Table 1.
Correlation of subclusters of pre- and post-implantation immune cells with previously described immune subtypes in the literature.
| Supercluster | Subcluster | Closest existing subset(s) | Known or presumed protein markers based on enriched genes | Additional enriched genes |
|---|---|---|---|---|
| B cells | B cells | Mature inexperienced liver B cells (50) | CD19+ | CD79A/B, CD22 |
| B cells | Plasma B cells | Plasmablasts/plasmacells(50) | CD79A, MS4A1, JCHAIN, XBP1, TNFRSF17 | |
| DCs | DC1 | Decidual DC1, CLEC9A+ DCs (51) | CLEC9A+HLhi | C1ORF54, XCR1, CADM1, CAMK2D |
| DCs | DC2 | Decidual DC2, Non-inflammatory CD1c+ DCs (51) | CD1c+HLAhi | FCER1A,CLEC10A |
| DCs | pDCs | Plasmacytoid DCs (52) | BDCA2+IL3RA+ | IRF7,IRF8,TCF4 |
| DCs | ToIDCs | Tolerogenic DCs (53, 54) | CD80+PD-L1+IDO1hi | CCL19, CCL22 |
| Fibroblasts/Granulocytes | Fibroblasts | Fibroblasts (55) | DCN+ | SPARC, APOD, CALD1 |
| Fibroblasts/Granulocytes | Mast cells | Mast cells (56) | CD117+ST2+ | TPSAB1, CPA3 |
| ILCs | CD16+NK | Decidual CD16bright NK cells, Decidual NK4 cells (32, 57) | CD56dim CD16bright | FGFBP2, SPON2, MYOM2 |
| ILCs | ILC3 | Decidual ILC3, LTi-like cells (58, 59) | CD117+CD127+CD56+/-NKp44+/-CD94- | IL7R, KIT, LTB, AHR, TOX2, TCF7, RORA, ID2 |
| ILCs | NK1a | Decidual NK1 cells, adaptive-like CD56bright NK cells (32, 33, 60) | CD56brightCD16dim
EomeshiT-bethi CD49ahiCD39+ |
CSF1, SPINK2, ID3, PRF1, GZMB |
| ILCs | NK1b | TTN, CDHR1 | ||
| ILCs | NK2a | Decidual NK2 cells (32, 33) | CD56brightCD16dim
CD39-CD103-KIRlow NKG2A/C/E+XCL1/2+ |
CCL5, CD9, ZNf683 |
| ILCs | NK2b | CCL4, KLRB1, CD7, ZNF683 | ||
| ILCs | NK3 | Decidual NK3 cells, ILC1 (32, 33, 41, 49) | CD56brightCD16dim CD103+CXCR4+CD161+NKp44+ Eomesint T-bethi | CCL3, CCL4, CCL5 |
| ILCs | Proliferating NK-a | (Proliferative) decidual NK2/3 (32, 33) | CD56dimCD16brightKi67+ | Predominantly cell cycle genes |
| ILCs | Proliferating NK-b | (Proliferative) decidual NK1/2/3 cells (32, 33) | ||
| ILCs | Proliferating NK-c | (Proliferative) decidual NK1/2/3 cells (32, 33) | ||
| Macrophages | M1a | Decidual M1 macrophages, angiogenic TAMs (32, 40, 61) | CD14+CD11chi | FCN1, OLR1, CLEC5A, VCAN, TIMP1, CTSB, CEBPB, EREG, VEGFA |
| Macrophages | M1b | Decidual M1 macrophages, inflammatory TAMs (32, 40, 61) | CD14+CD11chiHLA-DRlo | IL1A/B, NLRP3, CASP1, IL1RN, PYCARD |
| Macrophages | M2 | Decidual M2 macrophages, lipid-associated TAMs, regulatory TAMs (32, 40, 61) | CD14+CD11cloHLA-DRhi | C1QA, C1QB, C1QC, APOC1, APOE, RNASE1, FOLR2, F13A1, TREM2, MRC1, CD163, MERTK HLA-DR/DQ, CD86, CX3CR1 |
| Macrophages | M3 | Decidual M3 macrophages (32, 61) | CD14+HLA-DRhi | APOC1, APOE, C1QA, C1QB, C1QC, TREM2, FOLR2, GPNMB |
| Monocytes | cMono | Decidual monocytes, classical monocytes (32, 62) | CD14+CD16- | VCAN, S100A8, S100A9, S100A12, CSF3R, LYZ, FOS, AREG, IL1B |
| Monocytes | ncMono | Decidual monocytes, non-classical monocytes (32, 62) | CD14-CD16+ | FCGR3A, IFITM2, IFITM3, LST1, S100A4, S100A6, SERPINA1 |
| Monocytes | proliferating Mono/macs | Proliferating decidual monocytes/macropahges (63) | CD14+Ki67+ | Predominantly cell cycle genes |
| T cells | Activated/Stressed T cell | Highly activated CD8+ T cells (64) | CD3+CD8+ | MALAT1, SYNE1, SYNE2, MTRNR2L8/12, AAK1, NKTR |
| T cells | CD8 T cells | Decidual CD8 T cells, CD8 TCM/TEM (41, 65) | CD27, BCL11B, GZMA/K/M, TIGIT, TRGC2 | |
| T cells | DN T cells | Decidual DN T cells (41, 66) | CD3+CD4-CD8- | CD27, BCL11B, GZMA/K/M, TIGIT, IL7R, CD40LG, KLRB1 |
| T cells | Proliferating T cell A | (Proliferating) decidual CD8 T cells | CD3+CD8+ | Predominantly cell cycle genes |
| T cells | Proliferating T cell B | (Proliferating) decidual CD8 T cells |
Data are organized by supercluster. Shown are our proposed names for each subcluster and the closest existing subset(s) in the literature, along with transcriptional and phenotypic information for each subset.