Single‐cell transcriptomic analysis of PB and BM NK cells from severe aplastic anaemia patients

Abstract

Dear Editor,In recently, we reported the important contribution of nature killer (NK) cells in the pathogenesis of severe aplas-F I G U R E 1 Overview of eight types of nature killer (NK) cells. (A) UMAP of 76156 cells from eight types of NK cells (left) and the corresponding lesion type of their donors (right). (B) Violin plot showing the expression level of six markers (NCAM1, CD7, KLRD1, KLRF1, NKG7 and GNLY) in eight types of NK cells. (C) Heatmap displaying the expression level of 63 target genes in eight types of NK cells. (D) Visualizing expression of genes associated with biological pathways. A dot plot showing the log-transformed expression values of marker genes (y-axis) from five subsets (labelled with different colours) across eight types of NK cells (x-axis). (E) Stacked bar plots showing the percentage of different NK cells in four groups, from left to right, AA-BM-NK, AA-PB-NK, HC-BM-NK and HC-PB-NK. (F) RNA velocity unveils the dynamics of differentiation of eight types of NK cells. Terminal NK and cytokine-induced memory-like (CIML) had unique transcriptional characteristics, among which CIML NK2 was transformed from CIML NK1. (G) TFs (transcription factors) were identified by SCENIC across two CIML NK cells. Left: Relative-specific scores (RSS) plot of TFs in two CIML NK cells. Right: Visualizing the TF with the highest RSS in two CIML NK cells on UMAP plot. A high RSS value indicates high correlation between TF and cells.# Chunyan Liu and Yingying Chen contributed equally to the study.

Single-cell transcriptomic analysis of NK cell dynamics in myeloma patients reveal persistent reduction of cytotoxic NK cells from diagnosis to relapse

“…The developmental trajectory of MM BM NK cells was mapped by pseudotime analysis and revealed, when assigning the naïve GZMK + CD56 bright NK cell cluster as starting point, that trajectories progress via the transitional/active NK cell cluster and conventional cytotoxic CD56 dim NK cells into the direction of either the IFN-responsive or terminal and proliferating GZMB + CD56 dim clusters (Figure 1L). This validated the existence of a transitional NK cell cluster in MM BM, in line with previous studies 11,26,27,28 . Calculation of a module score based on the gene expression of helper ILC 29,30 did not identify helper ILCs in our dataset (Supplemental Figure 1I), which is likely due the exclusion of NKG7 low cells during in silico pre-processing 31 .…”

“…The terminal NK cluster was transcriptionally similar to the conventional cytotoxic CD56 dim cluster but had increased average expression of several cytotoxicity genes including FCGR3A and PRF1 (Supplemental Figures 1D-E). In line with other NK cell datasets 26,27,28 , transcription of CD57 (B3GAT1), the functionally distinguishing marker for terminally differentiated NK cells, was too low to differentiate conventional cytotoxic NK cells from terminal NK cells (Supplemental Figure 1E). The same was true for other maturation markers including ZEB2, CX3CR1 and HAVCR2 (Supplemental Figure 1E).…”

“…The conventional cytotoxic CD56 dim cluster was characterized by cytotoxicity markers (PRF1, FGFBP2, NKG7, GNLY, CST7, PRF1 and GZMB) and CX3CR1, while the transitional/recently activated NK cluster combined intermediate expression of these genes with the expression of immediate early genes (e.g. DUSP2, NR4A2 and FOSL2) (Figure 1G, Supplemental Figure 1D) 11,26,27,28 . The terminal NK cluster was transcriptionally similar to the conventional cytotoxic CD56 dim cluster but had increased average expression of several cytotoxicity genes including FCGR3A and PRF1 (Supplemental Figures 1D-E).…”

Unbiased Single‐Cell Sequencing of Hematopoietic and Immune Cells from Aplastic Anemia Reveals the Contributors of Hematopoiesis Failure and Dysfunctional Immune Regulation

“…[ 6 , 7 ] Natural killer (NK) cells have been identified as inhibitors of autologous CD8 + T‐cells, depending on the NKG2D (KLRK1)‐MICA axis, which is related to the disease state. [ 8 ] γδ T‐cells can inhibit erythroid development in patients with acquired pure red cell AA. [ 9 ] Although scRNA‐seq datasets of T‐cells, HSPCs, and NK cells have been provided, [ 8 ] the AA comprehensive and unbiased immune landscape remains unclear.…”

“…[ 8 ] γδ T‐cells can inhibit erythroid development in patients with acquired pure red cell AA. [ 9 ] Although scRNA‐seq datasets of T‐cells, HSPCs, and NK cells have been provided, [ 8 ] the AA comprehensive and unbiased immune landscape remains unclear.…”