Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries
2018; Cell Press; Volume: 172; Issue: 1-2 Linguagem: Inglês
10.1016/j.cell.2017.11.011
ISSN1097-4172
Autores Tópico(s)Neuroinflammation and Neurodegeneration Mechanisms
ResumoThe immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. In this Perspective, we consider recent and forthcoming technological and analytical advances in single-cell genomics and the potential impact of those advances on the future of immunology research and immunotherapy. The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. In this Perspective, we consider recent and forthcoming technological and analytical advances in single-cell genomics and the potential impact of those advances on the future of immunology research and immunotherapy. The immune system is a complex network composed of various interacting cell types and functional states (Figure 1). It is one of the most dynamic and plastic systems in the human body, present in nearly every tissue of the organism, and involved in a wide range of homeostatic activities—from tissue development and remodeling (Wynn et al., 2013Wynn T.A. Chawla A. Pollard J.W. 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Its function or dysfunction is even more pronounced in pathology, where various immune cells play a central role in pathogen and tumor clearance or escape, as well as in metabolic, autoimmune, and neurodegenerative diseases. Immune processes are mediated by the crosstalk between many types of cells—tissue resident as well as circulating immune cells—all interacting in specific micro-environmental contexts while communicating with the local tissue. Characterizing these cellular networks, the participating cell types, their unique pathways, and genes, as well as their interactions and responses to environmental cues, is key to successfully manipulating the immune system in order to harness its unique therapeutic potential (Sharma and Allison, 2015Sharma P. Allison J.P. Immune checkpoint targeting in cancer therapy: toward combination strategies with curative potential.Cell. 2015; 161: 205-214Abstract Full Text Full Text PDF PubMed Scopus (1506) Google Scholar). Since the 19th century, with efforts pioneered by Ilya Mechnikov, a major focus of immunology has been the characterization and categorization of immune cells into distinct types (Tauber, 2003Tauber A.I. Metchnikoff and the phagocytosis theory.Nat. Rev. Mol. Cell Biol. 2003; 4: 897-901Crossref PubMed Scopus (249) Google Scholar). Early classification efforts assigned cell types based on morphology and cellular functions. For example, macrophages were associated with phagocytosis, whereas dendritic cells were associated with antigen presentation (van Furth et al., 1972van Furth R. Cohn Z.A. Hirsch J.G. Humphrey J.H. Spector W.G. Langevoort H.L. The mononuclear phagocyte system: a new classification of macrophages, monocytes, and their precursor cells.Bull. World Health Organ. 1972; 46: 845-852PubMed Google Scholar, Steinman and Cohn, 1973Steinman R.M. Cohn Z.A. Identification of a novel cell type in peripheral lymphoid organs of mice. I. Morphology, quantitation, tissue distribution.J. 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Hematopoietic stem cell heterogeneity: subtypes, not unpredictable behavior.Cell Stem Cell. 2010; 6: 203-207Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar). The question of whether new and better markers could resolve this difficulty, or whether it requires the incorporation of additional experimental and analytical tools, was, until recently, subject to debate. Our working hypothesis was that, because of the high connectivity, heterogeneity, and plasticity of the immune system, current technologies were often limited in their abilities to fully characterize the various cell types and states involved in immune cell functions. This stemmed from the setbacks of the then-available molecular profiling tools; these allowed either genome-wide profiling of a population of cells, selected by expression of predefined markers, or detection of a small number of molecular features at the single-cell level. Single-cell RNA-seq seemed to be an ideal solution for immunology research, as it overcomes these previous technological limitations. Our study on unbiased characterization of spleen immune cell populations was the first step towards materializing this vision, demonstrating that single cell RNA-seq is an effective tool for comprehensive cellular decomposition of complex tissues without the need for predefined markers (Jaitin et al., 2014Jaitin D.A. Kenigsberg E. Keren-Shaul H. Elefant N. Paul F. Zaretsky I. Mildner A. Cohen N. Jung S. Tanay A. Amit I. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.Science. 2014; 343: 776-779Crossref PubMed Scopus (1095) Google Scholar). In the last few years, the single-cell genomics field dramatically advanced in overcoming the limiting factors that had previously hindered its utility in immunology research. 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Scrutinized under this newly established molecular microscope, immune cell types so far considered homogenous were shown to display functional heterogeneity, even within thoroughly studied models and well-recognized immune cell populations. Recent studies demonstrated that classically defined immune entities can consist of different cell populations sharing overlapping markers (Björklund et al., 2016Björklund Å.K. Forkel M. Picelli S. Konya V. Theorell J. Friberg D. Sandberg R. Mjösberg J. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat.Immunol. 2016; 17: 451-460Google Scholar, Gaublomme et al., 2015Gaublomme J.T. Yosef N. Lee Y. Gertner R.S. Yang L.V. Wu C. Pandolfi P.P. Mak T. Satija R. Shalek A.K. et al.Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.Cell. 2015; 163: 1400-1412Abstract Full Text Full Text PDF PubMed Scopus (366) Google Scholar, Gury-BenAri et al., 2016Gury-BenAri M. Thaiss C.A. 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Kenigsberg E. Keren-Shaul H. Winter D. Lara-Astiaso D. Gury M. Weiner A. et al.Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.Cell. 2015; 163: 1663-1677Abstract Full Text Full Text PDF PubMed Scopus (599) Google Scholar, Schlitzer et al., 2015Schlitzer A. Sivakamasundari V. Chen J. Sumatoh H.R. Schreuder J. Lum J. Malleret B. Zhang S. Larbi A. Zolezzi F. et al.Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow.Nat. Immunol. 2015; 16: 718-728Crossref PubMed Scopus (329) Google Scholar). For example, single-cell profiling of hematopoietic progenitor populations revealed a large degree of functional heterogeneity and commitment to various lineages (Paul et al., 2015Paul F. Arkin Y. Giladi A. Jaitin D.A.A. Kenigsberg E. Keren-Shaul H. Winter D. Lara-Astiaso D. Gury M. Weiner A. et al.Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.Cell. 2015; 163: 1663-1677Abstract Full Text Full Text PDF PubMed Scopus (599) Google Scholar, Schlitzer et al., 2015Schlitzer A. Sivakamasundari V. Chen J. Sumatoh H.R. Schreuder J. Lum J. Malleret B. Zhang S. Larbi A. Zolezzi F. et al.Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow.Nat. Immunol. 2015; 16: 718-728Crossref PubMed Scopus (329) Google Scholar). Similarly, single-cell analysis of innate lymphocytes (ILCs) from mouse intestine and human tonsils uncovered heterogeneity exceeding the accepted separation into ILC1-3, as well as plasticity within these subsets (Björklund et al., 2016Björklund Å.K. Forkel M. Picelli S. Konya V. Theorell J. Friberg D. Sandberg R. Mjösberg J. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat.Immunol. 2016; 17: 451-460Google Scholar, Gury-BenAri et al., 2016Gury-BenAri M. Thaiss C.A. Serafini N. Winter D.R. Giladi A. Lara-Astiaso D. Levy M. Salame T.M. Weiner A. David E. et al.The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome.Cell. 2016; 166: 1231-1246Abstract Full Text Full Text PDF PubMed Scopus (376) Google Scholar). Furthermore, characterization of Th17 cells revealed heterogeneity and transcription programs involved in pathogenicity or regulatory potentials (Gaublomme et al., 2015Gaublomme J.T. Yosef N. Lee Y. Gertner R.S. Yang L.V. Wu C. Pandolfi P.P. Mak T. Satija R. Shalek A.K. et al.Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.Cell. 2015; 163: 1400-1412Abstract Full Text Full Text PDF PubMed Scopus (366) Google Scholar). The discovery of disease-associated microglia (DAM), molecularly distinct microglia cells that interact with and phagocytize plaques in Alzheimer's disease, became possible due to the power of single-cell analysis to discover otherwise hidden and rare subsets of cells within immune populations (Keren-Shaul et al., 2017Keren-Shaul H. Spinrad A. Weiner A. Matcovitch-Natan O. Dvir-Szternfeld R. Ulland T.K. David E. Baruch K. Lara-Astaiso D. Toth B. et al.A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.Cell. 2017; 169: 1276-1290Abstract Full Text Full Text PDF PubMed Scopus (2021) Google Scholar). Further elucidating the pathways and checkpoints of this new cell type may have important implications for future treatment of Alzheimer's disease and other neurodegenerative disorders. 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