Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

• Published in: Cell 2015-12, Vol.163 (6), p.1400-1412
• Main Authors: Gaublomme, Jellert T., Yosef, Nir, Lee, Youjin, Gertner, Rona S., Yang, Li V., Wu, Chuan, Pandolfi, Pier Paolo, Mak, Tak, Satija, Rahul, Shalek, Alex K., Kuchroo, Vijay K., Park, Hongkun, Regev, Aviv
• Format: Article
• Language: English
• Subjects: Animals; Apoptosis Regulatory Proteins - metabolism; Carrier Proteins - metabolism; Central Nervous System - pathology; Encephalomyelitis, Autoimmune, Experimental - immunology; Encephalomyelitis, Autoimmune, Experimental - metabolism; Encephalomyelitis, Autoimmune, Experimental - pathology; Gene Expression Profiling; Humans; Kruppel-Like Transcription Factors - metabolism; Lymph Nodes - pathology; Membrane Proteins - metabolism; Mice; Mice, Inbred C57BL; Mice, Knockout; Myelin-Oligodendrocyte Glycoprotein - metabolism; Peptide Fragments - metabolism; Promyelocytic Leukemia Zinc Finger Protein; Receptors, G-Protein-Coupled - metabolism; Receptors, Immunologic - metabolism; Sequence Analysis, RNA; Single-Cell Analysis; Th17 Cells - immunology; Th17 Cells - metabolism; Th17 Cells - pathology
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2015.11.009

Extensive cellular heterogeneity exists within specific immune-cell subtypes classified as a single lineage, but its molecular underpinnings are rarely characterized at a genomic scale. Here, we use single-cell RNA-seq to investigate the molecular mechanisms governing heterogeneity and pathogenicity of Th17 cells isolated from the central nervous system (CNS) and lymph nodes (LN) at the peak of autoimmune encephalomyelitis (EAE) or differentiated in vitro under either pathogenic or non-pathogenic polarization conditions. Computational analysis relates a spectrum of cellular states in vivo to in-vitro-differentiated Th17 cells and unveils genes governing pathogenicity and disease susceptibility. Using knockout mice, we validate four new genes: Gpr65, Plzp, Toso, and Cd5l (in a companion paper). Cellular heterogeneity thus informs Th17 function in autoimmunity and can identify targets for selective suppression of pathogenic Th17 cells while potentially sparing non-pathogenic tissue-protective ones. [Display omitted] [Display omitted] •Atlas of Th17 single-cell RNA-seq profiles reveals extensive heterogeneity•Annotation approach relates single-cell profiles to legacy genomic signatures•Pathogenicity regulators co-vary with pro-inflammatory and regulatory modules•Functional validation of Th17 pathogenicity regulators: GRP65, TOSO, and PLZP Single-cell RNA-seq coupled to a new functional annotation approach identifies distinct functional states of Th17 cells and the underlying molecular mechanisms that regulate their pathogenicity.