Variable expression of lineage regulators in differentiated stromal cells indicates distinct mechanisms of differentiation towards common cell fate

Mesenchymal stem cells (MSCs) possess a multi-lineage differentiation capacity that makes them important players in the field of regenerative medicine. MSC populations derived from different tissues or donors have been shown to exhibit variable gene expression patterns. Further, it is widely acknowledged that MSC isolates are heterogeneous mixtures of cells at different developmental stages. However, the heterogeneity of expression of lineage regulators has not been linked to differentiation potential of different MSC populations towards mesenchymal lineages. Here, we analyzed variation of expression of differentiation markers across whole population and between single differentiating cells of multipotent stromal cell populations derived from adipose tissue (AdMSCs) and skin (FBs) of seven donors. The results of the analyses show that all cell populations exhibit similar differentiation potential towards adipocyte, osteoblast and chondrocyte lineages despite tissue type- and donor-specific variations of expression of differentiation-associated genes. Further, we detected variable expression of lineage regulators in individual differentiating cells. Together, our data indicate that single cells of stromal cell populations could use distinct molecular mechanisms to reach a common cell fate.     

Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns

Single-cell quantitative real-time PCR (qRT-PCR) combined with high-throughput arrays allows the analysis of gene expression profiles at a molecular level in approximately 11 h after cell sample collection. We present here a high-content microfluidic real-time platform as a powerful tool for comparatively investigating the regulation of developmental processes in single cells. This approach overcomes the limitations involving heterogeneous cell populations and sample amounts, and may shed light on differential regulation of gene expression in normal versus disease-related contexts. Furthermore, high-throughput single-cell qRT-PCR provides a standardized, comparative assay for in-depth analysis of the mechanisms underlying human pluripotent stem cell self-renewal and differentiation.     

单细胞转录组高通量测序分析新进展

细胞异质性是生物组织的普遍特征。常规转录组测序(RNA-Seq)技术需要上万个细胞,所测结果实际上是一群细胞基因表达的平均值,所以难以鉴别细胞之间基因表达的异质性。单细胞RNA-Seq技术的分辨率精确至单个细胞,为辨别异质性群体中各种细胞类型的转录组特征提供了有力的工具。近年来单细胞RNA-Seq技术发展迅速,在方法学上包括cDNA扩增方法的多样化、对灵敏度和技术噪声的定量分析、浅覆盖高通量单细胞RNA-Seq方法和原位RNA-Seq技术等;在技术应用方面应用范围从早期胚胎发育扩大到组织器官发育、免疫和肿瘤等多个领域。文章对单细胞RNA-Seq在方法学和技术应用两方面的研究进展进行了详细阐述。     

Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells

Ex vivo-expanded mesenchymal stem cells (MSCs) have been demonstrated to be a heterogeneous mixture of cells exhibiting varying proliferative, multipotential, and immunomodulatory capacities. However, the exact characteristics of MSCs remain largely unknown. By single-cell RNA sequencing of 61,296 MSCs derived from bone marrow and Wharton’s jelly, we revealed five distinct subpopulations. The developmental trajectory of these five MSC subpopulations was mapped, revealing a differentiation path from stem-like active proliferative cells (APCs) to multipotent progenitor cells, followed by branching into two paths: 1) unipotent preadipocytes or 2) bipotent prechondro-osteoblasts that were subsequently differentiated into unipotent prechondrocytes. The stem-like APCs, expressing the perivascular mesodermal progenitor markers CSPG4/MCAM/NES, uniquely exhibited strong proliferation and stemness signatures. Remarkably, the prechondrocyte subpopulation specifically expressed immunomodulatory genes and was able to suppress activated CD3⁺ T cell proliferation in vitro, supporting the role of this population in immunoregulation. In summary, our analysis mapped the heterogeneous subpopulations of MSCs and identified two subpopulations with potential functions in self-renewal and immunoregulation. Our findings advance the definition of MSCs by identifying the specific functions of their heterogeneous cellular composition, allowing for more specific and effective MSC application through the purification of their functional subpopulations.     

Proteomic Signature of Mesenchymal Stromal Cell‐Derived Small Extracellular Vesicles

Small extracellular vesicles (EVs) are 50–200 nm vesicles secreted by most cells. They are considered as mediators of intercellular communication, and EVs from specific cell types, in particular mesenchymal stem/stromal cells (MSCs), offer powerful therapeutic potential, and can provide a novel therapeutic strategy. They appear promising and safe (as EVs are non‐self‐replicating), and eventually MSC‐derived EVs (MSC‐EVs) may be developed to standardized, off‐the‐shelf allogeneic regenerative and immunomodulatory therapeutics. Promising pre‐clinical data have been achieved using MSCs from different sources as EV‐producing cells. Similarly, a variety EV isolation and characterization methods have been applied. Interestingly, MSC‐EVs obtained from different sources and prepared with different methods show in vitro and in vivo therapeutic effects, indicating that isolated EVs share a common potential. Here, well‐characterized and controlled, publicly available proteome profiles of MSC‐EVs are compared to identify a common MSC‐EV protein signature that might be coupled to the MSC‐EVs’ common therapeutic potential. This protein signature may be helpful in developing MSC‐EV quality control platforms required to confirm the identity and test for the purity of potential therapeutic MSC‐EVs.     

Single-cell analysis of tumors: Creating new value for molecular biomarker discovery of cancer stem cells and tumor-infiltrating immune cells

Biomarker-driven individualized treatment in oncology has made tremendous progress through technological developments, new therapeutic modalities and a deeper understanding of the molecular biology for tumors, cancer stem cells and tumor-infiltrating immune cells. Recent technical developments have led to the establishment of a variety of cancer-related diagnostic, prognostic and predictive biomarkers. In this regard, different modern OMICs approaches were assessed in order to categorize and classify prognostically different forms of neoplasia. Despite those technical advancements, the extent of molecular heterogeneity at the individual cell level in human tumors remains largely uncharacterized. Each tumor consists of a mixture of heterogeneous cell types. Therefore, it is important to quantify the dynamic cellular variations in order to predict clinical parameters, such as a response to treatment and or potential for disease recurrence. Recently, single-cell based methods have been developed to characterize the heterogeneity in seemingly homogenous cancer cell populations prior to and during treatment. In this review, we highlight the recent advances for single-cell analysis and discuss the challenges and prospects for molecular characterization of cancer cells, cancer stem cells and tumor-infiltrating immune cells.     

基于沟眶象属两近缘种不同虫态转录组的气味受体基因鉴定及表达分析

【目的】基于沟眶象属Eucryptorrhynchus两近缘种沟眶象E. scrobiculatus和臭椿沟眶象E. brandti不同虫态的转录组数据进行气味受体(odorant receptor, OR)基因的鉴定及表达特征分析,补充两种象甲的气味受体信息,为之后的功能研究提供理论依据。【方法】从沟眶象(幼虫、蛹和成虫)和臭椿沟眶象(卵、幼虫、蛹和成虫)不同虫态转录组数据库中筛选OR基因序列;基于两种象甲触角转录组数据,对两种象甲筛选得到的ORs进行种间和种内的序列比对;利用最大似然法对两种象甲新鉴定的ORs进行系统发育分析;根据两种象甲不同虫态转录组数据中OR基因的FPKM(fragments per kilobase per million mapped fragments)值对新鉴定的OR基因进行表达丰度分析;利用qPCR检测新鉴定的OR基因在沟眶象和臭椿沟眶象不同发育阶段和成虫不同组织中的表达谱。【结果】从沟眶象和臭椿沟眶象不同虫态转录组数据库中分别鉴定出6和4个OR基因,都具有完整的开放阅读框。根据与触角转录组数据的序列比对结果,从沟眶象和臭椿沟眶象分别新鉴定出4个(EscrOR50-53)和2个(EbraOR46-47)OR基因;在两象甲种间发现了一对可能的同源基因EscrOR53和EbraOR45。系统发育树显示,6个新鉴定的OR蛋白分属于鞘翅目OR亚家族2B和7。结合不同虫态转录组的FPKM数据及qPCR检测的时空表达谱得知,沟眶象3个和臭椿沟眶象2个新鉴定到的OR基因均在成虫的非嗅觉组织中高表达,且在卵、幼虫或蛹期也有表达。【结论】本研究明确了沟眶象和臭椿沟眶象不同虫态转录组中的气味受体基因及其时空表达谱,并且发现两种象甲的生殖器官中可能存在非嗅觉的功能性的ORs,提示其可能在发育的早期阶段就已发挥功能。     

Comparing the transcriptional profile of mesenchymal cells to cardiac and skeletal muscle cells

Marrow-derived stroma cells (MSCs) can differentiate into multiple lineages including myogenic cells. However, the molecular mechanisms that direct MSCs to each differentiation pathway are poorly understood. Our study was designed to gain insights into the potential regulatory pathways that may assist in defining MSC commitment and differentiation properties. This will delineate the similarities or differences in the expression of genes between several cell types of mesenchymal origin. In this study, we established in vitro models, which allow following the discrete stages of differentiation of cardio- and myogenic-cells compared with MSC. Gene expression of each cell type at several stages of their differentiation path was evaluated by means of Affymetrix Gene Chips. Bioinformatic clustering of genes confirmed that with time in culture the myogenic cells ceased proliferating and commenced with differentiation. The expression profile analysis revealed the similarity and differences between myogenic cells and MSCs. This research compared at the molecular levels snapshots of gene expression patterns and elaborated on the overlap or differences between the analyzed cellular systems. Our results shed light on gene profiles of cells throughout their differentiation pathways. Establishing the gene signature of the differentiation process of cells that belong to several mesenchymal lineages may contribute to the understanding of molecular pathways that underlay mesenchymal tissue remodeling.     

Differential Expression of Surface Markers in Mouse Bone Marrow Mesenchymal Stromal Cell Subpopulations with Distinct Lineage Commitment

Bone marrow mesenchymal stromal cells (BM MSCs) represent a heterogeneous population of progenitors with potential for generation of skeletal tissues. However the identity of BM MSC subpopulations is poorly defined mainly due to the absence of specific markers allowing in situ localization of those cells and isolation of pure cell types. Here, we aimed at characterization of surface markers in mouse BM MSCs and in their subsets with distinct differentiation potential. Using conditionally immortalized BM MSCs we performed a screening with 176 antibodies and high-throughput flow cytometry, and found 33 markers expressed in MSCs, and among them 3 were novel for MSCs and 13 have not been reported for MSCs from mice. Furthermore, we obtained clonally derived MSC subpopulations and identified bipotential progenitors capable for osteo- and adipogenic differentiation, as well as monopotential osteogenic and adipogenic clones, and thus confirmed heterogeneity of MSCs. We found that expression of CD200 was characteristic for the clones with osteogenic potential, whereas SSEA4 marked adipogenic progenitors lacking osteogenic capacity, and CD140a was expressed in adipogenic cells independently of their efficiency for osteogenesis. We confirmed our observations in cell sorting experiments and further investigated the expression of those markers during the course of differentiation. Thus, our findings provide to our knowledge the most comprehensive characterization of surface antigens expression in mouse BM MSCs to date, and suggest CD200, SSEA4 and CD140a as markers differentially expressed in distinct types of MSC progenitors.