Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

• Published in: Cell 2020-08, Vol.182 (4), p.872-885.e19
• Main Authors: Katzenelenbogen, Yonatan, Sheban, Fadi, Yalin, Adam, Yofe, Ido, Svetlichnyy, Dmitry, Jaitin, Diego Adhemar, Bornstein, Chamutal, Moshe, Adi, Keren-Shaul, Hadas, Cohen, Merav, Wang, Shuang-Yin, Li, Baoguo, David, Eyal, Salame, Tomer-Meir, Weiner, Assaf, Amit, Ido
• Format: Article
• Language: English
• Subjects: Animals; Arginase - genetics; Arginase - metabolism; cancer immunology; CD8-Positive T-Lymphocytes - cytology; CD8-Positive T-Lymphocytes - immunology; CD8-Positive T-Lymphocytes - metabolism; Dendritic Cells - cytology; Dendritic Cells - drug effects; Dendritic Cells - metabolism; Female; fixation; Gene Expression Regulation; Humans; immunotherapy; intracellular staining; Leukocytes, Mononuclear - cytology; Leukocytes, Mononuclear - metabolism; Lipopolysaccharides - pharmacology; MDSC; Membrane Glycoproteins - genetics; Membrane Glycoproteins - metabolism; Mice; Mice, Inbred C57BL; myeloid suppressive cells; Neoplasms - immunology; Neoplasms - metabolism; Neoplasms - pathology; p38 Mitogen-Activated Protein Kinases; Receptors, Immunologic - genetics; Receptors, Immunologic - metabolism; RNA, Small Cytoplasmic - chemistry; RNA, Small Cytoplasmic - metabolism; scRNA-seq; Sequence Analysis, RNA; single cell genomics; Single-Cell Analysis; Transcription Factors - metabolism; Trem2; Tumor Microenvironment; Tumor Necrosis Factor-alpha - metabolism
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2020.06.032

Cell function and activity are regulated through integration of signaling, epigenetic, transcriptional, and metabolic pathways. Here, we introduce INs-seq, an integrated technology for massively parallel recording of single-cell RNA sequencing (scRNA-seq) and intracellular protein activity. We demonstrate the broad utility of INs-seq for discovering new immune subsets by profiling different intracellular signatures of immune signaling, transcription factor combinations, and metabolic activity. Comprehensive mapping of Arginase 1-expressing cells within tumor models, a metabolic immune signature of suppressive activity, discovers novel Arg1+ Trem2+ regulatory myeloid (Mreg) cells and identifies markers, metabolic activity, and pathways associated with these cells. Genetic ablation of Trem2 in mice inhibits accumulation of intra-tumoral Mreg cells, leading to a marked decrease in dysfunctional CD8+ T cells and reduced tumor growth. This study establishes INs-seq as a broadly applicable technology for elucidating integrated transcriptional and intra-cellular maps and identifies the molecular signature of myeloid suppressive cells in tumors. [Display omitted] •INs-seq: a new technology for recording scRNA-seq and intracellular protein activity•INs-seq defines new immune subsets by TF combinations and metabolic activity•Mapping Arg1+ cells within tumors reveals novel Trem2+ suppressive myeloid cells•Genetic ablation of Trem2 decreases Mreg, exhausted CD8+ T cells and tumor growth INs-seq, an integrated technology for scRNA-seq and intracellular protein activity uncovers a novel Arg1+ Trem2+ regulatory myeloid cells (Mreg), genetic ablation of Trem2 inhibits the accumulation of intra-tumoral Mreg, leading to immune reactivation and reduced tumor growth.