In our cell type atlas, we define CD8 T cell, gdT cell, and MAIT cell types at 3 levels of resolution, from one Level 1 type (broadest) to 19 Level 3 types (highest resolution) based on marker gene expression and cell types previously described in literature. Note that additional cell types are also derived from the Level 1 T cell type class, and are described in a separate page for CD4, Treg, and DN T cell types .
The hierarchical relationships between types, the usage of labels at each level of our cell type hierarchy, and the number and proportion of cells relative to parent populations and the full dataset (All) are shown here:
| Cell Type | Level(s) | N cells | % of Parent | % of All |
|---|---|---|---|---|
| T cell | 1 | 1,150,345 | NA | 63.15% |
| ├ Naive CD8 T cell | 2 | 121,167 | 10.53% | 6.65% |
| ┆ ├ Core naive CD8 T cell | 3 | 115,126 | 95.01% | 6.32% |
| ┆ ├ SOX4+ naive CD8 T cell | 3 | 5,261 | 4.34% | 0.29% |
| ┆ └ ISG+ naive CD8 T cell | 3 | 780 | 0.64% | 0.04% |
| ├ Memory CD8 T cell | 2 | 183,096 | 15.92% | 10.05% |
| ┆ ├ CM CD8 T cell | 3 | 28,453 | 15.54% | 1.56% |
| ┆ ├ GZMK- CD27+ EM CD4 T cell | 3 | 4,634 | 2.53% | 0.25% |
| ┆ ├ GZMK+ CD27+ EM CD4 T cell | 3 | 62,099 | 33.92% | 3.41% |
| ┆ ├ KLRF1- GZMB+ CD27- EM CD8 T cell | 3 | 65,156 | 35.59% | 3.58% |
| ┆ ├ KLRF1+ GZMB+ CD27- EM CD8 T cell | 3 | 21,471 | 11.73% | 1.18% |
| ┆ └ ISG+ memory CD8 T cell | 3 | 1,283 | 0.70% | 0.07% |
| ├ CD8aa | 2, 3 | 5,737 | 0.50% | 0.32% |
| ├ gdT | 2 | 50,587 | 4.40% | 2.78% |
| ┆ ├ Naive Vd1 gdT | 3 | 4,160 | 8.22% | 0.23% |
| ┆ ├ SOX4+ Vd1 gdT | 3 | 1,577 | 3.12% | 0.09% |
| ┆ ├ KLRF1- effector Vd1 gdT | 3 | 4,181 | 8.27% | 0.23% |
| ┆ ├ KLRF1+ effector Vd1 gdT | 3 | 4,955 | 9.80% | 0.27% |
| ┆ ├ GZMB+ Vd2 gdT | 3 | 15,665 | 30.97% | 0.86% |
| ┆ └ GZMK+ Vd2 gdT | 3 | 20,049 | 39.63% | 1.10% |
| └ MAIT | 2 | 46,143 | 4.01% | 2.53% |
| ├ CD4 MAIT | 3 | 2,527 | 5.48% | 0.14% |
| ├ CD8 MAIT | 3 | 42,536 | 92.18% | 2.34% |
| └ ISG+ MAIT | 3 | 1,080 | 2.34% | 0.06% |
Cell type definitions
Level 1
Here, we capture all peripheral blood mononuclear cells with a T cell identity under a single label, spanning the full spectrum of T cell maturation and differentiation. We applied our knowledge of the distinct transcriptional and phenotypic features of human T cell populations to establish a subset classification based on single cell gene expression profiles.
In this reference we have one Level 1 label:
- T cell: We distinguished T cells from other peripheral immune cell populations based on expression of T cell receptor (TCR) complex genes, including TRAC or TRDC as well as CD3 genes (CD3D, CD3E, CD3G). Of note, T cells are defined by high expression of CD3D, CD3E and CD3G, whereas NK cells express CD3E at high levels but are distinguished from T cells by low to no expression of CD3D and CD3G.
Level 2
We separate the T cell compartment into its major sub-subpopulations based on the expression of T cell receptor complexes (TRAC, TRDC), major co-receptors CD4 and CD8 (CD4, CD8A, CD8B) and basic gene programming. We also began to distinguish antigen-inexperienced T cell subsets, namely Naive T cells, from antigen-experienced subsets, Memory T cells.
At Level 2, we subdivided T cells into 10 major subclasses, 5 of which are described here, and 5 of which are described on a separate page.
- Naive CD8 T cell: Naive CD8 T cells are an antigen-inexperienced alpha-beta-expressing CD8 T cell population. This population is defined by expression of CD27, CCR7, SELL, TCF7 and LEF1, and the lack of granzyme genes GZMA, GZMK, or GZMB, as well as a lack of ITGB1, an integrin specifically expressed on memory T cells.
- Memory CD8 T cell: Memory CD8 T cells arise when Naive CD8 T cells encounter their cognate antigen and receive further activating signals that support differentiation. This population is delineated in scRNA-seq by the expression of ITGB1, high expression of granzyme genes GZMA, GZMB, or GZMK, and reduced or no expression of CCR7 in conjunction with TRAC (TCR alpha subunit) expression.
- CD8aa: CD8 alpha-alpha (CD8aa) T cells are a recently-described subset of alpha-beta T cells with effector-like properties (Thomson, et al., 2023; Terekhova, et al., 2023). These cells are defined by expression of high CD8A, KLRC2, IKZF2, and IL21R, and is closely associated with certain gdT cell subsets. (Thomson, et al., 2023)
- MAIT: Mucosal-associated invariant T (MAIT) cells are a subset of alpha-beta T cells with a semi-invariant TCR and innate-like features. This population is defined by the expression of the marker gene SLC4A10 and high expression of KLRB1 (i.e. CD161).
- gdT: Gamma-delta T cells (gdT) are a subset of T cells that express a T cell receptor (TCR) composed of gamma and delta subunits instead of alpha and beta subunits. This population is delineated from alpha-beta T cells by high expression of TRDC (TCR delta subunit) as well as TRGC1 and TRGC2 (TCR gamma subunits) in the absence of TRAC (TCR alpha subunit) expression. gdT cells are classically known for the ability to recognize soluble proteins and endogenous non-protein antigens.
Level 3
At Level 3 of our annotations, we further divided the Naive CD8, Memory CD8, gdT, and MAIT cells based on expression of specific gene programs. CD8aa cells were not subdivided further.
Naive CD8 T cells were divided into 3 subpopulations:
- Core naive CD8 T cell: Core naive CD8 T cells are the major antigen-inexperienced CD8 T cell population. This population is defined by expression of CD27, CCR7, SELL, TCF7 and LEF1, and the lack of ITGB1, an integrin specifically expressed on memory T cells.
- SOX4+ naive CD8 T cell: This Naive CD8 T cell population is delineated from Core Naive CD8 T cell via its more immature T cell gene expression profile, in particular SOX4 expression.
- ISG+ naive CD8 T cell: This Naive CD8 T cell population is delineated from Core Naive CD8 T cell via its expression of type-I interferon signaling genes (ISG), such as MX1 and IFI44.
Memory CD8 T cells were divided into 6 subpopulations based of expression of CD27, GZMK, GZMB, and KLRF1:
- CM CD8 T cell: Central memory (CM) CD8 T cells are defined by their higher expression of CCR7, SELL and LEF1 compared with other memory CD8 T cell populations.
- GZMK- CD27+ EM CD8 T cell: This memory CD8 T cell population is defined by high expression of CD27, low expression of CCR7, SELL, and LEF1 and no expression of GZMK or GZMB.
- GZMK+ CD27+ EM CD8 T cell: This memory CD8 T cell population is defined by high expression of CD27 and GZMK in the absence of GZMB expression and low CCR7, SELL, and LEF1 expression.
- KLRF1- GZMB+ CD27- EM CD8 T cell: This memory CD4 T cell population is defined by high expression of GZMB and CCL5 with no KLRF1, CD27, or GZMK expression.
- KLRF1+ GZMB+ CD27- EM CD8 T cell: This memory CD8 T cell population is defined by high expression of KLRF1, GZMB, and CCL5 with no CD27 or GZMK expression.
- ISG+ memory CD8 T cell: This memory CD8 T cell population is delineated from other memory CD8 T cells via its expression of type-I interferon signaling genes (ISG), such as MX1 and IFI44.
gdT cells were divided into 6 subpopulations, with major separation based on enrichment in expression of distinct variable region of the delta subunit of TCR (TRDV1, TRDV2):
- Naive Vd1 gdT: This gdT cell subset is delineated by high expression of CCR7, SELL, and LEF1 with low ITGB1 expression. This subset is transcriptionally similar to CD8aa T cells.
- SOX4+ Vd1 gdT: This Naive-like gdT cell population is delineated from Naive Vd1 gdT cells by an immature T cell gene expression profile, in particular SOX4 expression.This subset is also transcriptionally similar to CD8aa T cells.
- KLRF1- effector Vd1 gdT: This gdT cell subset is defined by expression of TRDC, TRDV1 and the lack of KLRF1 expression. This subset is transcriptionally similar to GZMB+ effector memory CD8 and CD4 T cell subsets.
- KLRF1+ effector Vd1 gdT: This gdT cell subset is defined by expression of TRDC, TRDV1, and KLRF1. This subset is transcriptionally similar to GZMB+ CD8 and CD4 T cell subsets.
- GZMB+ Vd2 gdT: This gdT cell subset is defined by their expression of TRDC, TRDV2, and GZMB. This subset is transcriptionally similar to MAIT cells.
- GZMK+ Vd2 gdT: This gdT cell subset is defined by their expression of TRDC, TRDV2, and GZMK. This subset is transcriptionally similar to MAIT cells.
MAIT cells were divided into 3 subpopulations:
- CD8 MAIT: CD8 MAIT cells, the main population of MAIT cells in the blood, are delineated from CD4 MAIT cells by expression of CD8A.
- CD4 MAIT: CD4 MAIT cells are delineated from CD8 MAIT cells by expression of CD4.
- ISG+ MAIT: This MAIT cell population is delineated from L2 MAIT cells via its expression of type-I interferon signaling genes, such as MX1 and IFI44.
Marker visualizations
Key markers used to define NK and ILC cell types are shown in this figure, where we display a violin plot for each marker gene and each Level 3 cell type:
Expression of key marker genes shown on our UMAP projection:
References
Terekhova M, Swain A, Bohacova P, Aladyeva E, Arthur L, Laha A, et al. Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB-CD8+ memory T cells and accumulation of type 2 memory T cells. Immunity. 2024;57: 188–192.
doi:10.1016/j.immuni.2023.12.014
Thomson Z, He Z, Swanson E, Henderson K, Phalen C, Zaim SR, et al. Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment. Nat Immunol. 2023;24: 1947–1959.
doi:10.1038/s41590-023-01641-8