Dissection of immune cell subtypes in the cellular aging ecosystem
To classify each cell subpopulation in an unbiased manner, we separately reclustered the cells of each lineage. By analyzing the most significantly upregulated genes in each cluster in scRNA-seq analysis, we identified five distinct subsets of CD3+ TCs (Fig. S3A), five distinct subsets of CD4+ TCs (Fig. S3B), four distinct subsets of CD8+ TCs (Fig. S3C), three distinct subsets of NKs (Fig. S3D), four distinct subsets of BCs (Fig. S3E), three distinct subsets of MCs (Fig. S3F) and four distinct subsets of DCs (Fig. S3G, see Table S3A for the details).
Aging affects the development and function of TCs and NKs (Pinti et al., 2016). We identified known T cell subsets, including CD4+, CD8+, CD4+CD8+, CD4−CD8− and proliferative T cells (mitotic T cells, T-mito), based on the expression of canonical lineage markers (Fig. S3H). The CD4+ T cells were subdivided into five classes: CCR7high CD69low naive CD4+ T cells (CD4 Naive); CCR7med CD69high CCR6− central memory CD4+ T cells (CD4 Tcm); CCR6+ effector memory CD4+ T cells (CD4 Tem); FOXP3+ regulatory T cells (CD4 Treg) and PDCD1+ exhausted CD4+ T cells (CD4 Tex) (Fig. S3I). The CD8+ T cells were subdivided into four classes: CCR7+ naive CD8+ T cells (CD8 Naive); GZMK+ effector memory CD8+ T cells (CD8 Tem); GZMB+ GNLY+ cytotoxic CD8+ TCs (CD8 CTL) and PDCD1+ exhausted CD8+ T cells (CD8 Tex) (Fig. S3J).
Analysis of NK cell-status identified circulating NKs with three separate immune states (Fig. S 3D): the CD16 (FCGR3A)low CD56 (NCAM1)bright NK population (NK1), the CD16high CD56dim CD57 (B3GAT1)− low-cytotoxic NK compartment (NK2) and the CD16high CD56dim CD57+ late NK population (NK3) (Fig. S3K). In addition, we identified four major peripheral B cell subsets: IL4R+ IGHD+ naive B cells (Naive BCs); CD27+ IGHG1+ memory B cells (Memory BCs); plasma cells or so-called antibody-secreting cells (ASCs), expressing high level of immunoglobulin genes MZB1; and a subset of ITGAX+ B cells defined as age-associated B cells (ABCs) (Fig. S3L).
In human peripheral blood myeloid cells (including MCs and DCs), known to promote antigen presentation and inflammatory activities, we identified seven transcriptionally distinct subsets: CD14high CD16− classical monocytes (CD14 MCs), CD14+/− CD16high nonclassical monocytes (CD16 MCs), CD14+ CD16+/− intermediate monocytes (Intermed MCs) (Fig. S3M), CLEC9A+ conventional DC1 (cDC1), CD1c+ cDC2 conventional DC2 (cDC2), CD123 (IL3RA)+ CLEC4C+ plasmacytoid DCs (pDCs) (Fig. S3N), and dendritic cell precursors (pre-DCs) expressing AXL and CD123 (Grabiec and Hussell, 2016; Ruffin et al., 2019) (Fig. S3N). Therefore, we targeted the immune cell changes based on more precise classification of each subgroup.
To further verify the aging-associated change in the cell ratio, we performed single-cell analysis at the protein level. Similar to the cell clusters and subsets in scRNA-seq results, in CyTOF analysis, we identified 21 sub-clusters with nine subsets of TCs (CD4 Naive, CD4 Tcm, CD4 Tem, CD4 Treg, CD8 Naive, CD8 Tem, CD8 CTL, CD4+ CD8+, CD4− CD8−), three subsets of NKs (CD56bright NK1, CD16+CD57− NK2 and CD16+CD57+ NK3), four subsets of BCs (Naive BC, Memory BC, ASCs, and ABCs), three subsets of MCs (CD14high MCs, CD16high MCs and intermediate MCs), and two subsets of DCs (pDCs and cDCs) (Fig. S4A–K, see Table S3B for the details).