-cell whole genome amplification technology,single The principles and applications of cell whole transcriptome amplification technology and single cell transcriptome sequencing are summarized and summarized.

Investigating intratumour heterogeneity by single-cell sequencing

Intratumour heterogeneity is a longstanding field of focus for both researchers and clinicians. It refers to the diversity amongst cells within the same tumour. Two major hypotheses have attempted to explain the existence of intratumour heterogeneity： （i） the clonal evolution （CE） theory and （ii） the cancer stem cell （CSC） model. CE theory emphasizes the evolutionary biological characteristics of the tumour, underscoring the initiation and progression of the disease. In contrast, the CSC model focuses on stem cell differentiation into distinct functions in order to stabilize the tumour microenvironment. Here we consider single-cell sequencing （SCS） as a newly developed technique for application to the investigation of intratumour heterogeneity and assess its relevance within research and clinical environments. Early detection of rare tumour cells, monitoring of circulating tumour cells （CTCs） and control of the occurrence of drug resistance are imoortant goals in early diagnosis, prognosis prediction and individualized medicine.

Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development

BACKGROUND Accumulating evidence suggests that the maxillary process,to which cranial crest cells migrate,is essential to tooth development.Emerging studies indicate that Cd271 plays an essential role in odontogenesis.However,the underlying mechanisms have yet to be elucidated.AIM To establish the functionally heterogeneous population in the maxillary process,elucidate the effects of Cd271 deficiency on gene expression differences.METHODS p75NTR knockout(Cd271-/-)mice(from American Jackson laboratory)were used to collect the maxillofacial process tissue of p75NTR knockout mice,and the wildtype maxillofacial process of the same pregnant mouse wild was used as control.After single cell suspension,the cDNA was prepared by loading the single cell suspension into the 10x Genomics Chromium system to be sequenced by NovaSeq6000 sequencing system.Finally,the sequencing data in Fastq format were obtained.The FastQC software is used to evaluate the quality of data and CellRanger analyzed the data.The gene expression matrix is read by R software,and Seurat is used to control and standardize the data,reduce the dimension and cluster.We search for marker genes for subgroup annotation by consulting literature and database;explore the effect of p75NTR knockout on mesenchymal stem cells(MSCs)gene expression and cell proportion by cell subgrouping,differential gene analysis,enrichment analysis and protein-protein interaction network analysis;understand the interaction between MSCs cells and the differentiation trajectory and gene change characteristics of p75NTR knockout MSCs by cell communication analysis and pseudo-time analysis.Last we verified the findings single cell sequencing in vitro.RESULTS We identified 21 cell clusters,and we re-clustered these into three subclusters.Importantly,we revealed the cell–cell communication networks between clusters.We clarified that Cd271 was significantly associated with the regulation of mineralization.CONCLUSION This study provides comprehensive mechanistic insights into the maxillary-process-derived MSCs and demonstrates that Cd271 is significantly associated with the odontogenesis in mesenchymal populations.

A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling

Although vaccines have been developed,mutations of SARS-CoV-2,especially the dominant B.1.617.2(delta)and B.1.529(omicron)strains with more than 30 mutations on their spike protein,have caused a significant decline in prophylaxis,calling for the need for drug improvement.Antibodies are drugs preferentially used in infectious diseases and are easy to get from immunized organisms.The current study combined molecular modeling and single memory B cell sequencing to assess candidate sequences before experiments,providing a strategy for the fabrication of SARS-CoV-2 neutralizing antibodies.A total of 128 sequences were obtained after sequencing 196 memory B cells,and 42 sequences were left after merging extremely similar ones and discarding incomplete ones,followed by homology modeling of the antibody variable region.Thirteen candidate sequences were expressed,of which three were tested positive for receptor binding domain recognition but only one was confirmed as having broad neutralization against several SARS-CoV-2 variants.The current study successfully obtained a SARS-CoV-2 antibody with broad neutralizing abilities and provided a strategy for antibody development in emerging infectious diseases using single memory B cell BCR sequencing and computer assistance in antibody fabrication.

Extensive exploration of T cell heterogeneity in cancers by single cell sequencing

Human T cells are a highly heterogeneous population and can recognize a wide variety of antigens by their T cell receptors(TCRs). Tumor cells display a large repertoire of antigens that serve as potential targets for recognition,thus making T cells in the tumor micro-environment more complicated. Making a connection between TCRs and the transcriptional information of individual T cells will be interesting for investigating clonal expansion within T cell populations under pathologic conditions. Advances in single cell RNA-sequencing(scRNA-seq) have allowed for comprehensive analysis of T cells. In this review, we briefly describe the research progress on tumor microenvironment T cells using single cell RNA sequencing, and then discuss how scRNA-seq can be used to resolve immune system heterogeneity in health and disease. Finally, we point out future directions in this field and potential for immunotherapy.

Alzheimer’s disease, neural stem cells and neurogenesis: cellular phase at single-cell level

Alzheimer’s disease cannot be cured as of yet.Our current understanding on the causes of Alzheimer’s disease is limited.To develop treatments,experimental models that represent a particular cellular phase of the disease and more rigorous scrutiny of the cellular pathological mechanisms are crucial.In recent years,Alzheimer’s disease research underwent a paradigm shift.According to this tendency,Alzheimer’s disease is increasingly being conceived of a disease where not only neurons but also multiple cell types synchronously partake to manifest the pathology.Knowledge on every cell type adds an alternative approach and hope for the efforts towards the treatment.Neural stem cells and their neurogenic ability are making an appearance as a new aspect of the disease manifestation based on the recent findings that neurogenesis reduces dramatically in Alzheimer’s disease patients compared to healthy individuals.Therefore,understanding how neural stem cells can form new neurons in Alzheimer’s disease brains holds an immense potential for clinics.However,this provocative idea requires further evidence and tools for investigation.Recently,single cell sequencing appeared as a revolutionary tool to understand cellular programs in unprecedented resolution and it will undoubtedly facilitate comprehensive investigation of different cell types in Alzheimer’s disease.In this mini-review,we will touch upon recent studies that use single cell sequencing for investigating cellular response in Alzheimer’s disease and some consideration pertaining to the utilization of neural regeneration for Alzheimer’s disease research.

Single-cell transcriptomic dissection of the cellular and molecular events underlying the triclosan-induced liver fibrosis in mice

Background: Triclosan [5-chloro-2-(2,4-dichlorophenoxy) phenol, TCS], a common antimicrobial additive in many personal care and health care products, is frequently detected in human blood and urine. Therefore, it has been considered an emerging and potentially toxic pollutant in recent years. Long-term exposure to TCS has been suggested to exert endocrine disruption effects, and promote liver fibrogenesis and tumorigenesis. This study was aimed at clarifying the underlying cellular and molecular mechanisms of hepatotoxicity effect of TCS at the initiation stage.Methods: C57BL/6 mice were exposed to different dosages of TCS for 2 weeks and the organ toxicity was evaluated by various measurements including complete blood count, histological analysis and TCS quantification. Single cell RNA sequencing(scRNA-seq) was then carried out on TCS-or mock-treated mice livers to delineate the TCS-induced hepatotoxicity. The acquired single-cell transcriptomic data were analyzed from different aspects including differential gene expression, transcription factor(TF) regulatory network, pseudotime trajectory, and cellular communication, to systematically dissect the cellular and molecular events after TCS exposure. To verify the TCS-induced liver fibrosis,the expression levels of key fibrogenic proteins were examined by Western blotting, immunofluorescence, Masson’s trichrome and Sirius red stainings. In addition, normal hepatocyte cell MIHA and hepatic stellate cell LX-2 were used as in vitro cell models to experimentally validate the effects of TCS by immunological, proteomic and metabolomic technologies.Results: We established a relatively short term TCS exposure murine model and found the TCS mainly accumulated in the liver. The scRNA-seq performed on the livers of the TCS-treated and control groups profiled the gene expressions of > 76,000 cells belonging to 13 major cell types. Among these types, hepatocytes and hepatic stellate cells(HSCs)were significantly increased in TCS-treated group. We found that TCS promoted fibrosis-associated proliferation of hepatocytes, in which Gata2 and Mef2c are the key driving TFs. Our data also suggested that TCS induced the proliferation and activation of HSCs, which was experimentally verified in both liver tissue and cell model. In addition,other changes including the dysfunction and capillarization of endothelial cells, an increase of fibrotic characteristics in B plasma cells, and M2 phenotype-skewing of macrophage cells, were also deduced from the scRNA-seq analysis, and these changes are likely to contribute to the progression of liver fibrosis. Lastly, the key differential ligand-receptor pairs involved in cellular communications were identified and we confirmed the role of GAS6_AXL interactionmediated cellular communication in promoting liver fibrosis.Conclusions: TCS modulates the cellular activities and fates of several specific cell types(including hepatocytes, HSCs,endothelial cells, B cells, Kupffer cells and liver capsular macrophages) in the liver, and regulates the ligand-receptor interactions between these cells, thereby promoting the proliferation and activation of HSCs, leading to liver fibrosis.Overall, we provide the first comprehensive single-cell atlas of mice livers in response to TCS and delineate the key cellular and molecular processes involved in TCS-induced hepatotoxicity and fibrosis.

Single-cell analyses of circulating tumor cells

Circulating tumor cells(CTCs) are a population of tumor cells mediating metastasis, which results in most of the cancer related deaths. The number of CTCs in the peripheral blood of patients is rare, and many platforms have been launched for detection and enrichment of CTCs. Enumeration of CTCs has already been used as a prognosis marker predicting the survival rate of cancer patients. Yet CTCs should be more potential. Studies on CTCs at single cell level may help revealing the underlying mechanism of tumorigenesis and metastasis. Though far from developed, this area of study holds much promise in providing new clinical application and deep understanding towards metastasis and cancer development.

Discovering myeloid cell heterogeneity in the lung by means of next generation sequencing

The lung plays a vital role in maintaining homeostasis,as it is responsible for the exchange of oxygen and carbon dioxide.Pulmonary homeostasis is maintained by a network of tissue-resident cells,including epithelial cells,endothelial cells and leukocytes.Myeloid cells of the innate immune system and epithelial cells form a critical barrier in the lung.Recently developed unbiased next generation sequencing(NGS)has revealed cell heterogeneity in the lung with respect to physiology and pathology and has reshaped our knowledge.New phenotypes and distinct gene signatures have been identified,and these new findings enhance the diagnosis and treatment of lung diseases.Here,we present a review of the new NGS findings on myeloid cells in lung development,homeostasis,and lung diseases,including acute lung injury(ALI),lung fibrosis,chronic obstructive pulmonary disease(COPD),and lung cancer.

Next-generation sequencing traces human induced pluripotent stem cell lines clonally generated from heterogeneous cancer tissue

AIM To investigate genotype variation among induced pluripotent stem cell(iPSC) lines that were clonally generated from heterogeneous colon cancer tissues using next-generation sequencing. METHODS Human iPSC lines were clonally established by selecting independent single colonies expanded from heterogeneous primary cells of S-shaped colon cancer tissues by retroviral gene transfer(OCT3/4, SOX2, and KLF4). The ten iPSC lines, their starting cancer tissues, and the matched adjacent non-cancerous tissues were analyzed using nextgeneration sequencing and bioinformatics analysis using the human reference genome hg19. Non-synonymous single-nucleotide variants(SNVs)(missense, nonsense,and read-through) were identified within the target region of 612 genes related to cancer and the human kinome. All SNVs were annotated using dbS NP135, CCDS, RefSeq, GENCODE, and 1000 Genomes. The SNVs of the iPSC lines were compared with the genotypes of the cancerous and non-cancerous tissues. The putative genotypes were validated using allelic depth and genotype quality. For final confirmation, mutated genotypes were manually curated using the Integrative Genomics Viewer. RESULTS In eight of the ten iPSC lines, one or two non-synonymous SNVs in EIF2AK2, TTN, ULK4, TSSK1 B, FLT4, STK19, STK31, TRRAP, WNK1, PLK1 or PIK3R5 were identified as novel SNVs and were not identical to the genotypes found in the cancer and non-cancerous tissues. This result suggests that the SNVs were de novo or pre-existing mutations that originated from minor populations, such as multifocal pre-cancer(stem) cells or pre-metastatic cancer cells from multiple, different clonal evolutions, present within the heterogeneous cancer tissue. The genotypes of all ten iPSC lines were different from the mutated ERBB2 and MKNK2 genotypes of the cancer tissues and were identical to those of the noncancerous tissues and that found in the human reference genome hg19. Furthermore, two of the ten iPSC lines did not have any confirmed mutated genotypes, despite being derived from cancerous tissue. These results suggest that the traceability and preference of the starting single cells being derived from pre-cancer(stem) cells, stroma cells such as cancer-associated fibroblasts, and immune cells that co-existed in the tissues along with the mature cancer cells.CONCLUSION The genotypes of iPSC lines derived from heterogeneous cancer tissues can provide information on the type of starting cell that the iPSC line was generated from.

COVID-19 Related Research by Data Mining in Single Cell Transcriptome Profiles

The outbreak of coronavirus disease 2019(COVID-2019)has drawn public attention all over the world.As a newly emerging area,single cell sequencing also exerts its power in the battle over the epidemic.In this review,the up-to-date knowledge of COVID-19 and its receptor is summarized,followed by a collection of the mining of single cell transcriptome profiling data for the information in aspects of the vulnerable cell types in humans and the potential mechanisms of the disease.

Biological significance of RNA-seq and single-cell genomic research in woody plants

RNA-seq and single-cell genomic research emerge as an important research area in the recent years due to its ability to examine genetic information of any number of single cells in all living organisms.The knowledge gained from RNA-seq and single-cell genomic research will have a great impact in many aspects of plant biology.In this review,we summary and discuss the biological significance of RNA-seq and single-cell genomic research in plants including the single-cell DNA-sequencing,RNA-seq and single-cell RNA sequencing in woody plants,methods of RNA-seq and single-cell RNA-sequencing,single-cell RNA-sequencing for studying plant development,and single-cell RNA-sequencing for elucidating cell type composition.We will focus on RNA-seq and single-cell RNA sequencing in woody plants,understanding of plant development through single-cell RNAsequencing,and elucidation of cell type composition via single-cell RNA-sequencing.Information presented in this review will be helpful to increase our understanding of plant genomic research in a way with the power of plant single-cell RNA-sequencing analysis.

内皮细胞特异性骨形态发生蛋白2对血管新生的影响:生物信息学分析和实验验证

背景:血管新生是心血管疾病的主要干预靶点,骨形态发生蛋白2具有调控血管新生作用,但内皮细胞特异性骨形态发生蛋白2对血管新生的调控作用不清楚。目的:探讨内皮细胞特异性骨形态发生蛋白2对血管新生的影响。方法:(1)生物信息学分析:通过Panglao DB公共基因表达数据库单细胞转录组荟萃分析观察骨形态发生蛋白2细胞群表达丰度和定位。血管新生小鼠和内皮(心内膜)过表达骨形态发生蛋白2小鼠转录组测序数据集探索内皮细胞骨形态发生蛋白2对血管新生信号通路的调控作用。(2)体内实验验证:建立小鼠后肢缺血模型,对比模型小鼠患侧与健侧缺血后肢7,14和21 d血流灌注情况,免疫荧光和免疫组织化学染色评估小鼠骨形态发生蛋白2和CD31的表达定位情况。(3)体外实验验证:体外培养人脐静脉内皮细胞,分为对照组、缺氧组和骨形态发生蛋白2抑制剂(Noggin蛋白)干预组,培养24 h,观察各组内皮细胞血管新生情况。结果与结论:(1)内皮细胞是表达骨形态发生蛋白2的重要细胞亚群,在血管新生内皮细胞和骨形态发生蛋白2过表达内皮细胞转录组再分析均发现骨形态发生蛋白2表达明显升高,血管新生通路明显激活。(2)缺血7 d小鼠新生血管周围骨形态发生蛋白2阳性血管明显增加(P<0.05),缺血2周骨形态发生蛋白2阳性血管明显减少(P<0.001)。(3)体外培养人脐静脉内皮细胞,缺氧干预后,内皮细胞迁移能力和血管出芽明显增加,血管新生因子血管内皮生长因子和血小板衍生生长因子的表达明显升高,Noggin明显减少了缺氧诱导的内皮细胞血管新生(P<0.001),并下调血管内皮生长因子和血小板衍生生长因子的表达(P<0.01)。(4)结果证实,内皮细胞特异性骨形态发生蛋白2具有调控血管新生作用,靶向性内皮细胞骨形态发生蛋白2可望改善血管新生。

单细胞转录组测序技术在骨质疏松症研究中的应用与进展

背景:骨质疏松导致的脆性骨折发病率逐年上升,亟需探索其病理生理、潜在生物标志物、治疗靶点及有效药物。骨微环境中存在多种细胞,对骨代谢的维持至关重要。近几年,单细胞RNA测序(scRNA-seq)技术被开发用于表征单个细胞的转录组,并逐步应用到骨质疏松症防治的研究。目的:综述单细胞转录组测序技术在骨质疏松症研究中的应用与进展。方法:由第一作者使用计算机检索Web of Science,PubMed和中国知网数据库中2009-2023年出版的文献,英文检索词为:“single-cell RNA sequencing,bone marrow derived stromal cells,osteoblasts,osteocytes,osteoclasts,immune cells,Bone marrow vascular endothelial cells”;中文检索词为:“单细胞转录组测序,骨髓间充质干细胞,成骨细胞,骨细胞,破骨细胞,免疫细胞,骨髓血管内皮细胞”;通过阅读筛选相关文献,最终纳入89篇文献进行综述分析。结果与结论:①单细胞转录组测序技术能够深入了解细胞发育、增殖、分化的轨迹及其调控机制。②影响骨密度的候选基因主要富集在骨髓间充质干细胞亚群,其中Sox9是关键的转录因子。③成骨细胞不同亚群中差异表达Runx2控制骨髓间充质干细胞向成骨细胞方向分化。④破骨细胞分化过程中RAB38与组蛋白修饰和转录调控动态变化有关。⑤单细胞层面研究证实,骨微环境中存在多种细胞间通讯,破骨细胞可能通过CD160-TNFRSF14配体-受体结合进行细胞间通讯;中性粒/单核细胞与成骨细胞间可能通过RESISTIN通路进行交互;浆样树突状细胞与成骨细胞系通过表皮生长因子通路进行交流;均可以为靶点预测和药物研发提供方向。⑥新的骨髓毛细血管内皮细胞亚群,称为S型内皮细胞,完全起源于骨骺次级骨化中心,甚至比H型血管更具有可塑性。⑦文章从细胞角度总结单细胞转录组测序技术在表征不同骨组织细胞的分化命运和分化轨迹、识别新的细胞亚群、鉴定细胞调控因子及明确细胞间通讯的研究进展,为探讨骨质疏松症的病理机制、筛选潜在诊断标志物、预测治疗靶点及探究药物作用机制提供细胞层面的信息。⑧未来单细胞测序技术将向单细胞多组学(基因组、蛋白组学及代谢组学)方向及结合其他诸如空间转录组技术为骨组织细胞变化提供更有价值的信息。

单细胞转录组测序技术在帕金森病中的应用

背景:帕金森病以中脑特别是黑质致密部为主要病理改变,导致患者运动和非运动功能受损。目前研究受制于细胞异质性,其发病机制仍需要更深入的阐明。近些年,单细胞转录组测序(single-cell RNA sequencing,scRNA-seq)逐渐应用于神经退行性疾病中,对于理解细胞间异质性、疾病发展机制和治疗策略有重要意义。目的:综述近些年scRNA-seq技术应用于帕金森病的研究进展,为scRNA-seq在帕金森病诊断和治疗中应用提供理论基础。方法:由第一作者应用计算机系统检索中国知网、万方医学网数据库、PubMed、Web of Science数据库的相关文献,中文检索词为“单细胞RNA测序,帕金森病,细胞异质性,细胞亚型,多巴胺能神经元,胶质细胞”;英文检索词为“single-cell RNA-seq,Parkinson Disease,heterogeneity,subtypes,dopaminergic neurons,glial cells”,最终纳入71篇文献进行综述分析。结果与结论:(1)scRNA-seq是一种在单细胞水平上利用RNA测序对特定细胞群体进行基因表达谱定量的高通量实验技术,从分子水平揭示细胞奥秘。与传统的测序技术相比,scRNA-seq技术通过对细胞转录组进行自动聚类分析,从而揭示各种生理和病理情况下复杂组织中细胞类型多样性和特异性基因表达的变化。(2)通过scRNA-seq阐明多巴胺能神经元发育过程以及各种细胞亚型的独特功能特性,从而更好地了解具有潜在治疗作用的分子靶点。(3)利用scRNA-seq分析,提高了研究者对帕金森病胶质细胞反应的了解,从而全面表征了不同的细胞类型群体,并鉴定出与神经变性相关的胶质细胞亚群,绘制了有价值的单细胞图谱,作为未来研究的参考数据。(4)应用scRNA-seq检测胚胎小鼠以及干细胞,将有助于改善细胞治疗的体外分化方案和质量控制,以及评估干细胞衍生的中脑多巴胺能神经元的整体细胞质量和发育阶段。

单细胞转录组测序技术在脊髓损伤研究中的应用

背景:近年来,单细胞转录组测序技术在脊髓损伤的研究为创伤后中枢神经系统的细胞和分子异质性以及结构变化提供了新的见解。目的:就单细胞转录组测序技术在脊髓损伤的研究进展进行综述,更加全面、深入地阐述单细胞转录组测序技术在脊髓损伤领域的应用。方法:应用计算机系统检索PubMed、Web of Science、中国知网和万方数据库中2009-2023年出版的文献,英文检索词为“single-cell RNA sequencing,spinal cord injury,sequencing technology”;中文检索词为“单细胞转录组测序,脊髓损伤,测序技术”。排除质量较差、内容重复及不相关的文献,最终纳入57篇文献进行综述分析。结果与结论:目前,单细胞转录组测序技术在脊髓损伤的研究可归纳为以下几点:①鉴定了小胶质细胞、星形胶质细胞、少突胶质细胞、巨噬细胞、B细胞、神经元和神经干细胞等细胞亚群,并识别了这几种亚群的特异性标记基因。②小胶质细胞在脊髓损伤后保持永久活跃,通过增殖、免疫和稳态功能来协调脊髓损伤后的早期阶段。星形胶质细胞以激活的方式在脊髓损伤中发挥许多重要功能,包括维持微环境平衡、清除坏死组织、形成保护屏障以及胶质瘢痕等。巨噬细胞和小胶质细胞均在脊髓损伤后的慢性神经炎症中起重要作用。③神经干细胞和神经元亚群能够在脊髓损伤后进行自我更新,新发现的SCV^(sx2::Hoxa7:Zfhx3→lumbar)和SCV^(sx2::Hoxa10)等神经元亚群可再生到自然靶区,有利于运动功能的恢复。④发现细胞亚群的动态变化提高了研究者们对脊髓损伤病变进程的理解,并为脊髓损伤在不同时间点的治疗提供了新见解。截至目前,这些研究结果均还需要更多的基础研究和足够的临床试验来验证。在未来,单细胞转录组测序技术通过与生物信息学、计算机科学、组织工程学和临床医学等跨学科合作,有望为脊髓损伤的诊疗打开新的一扇窗户。

Advances in single-cell sequencing technology in microbiome research

With the rapid development of histological techniques and the widespread applica-tion of single-cell sequencing in eukaryotes,researchers desire to explore individual microbial.genotypes and functional expression,which deepens our understanding of microorganisms.In this review,the history of the development of microbial detection technologies was revealed and the difficulties in the application of single-cell sequencing in microorganisms were dissected as well.Moreover,the characteristics of the currently emerging microbial single-cell sequencing(Microbe-seq)technology were summarized,and the prospects of the application of Microbe-seq in microorganisms were distilled based on the current development status.Despite its mature development,the Microbe-seq technology was still in the optimization stage.A retrospective study was conducted,aiming to promote the widespread application of single-cell sequencing in microorganisms and facilitate further improvement in the technol-ogy.

FSPAM:A Feature Construction Method to Identifying Cell Populations in ScRNA-seq Data

The emergence of single-cell RNA-sequencing(scRNA-seq)technology has introduced new information about the structure of cells,diseases,and their associated biological factors.One of the main uses of scRNA-seq is identifying cell populations,which sometimes leads to the detection of rare cell populations.However,the new method is still in its infancy and with its advantages comes computational challenges that are just beginning to address.An important tool in the analysis is dimensionality reduction,which transforms high dimensional data into a meaningful reduced subspace.The technique allows noise removal,visualization and compression of high-dimensional data.This paper presents a new dimensionality reduction approach where,during an unsupervised multistage process,a feature set including high valuable markers is created which can facilitate the isolation of cell populations.Our proposed method,called fusion of the Spearman and Pearson affinity matrices(FSPAM),is based on a graph-based Gaussian kernel.Use of the graph theory can be effective to overcome the challenge of the nonlinear relations between cellular markers in scRNA-seq data.Furthermore,with a proper fusion of the Pearson and Spearman correlation coefficient criteria,it extracts a set of the most important features in a new space.In fact,the FSPAM aggregates the various aspects of cell-to-cell similarity derived from the Pearson and Spearman metrics,and reveals new aspects of cell-to-cell similarity,which can be used to extract new features.The results of the identification of cell populations via k-means++clustering method based on the features extracted from the FSPAM and different datasets of scRNA-seq suggested that the proposed method,regardless of the characteristics that govern each dataset,enjoys greater accuracy and better quality compared to previous methods.