Single Cell RNA Seq Provides Information On New Types Of Human Blood Cells.

Single-cell-RNA-sequence is successfully implementing the dissect molecular and cellular features that are present underlying the hematopoiesis. However, there is a lack of comprehensive and elaborate reference of the transcriptome for the entire body system. In the following study, the scientists profiled the 7,551 transcriptomes of human body cells, which demonstrate 32 immunophenotypic types of cells, which include progenitors, mature blood cells, and hematopoietic stem cells from a total of 21 healthy physicians. With high coverage and depth, scientists constructed an atlas of single-cell transcriptional blood cells, based on a couple of things, the long non-coding RNAs protein-coding genes, and the long noncoding RNAs. Furthermore, the atlas had also revealed a consistency present in between.  

It was noted that the putative long non-coding RNAs and the regulating factors of transcription factors were also revealed. Although the regulatory networks of transcription factors were activated in both monocytes and neutrophils, this dramatically changed the lymphoid cells and the regulatory networks in between their differentiation.

Moreover, the scientists also revealed a subset of nucleated erythrocytes that are actively showing immune signals, which reflect the existence of precursors of erythroid with their immune functions. Finally, there has been an establishment of a web portal offering the browsing of the transcriptome as well as prediction of blood cell type. Hence, the work of the scientists successfully provides a map of human transcriptional blood cells, that are situated at single-cell resolution. Therefore, it offers a very comprehensive reference to explore pathological and physiological hematopoiesis.

Role of the hematopoietic system in generating red blood cells and single-cell RNA in identifying them

Hematopoietic progenitor cells give birth to a hematopoietic system that continues to generate myeloid cells, erythrocytes, lymphocytes, and megakaryocytes. Sudden or gradual dysregulation in hematopoiesis spur several grave diseases like blood cancers and immunodeficiency. Recently, single-cell sequencing has provided ease in the exploration of molecular and cellular heterogeneity during cell differentiation in hematopoiesis.  Researchers have highlighted the differentiation in the hierarchy during the early hematopoiesis.  Meanwhile, other cells have been identified as a transcriptional continuum of undifferentiated and low-primed progenitor cells and hematopoietic stem cells. 

Studies such as these have raised our perception about hematopoiesis, but in reality, a systemic view regarding hematopoietic cell differentiation based on various blood cell types and multiple individuals by deep single-cell RNA sequence has been lacking.

Functions of LncRNAs are very important regulators during cell differentiation and development, which include differentiation of hematopoietic stem cells, development of T and B lymphocytes, and erythropoiesis.  Lately, long non-coding RNAs were defined at the single-cell level and they displayed a dynamic expression and high-lineage specific during the differentiation of human HSPC. 

The embryonic hematopoietic landscape of single-cell long non-coding RNA was profiled. Also, Long non-coding RNA was given recognition as pivotal for the emergence of HSC. Nonetheless, the entire repertoire about Long non-coding RNAs inside human blood cells has not been elucidated.

In the study, the researchers had constructed a very comprehensive transcriptome as a human blood cell reference. The hierarchy of hematopoiesis was dissected based on two things, long non-coding RNA and the coding genes. Besides, it was also elaborated that the dynamic regulatory differentiations and network trajectories for every lineage. This entire work has contributed to a complete understanding of the molecular dynamics during lineage differentiation. It also provides valuable references for transcriptome and hematopoiesis under disease or homeostasis. 

Reference of Human hematopoietic transcriptome

To establish a complete transcriptome reference about the human blood system, the researchers had profiled transcriptomes of peripheral blood-derived from hematopoietic cells and the transcriptome bone marrow from more than 20 donors. It was then combined with Florence activated cell sorting of single cells present in 32 well-defined types of cells and also the strategy of a single-cell tagged reverse transcription RNA sequencing.

If we talk specifically, the scientist had harvested bone marrow that is derived from progenitors and the differentiated cells that include  B, cells, NK cells, monocytes, erythrocytes and the neutrophils etc. Furthermore, all of these cells were made sure to be harvested together along with peripheral blood-derived differentiated cells which include naive B,  cytotoxic, regulatory B, cytotoxic NK, T cells and cytokine NK. All in all, there were estimated to be 7551 single cells that profiled so transcriptional atlas of human hematopoietic cells could be constructed. By increasing the sequencing depth and limiting the count of single-cells that are mixed in each library, the researcher was enabled to identify 3000 protein-coding genes for each cell. Such data of high-quality transcriptome made sure an absolute construction of hematopoietic hierarchy cells. By reducing the number of single-cells that are mixed in every library and raising the sequencing depth,  it was made possible to detect 3000 protein-coding genes in every single cell.  This data of transcriptome made sure there is the right construction of the hematopoietic hierarchy with more detailing of gene expression. Monocytes and HSPCs were able to express the highest quantity of genes whereas other cells like neutrophils, T cells and NK cells were quiescent in terms of transcription. 

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Hematopoietic differentiation underlying the regulatory networks

To make sure the transcription factor of regulatory networks is underlying the hematopoietic differentiation, the calculation of regulon activated scores for a transcription factor in every single-cell differentiation was done by the use of SCENIC.  This was then submitted for the construction of the regulatory atlas of blood cells in humans. It was also revealed that all in all transcription differentiation trajectory for hematopoiesis regulons is coinciding with the reveal of single-cell transcriptomes.  Furthermore, SPRING was also used for the visualization of hematopoietic hierarchy which was deduced from not only the regulons but also recapitulation of the trajectory of lineage branchings.  The single cells were spread in accord with the cell types rather than according to the donors. This suggested no effects on the batch or the individual diversities if regulons are related to hematopoiesis. The hematopoietic cells were added into the group of 20 regulatory clusters by the unsupervised clusterings especially in terms of C1 to C20 henceforth (Xiaowei, 2020).

Reference

Xiaowei Xie, Mengyao Liu, Yawen Zhang, Bingrui Wang, Caiying Zhu, Chenchen Wang, Qing Li, Yingying Huo, Jiaojiao Guo, Changlu Xu, Linping Hu, Aiming Pang, Shihui Ma, Lina Wang, Wenbin Cao, Shulian Chen, Qiuling Li, Sudong Zhang, Xueying Zhao, Wen Zhou, Hongbo Luo, Guoguang Zheng, Erlie Jiang, Sizhou Feng, Lixiang Chen, Xiuli An, Lihong Shi, Hui Cheng, Sha Hao, Ping Zhu, Tao Cheng, Single-cell transcriptomic landscape of human blood cells, National Science Review, 2020; nwaa180, https://doi.org/10.1093/nsr/nwaa180