Primitive genotypic characteristics in umbilical cord neutrophils identified by single-cell transcriptome profiling and functional prediction

Abstract

The function and heterogeneity of neutrophils in neonatal umbilical cord blood (UCB) have not been characterized. In this study, we analyzed the neutrophils in UCB and healthy adults using single-cell RNA sequencing analysis for the first time. We found that neutrophils divided into six subpopulations (G2, G3, G4, G5a, G5b, and G5c) with different marker genes and different functions under homeostasis. Compared with healthy adults, neutrophils of UCB were more naïve and have more obvious degranulation and activation functions. Moreover, we found significant differences in the amount and function of G5b cells between healthy adults and UCB. The amount of G5b group in UCB was lower, but it has more degranulation, secretion and activation functions. In addition, we noted a new subset of G5c labeled by CD52, which almost did not exist in UCB. Besides, its differential genes were enriched in terms such as protein synthesis and mRNA transcription. Furthermore, uncharacteristic transcription factors ZNF-276, ZNF-319 and ZNF-354A were identified in our study. In summary, we first examined the heterogeneity and functional diversity of neutrophils in UCB, and these data provided new insights into the mechanism of neutrophil-mediated diseases of neonates and the wider use of neutrophils in UCB.

Single-cell analysis of uterosacral ligament revealed cellular heterogeneity in women with pelvic organ prolapse

“…Based on several clusters enriched in pathway neutrophils activation, we did find that neutrophils increased significantly at the same time. We divided neutrophils into four clusters and found that these four clusters can correspond to the neutrophils in Chen and Xie et al’s scRNA-seq studies 38 , 39 , which further verified the phenotype of neutrophils in the human body. In addition, according to a widely used previous classification scheme, macrophages were grouped into pro-inflammatory (M1) and anti-inflammatory (M2) phenotypes.…”

“…Correlation analysis showed Neutrophils4 were different from any subpopulation of G0–G5. However, according to the known neutrophil typing markers provided by Chen et al 39 , we suggested that Neutrophils4 had the characteristics of G5c (Fig. 5i , Supplementary Data 1 ).…”

Single-cell analysis of uterosacral ligament revealed cellular heterogeneity in women with pelvic organ prolapse

“…Based on several clusters enriched in pathway neutrophils activation, we did nd that neutrophils increased signi cantly at the same time. We divided neutrophils into four clusters and found that these four clusters can correspond to the neutrophils in Chen and Xie et al's single cell RNA sequencing studies 38,39 , which further veri ed the phenotype of neutrophils in the human body. In addition, according to a widely used previous classi cation scheme, macrophages were grouped into pro-in ammatory (M1) and an anti-in ammatory (M2) phenotypes.…”

“…Correlation analysis showed Neutrophils4 were different from any subpopulation of G0-G5. However, according to the known neutrophil typing markers provided by Chen + et al 39 , we suggested that Neutrophils4 were G5c (Fig. 3G).…”

Protocol for enrichment and functional analysis of human hematopoietic cells from umbilical cord blood

“… Optional: The high-density cell pellet (which contains non-nucleated red blood cells and high density polymorphonuclear cells, such as granulocytes) can be used for analysis or cryopreserved for later analysis. As our focus in this protocol is on the LDCB fraction, we direct you to additional publications 9 , 10 for these types of analyses. After transferring to new tubes, add 1× PBS so the final volume is approximately 45 mL.…”