scholarly journals Single-cell atlas of major haematopoietic tissues sheds light on blood cell formation from embryonic endothelium

2019 ◽  
Author(s):  
Maya Shvartsman ◽  
Polina V. Pavlovich ◽  
Morgan Oatley ◽  
Kerstin Ganter ◽  
Rachel McKernan ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Blood Cell ◽  
Single Cell ◽  
Ectopic Expression ◽  
Cell Formation ◽  
Marker Genes ◽  
Computational Tool ◽  
Single Cell Rna Sequencing ◽  
The Difference ◽  
Blood Cell Formation

AbstractThe Yolk Sac (YS) and Aorta-Gonad-Mesonephros (AGM) are two major haematopoietic regions during embryonic development. Interestingly, AGM is the only one generating haematopoietic stem cells (HSCs). To identify the difference between AGM and YS, we compared them using single-cell RNA sequencing between 9.5 and 11.5 days of mouse embryonic development and identified cell populations using CONCLUS, a new computational tool. The AGM was the only one containing neurons and a specific mesenchymal population, while the YS major component was an epithelial population expressing liver marker genes. In addition, the YS contained a major endothelial population expressing Stab2, a hyaluronan receptor, also highly expressed by liver endothelium. We demonstrated that the YS haematopoietic potential was restricted to Stab2-negative cells and that ectopic expression of Stab2 could reduce blood cell formation from endothelium. Our results indicate that the AGM is a tissue more favourable to HSCs development than the YS because of its microenvironment and the nature of its endothelial cells.

scholarly journals Evaluation of single-cell classifiers for single-cell RNA sequencing data sets

2019 ◽  
Vol 21 (5) ◽  
pp. 1581-1595 ◽  
Author(s):  
Xinlei Zhao ◽  
Shuang Wu ◽  
Nan Fang ◽  
Xiao Sun ◽  
Jue Fan
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Reference Data ◽  
Predictive Accuracy ◽  
Cell Types ◽  
Superior Performance ◽  
Marker Genes ◽  
Data Sets ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing

Abstract Single-cell RNA sequencing (scRNA-seq) has been rapidly developing and widely applied in biological and medical research. Identification of cell types in scRNA-seq data sets is an essential step before in-depth investigations of their functional and pathological roles. However, the conventional workflow based on clustering and marker genes is not scalable for an increasingly large number of scRNA-seq data sets due to complicated procedures and manual annotation. Therefore, a number of tools have been developed recently to predict cell types in new data sets using reference data sets. These methods have not been generally adapted due to a lack of tool benchmarking and user guidance. In this article, we performed a comprehensive and impartial evaluation of nine classification software tools specifically designed for scRNA-seq data sets. Results showed that Seurat based on random forest, SingleR based on correlation analysis and CaSTLe based on XGBoost performed better than others. A simple ensemble voting of all tools can improve the predictive accuracy. Under nonideal situations, such as small-sized and class-imbalanced reference data sets, tools based on cluster-level similarities have superior performance. However, even with the function of assigning ‘unassigned’ labels, it is still challenging to catch novel cell types by solely using any of the single-cell classifiers. This article provides a guideline for researchers to select and apply suitable classification tools in their analysis workflows and sheds some lights on potential direction of future improvement on classification tools.

scholarly journals Multi-Agent Systems and Blood Cell Formation

10.5772/15950 ◽  
2011 ◽  
Author(s):  
Bessonov Nikolai ◽  
Demin Ivan ◽  
Kurbatova Polina ◽  
Pujo-Menjouet Laurent ◽  
Volpert Vitaly
Keyword(s):  
Blood Cell ◽  
Cell Formation ◽  
Multi Agent Systems ◽  
Agent Systems ◽  
Multi Agent ◽  
Blood Cell Formation

Expression of connexin 43 (Cx43) is critical for normal hematopoiesis

Blood ◽  
2000 ◽  
Vol 96 (3) ◽  
pp. 917-924 ◽  
Author(s):  
Encarnacion Montecino-Rodriguez ◽  
Hyosuk Leathers ◽  
Kenneth Dorshkind
Keyword(s):  
Bone Marrow ◽  
T Cell ◽  
Blood Cell ◽  
Gap Junctions ◽  
Connexin 43 ◽  
Cell Formation ◽  
Cx43 Expression ◽  
Hematopoietic System ◽  
Blood Cell Formation

Abstract Gap junctions are intercellular channels, formed by individual structural units known as connexins (Cx), that allow the intercellular exchange of various messenger molecules. The finding that numbers of Cx43-type gap junctions in bone marrow are elevated during establishment and regeneration of the hematopoietic system has led to the hypothesis that expression of Cx43 is critical during the initiation of blood cell formation. To test this hypothesis, lymphoid and myeloid development were examined in mice with a targeted disruption of the gene encoding Cx43. Because Cx43−/− mice die perinatally, initial analyses were performed on Cx43−/−, Cx43+/−, and Cx43+/+ embryos and newborns. The data indicate that lack of Cx43 expression during embryogenesis compromises the terminal stages of primary T and B lymphopoiesis. Cx43−/− embryos and neonates had a reduced frequency of CD4+ and T-cell receptor-expressing thymocytes and surface IgM+cells compared to their Cx43+/+ littermates. Surprisingly, Cx43+/− embryos/neonates also showed defects in B- and T-cell development similar to those observed in Cx43−/− littermates, but their hematopoietic system was normal at 4 weeks of age. However, the regeneration of lymphoid and myeloid cells was severely impaired in the Cx43+/− mice after cytoablative treatment. Taken together, these data indicate that loss of a single Cx43 allele can affect blood cell formation. Finally, the results of reciprocal bone marrow transplants between Cx43+/+ and Cx43+/− mice and examination of hematopoietic progenitors and stromal cells in vitro indicates that the primary effects of Cx43 are mediated through its expression in the hematopoietic microenvironment.

scholarly journals Unveiling the heterogeneity of NKT cells in the liver through single cell RNA sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hao Shen ◽  
Chan Gu ◽  
Tao Liang ◽  
Haifeng Liu ◽  
Fan Guo ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Subset ◽  
Nkt Cells ◽  
Organ Distribution ◽  
Marker Genes ◽  
Type I ◽  
Nkt Cell ◽  
Single Cell Rna Sequencing

Abstract CD1d-dependent type I NKT cells, which are activated by lipid antigen, are known to play important roles in innate and adaptive immunity, as are a portion of type II NKT cells. However, the heterogeneity of NKT cells, especially NKT-like cells, remains largely unknown. Here, we report the profiling of NKT (NK1.1+CD3e+) cells in livers from wild type (WT), Jα18-deficient and CD1d-deficient mice by single-cell RNA sequencing. Unbiased transcriptional clustering revealed distinct cell subsets. The transcriptomic profiles identified the well-known CD1d-dependent NKT cells and defined two CD1d-independent NKT cell subsets. In addition, validation of marker genes revealed the differential organ distribution and landscape of NKT cell subsets during liver tumor progression. More importantly, we found that CD1d-independent Sca-1−CD62L+ NKT cells showed a strong ability to secrete IFN-γ after costimulation with IL-2, IL-12 and IL-18 in vitro. Collectively, our findings provide a comprehensive characterization of NKT cell heterogeneity and unveil a previously undefined functional NKT cell subset.

Blood Cell Formation in Certain Teleost Fishes

Blood ◽  
1951 ◽  
Vol 6 (1) ◽  
pp. 39-60 ◽  
Author(s):  
W. T. CATTON
Keyword(s):  
Blood Cell ◽  
Blood Cells ◽  
Cell Formation ◽  
Large Cell ◽  
Progressive Increase ◽  
Mitotic Division ◽  
Teleost Fishes ◽  
Epithelial Surface ◽  
Alternative Hypotheses ◽  
Blood Cell Formation

Abstract 1. The blood cells of trout and roach consist of nucleated erythrocytes and reticulocytes, nucleated thrombocytes, coarse and fine granulocytes, and lymphocytes of varying sizes. It is difficult to distinguish any cells showing characteristics similar to those of the monocytes of mammals. Immature cells occur more frequently in the blood than is the case in mammals. 2. The coarse granulocytes very commonly escape from the blood vessels, and have been observed in large numbers in the intestinal mucosa and submucosa, in the gill epithelia, and in the peritoneum. These cells migrate to the epithelial surface, where they undergo changes in structure leading to the formation of a characteristic discharge pattern of their granules. It is proposed that the "granules" are in reality vesicles with fluid contents, which are ultimately discharged at epithelial surfaces. 3. The hematopoietic organs of these fishes are chiefly the intertubular tissues of the kidneys; in the trout the spleen is also active; in the roach, only the kidney is active; in the perch, only the spleen is active. 4. Two alternative hypotheses of blood cell formation are proposed. On the first hypothesis, the common stem cell is described as a "large lymphoid hemoblast," which gives rise to granulocytes by direct transformation and undergoes mitotic division to give rise to "small lymphoid hemoblasts." From the latter develop the erythrocytes, thrombocytes and blood lymphocytes. On the second hypothesis, the large lymphoid hemoblast, derived by transformation of reticular cells is the precursor solely of the granulocytes, and the small lymphoid hemoblast is to be derived from endothelial cells and is the precursor of erythrocytes and thrombocytes. In this case the large cell is to be compared with the "primitive white cell" of Doan, Cunningham and Sabin, and the small cell with the "megaloblast" of the same authors. No evidence however is available of the derivation of small hemoblasts from endothelial cell components of the reticulo-endothelium. 5. In the maturation of the erythrocyte in teleost fishes, there is a progressive increase in the size of the cell; in mammals and birds there is a decrease in size. In both cases there is a decrease in size in granulocyte maturation. 6. There are no essential differences between the blood cells and hematopoietic processes of the freshwater and marine teleost fishes examined.

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