Single-cell RNA-seq Immune Cell Profiling

Major cell types were annotated based on expression of canonical marker genes (AMp: CD68, CD163, FABP4, MARCO; monocytes: VCAN, FCN1; mDC: CD1C, CD1E, FLT3, LGALS2; cDC1: FLT3, LGALS2, CLEC9A, XCR1; neutrophils: FCGR3B, CXCL8, CSF3R; G0S2; Mast cells: TPSAB1, TPSB2, MS4A2, GATA2; T-cells: CD3D, CD3E, IL32; CD4 T-cells: CD4; CD8 T-cells: CD8A, CD8B; Tregs: FOXP3, IL2RA; NK-cells: TRDC, NKG7, KLRC1, XCL1, XCL2, KLRF1; B-cells: MS4A1, SPIB; Plasma-cells: JCHAIN, SDC1, MZB1, TNFRSF17, XBP1; Fibroblasts: COL3A1, COL2A1, MFAP5; proliferating cells: MKI67, TOP2A). T-cell subpopulations were annotated upon careful assessment of expressed genes. particularly, expression of canonical lineage and cell state markers was interrogated (Th1: IFNG, TNF, TBX21, CXCR3; Th17: IL17A, CCL20, RORC, CCR6, KLRB1; central memory T-cell (TCM): CCR7, TCF7, S1PR1, IL7R, SELL; naive T-cells: CCR7, TCF7, LEF1; MAIT: SLC4A10, ME1; cytotoxic lymphocytes (CTL): Granzymes, PRF1; CD4 CTL: CD4, CCL4, CCL5, PRF1; IFN-responsive: ISG15, MX1, RSAD2). Macrophage subpopulations were annotated in an analogous fashion (CD163/LGMN Mp: SPP1, LGMN; pro-inflammatory AMp: CCL3, CCL4, CCL20, TNFAIP6, SOD2; metallothionein AMp: metallothioneins, e.g. MT1G, MT2A, MT1X; IFN-responsive: ISG15, MX1, RSAD2; Foam cells: LDLR, SQLE, HMGCR, MSMO1).

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Leipold A.M., Werner R.A., Düll J., Jung P., John M., Stanojkovska E., Zhou X., Hornburger H., Ruckdeschel A., Dietrich O., Imdahl F., Krammer T., Knop S., Rosenwald A., Buck A., Sander L.E., Einsele H., Kortüm K.M., Saliba A.E, & Rasche L. (2023). Th17.1 cell driven sarcoidosis-like inflammation after anti-BCMA CAR T cells in multiple myeloma. Leukemia, 37(3), 650-658.

Publication 2023

B cells Ccl20 Ccl3 Ccl4 Ccl5 Ccr6 Cd163 Cd1c Cd4 lymphocytes Cd8 t cells Cell Central memory t cell Csf3r Cxcl8 Cxcr3 Expression genes Fabp4 Fibroblasts Flt3 Foam cells Gata2 Genes Granzymes Hmgcr Ifng Il17a Il2ra Il32 Il7r Inflammatory Klrb1 Ldlr Lef1 Lgals2 Lymphocytes Macrophage Mast cells Metallothioneins Mki67 Monocytes Neutrophils Nk cells Plasma cells Prf1 Sell Sod2 Spp1 Subpopulations T cells Tbx21 Tcf7 Th17 Tnfrsf17 Top2a Xbp1 Xcl1 Xcl2 Xcr1

Corresponding Organization :

Other organizations : Helmholtz Institute for RNA-based Infection Research, Universitätsklinikum Würzburg, University of Würzburg, Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin, Freie Universität Berlin

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