Review
Systems immunology allows a new view on human dendritic cells

https://doi.org/10.1016/j.semcdb.2018.02.017Get rights and content

Highlights

  • Systems immunology is needed to delineate properties of unknown cell populations.

  • ScRNA-seq is an unbiased approach to best describe rare immune cells such as DCs.

  • Systems immunology revealed early and predefined precursors for cDCs in humans.

  • Monocytes can differentiate into DC-like cells, but remain monocytic in lineage.

Abstract

As the most important antigen-presenting cells, dendritic cells connect the innate and adaptive part of our immune system and play a pivotal role in our course of action against invading pathogens as well as during successful vaccination. Immunologists have therefore studied these cells in great detail using flow cytometry-based analyses, in vitro assays and in vivo models, both in murine models and in humans. Albeit, sophisticated, classical immunological, and molecular approaches were often unable to unequivocally determine the subpopulation structure of the dendritic cell lineage and not surprisingly, conflicting results about dendritic cell subsets co-existed throughout the last decades. With the advent of systems approaches and the most recent introduction of -omics approaches on the single cell level combined with multi-colour flow cytometry or mass cytometry, we now enter an era allowing us to define cell population structures with an unprecedented precision. We will report here on the most recent studies applying these technologies to human dendritic cells. Proper delineation of and definition of molecular signatures for the different human dendritic cell subsets will greatly facilitate studying these cells in the future: understanding their function under physiological as well as pathological conditions.

Introduction

In 2014, Guilliams et al. suggested a new nomenclature for dendritic cells (DCs), monocytes, and macrophages as members of the mononuclear phagocyte system [1]. They proposed to define the different cell lineages primarily based on ontogeny followed by location, function, and phenotype. In contrast, the first description of murine DCs by Ralph Steinman in 1973 was entirely focused on the morphological characteristics and the location of these exciting cells [2], followed by two consecutive publications on the in vitro [3] and in vivo [4] functions of DCs. DCs were shown to effectively present antigen via MHC molecules to T cell receptors, thereby even activating naïve T cells [5]. As for any other immune cell, with the advent of flow cytometry, the search for DC-specific cell markers was initiated and numerous genes have been suggested as DC-specific [6]. Until recently, murine DCs were characterized to express high levels of MHC class II molecules and CD11c [6] while human DCs are highly expressing HLA-DR but only some subsets express CD11c [1,6]. Further exploitation using numerous other cell surface markers suggested significant heterogeneity within the DC compartment [[6], [7], [8], [9], [10]] with sometimes even conflicting results concerning the functionality of certain cell subsets [11,12]. Nevertheless, both in the murine and the human system, the DC compartment could be divided up in several independent subsets including plasmacytoid DCs (pDCs) and conventional or classical DCs (cDCs) with two further subsets, cDC1 and cDC2 [1,6] (see also Fig. 1). Mainly established in the murine system, DC subsets were shown to derive from a common dendritic cell precursor (CDP), which further differentiates into either a pre-pDC as the precursor for pDC or an early precursor of cDCs, called early pre-cDC [13]. This early pre-cDC further differentiates into either pre-cDC1 or pre-cDC2, which are the respective precursors for cDC1 and cDC2s [13]. While the murine system is well suited for cell ontogeny studies, the precursor landscape of human DCs was rather obscure until recently [14]. In fact, for a long time, it was postulated that human DCs are derived directly from monocytes [[15], [16], [17]].

In 1994, Sallusto and Lanzavecchia introduced an in vitro culture system of human monocyte-derived DCs (moDCs), which revolutionized subsequent studies into human DC biology [16] laying also the ground for the development of DC vaccines [18]. MoDCs show many of the characteristics of ex vivo isolated human DCs including phenotype, morphology, and function [6]. Yet, with the advent of genomic technologies, particularly global assessment of transcriptional regulation, it became more and more evident that moDCs show differences to their in vivo counterparts. Whether this is solely due to in vitro culture conditions or whether these cells have – yet unrecognized – in vivo counterparts remains unresolved.

Clearly, systems immunology approaches, integrating computational modelling based on high throughput data with the assessment of classical parameters describing morphology, phenotype, and function of DCs, opens completely new avenues to better characterize the human DC compartment, particularly since experimental settings possible in murine model systems (fate mapping, genetic engineering for research), will never be available. Furthermore, the development of novel genomic technologies allowing the assessment of transcriptomes on the single cell level have already revolutionized our knowledge of murine DCs [[19], [20], [21], [22]].

A detailed outline of an integrated functional system of DCs and monocyte-derived cells as well as the distinct pDC system has been recently reviewed elsewhere [6,23], and we refer the reader to these publications for further information. Here, we will focus on the most recent developments in human DC biology. Indeed, systems immunology approaches have revealed the relationship of different human DC subsets throughout hematopoietic and non-hematopoietic tissues and organs [24,25]. Single cell RNA-sequencing (scRNA-seq) combined with mass cytometry (CyTOF) and assessment of classical parameters was instrumental to map the human DC lineage [14]. Lastly, systems approaches unequivocally revealed that moDCs are closely related to inflammatory myeloid cells in vivo, but not to in vivo DCs under homeostatic conditions ([26] and own published results).

Section snippets

Human dendritic cells in lymphoid tissues

Based on many studies performed during the last two decades, a consensus of the cell population structure within the human DC compartment has been established. In lymphoid – but also non-lymphoid – tissues, two main groups, namely plasmacytoid DCs (pDCs) and classical or myeloid DCs (cDCs) are recognized. Based on phenotypic and functional characterization, myeloid DCs have been further subdivided into two subsets: What is now known as the human cDC1 population was defined by the expression of

Human dendritic cells in non-lymphoid tissues

DC populations in non-lymphoid tissues had long been thought to be far less heterogeneic. Yet, more detailed multi-parameter flow cytometry analyses in recent years - particularly in the murine system - led to the identification of several newly defined subsets based upon surface marker expression suggested to be unique identifiers [7]. In 2010, Guilliams et al. proposed a unifying classification across tissues and species defining five major DC subsets [42] which resemble the currently used

Single cell analysis of human dendritic cells

Single cell RNA-sequencing is currently revolutionizing our understanding of the cell as the basic unit of any multi-cellular organism [[65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75]]. While such studies are more easily performed in animal models, the mapping of human cells on the single cell level applying sequencing technologies is more challenging. This is particularly true for tissues that are not easily obtained from healthy individuals or even patient biopsies. Not

Ontogeny of human dendritic cells

During haematopoiesis, that takes place within the bone marrow, stem cells give rise to progenitor cells that consequently differentiate into more specialized subtypes. Single cell-based analysis of murine bone marrow revealed a continuous development of distinct transcriptionally primed progenitor populations from an early precursor [77] suggesting that previously described distinct intermediates (e.g. CMPs, GMPs) are heterogenous albeit individual cells are already predetermined towards a

Functional studies of newly defined human DC subsets

Recent studies have started to address functional analyses of the now defined DC subsets. Harnessing an organ donor tissue resource, DC subsets were analysed in various tissues from nearly 80 individuals covering an age range from less than 1–93 years [84]. cDC1 and cDC2 subsets were found to be tissue-specifically distributed and, as this was conserved between the various donors, found to be retained over life. cDC2s were a common feature of draining lymph nodes with the highest prevalence in

What are monocyte-derived human dendritic cells?

Although it is now rather clear that tissue macrophages and dendritic cells are not derived from monocytes, blood monocytes can enter tissues and get reprogrammed when doing so, particularly under inflammatory conditions [88]. During this progress monocytes can gain many properties associated with either tissue macrophages or dendritic cells. According to a marker-based nomenclature, human blood monocytes have been subdivided into CD14+CD16 classical, CD14+CD16+ intermediate and CD14loCD16+

Conclusions and future directions

The application of systems immunology approaches in the last five to seven years has been critical to delineate the human dendritic cell system. The historical characterization of cell populations based on known cell surface markers has proven to be insufficient for a comprehensive functional discrimination of distinct cell subsets, especially with respect to the definition of progenitor populations. In contrast, an unsupervised analysis of conventional multi-colour flow cytometry, CyTOF, bulk

Funding sources

This work was supported by the German Research Foundation (DFG) to JLS (SFB704, Excellence Cluster ImmunoSensation).

Acknowledgements

JLS is a member of the Excellence Cluster ImmunoSensation.

References (95)

  • C.I. Yu et al.

    Human CD1c+ dendritic cells drive the differentiation of CD103+ CD8+ mucosal effector T cells via the cytokine TGF-beta

    Immunity

    (2013)
  • B. Cisse et al.

    Transcription factor E2-2 is an essential and specific regulator of plasmacytoid dendritic cell development

    Cell

    (2008)
  • L.F. Poulin et al.

    DNGR-1 is a specific and universal marker of mouse and human Batf3-dependent dendritic cells in lymphoid and nonlymphoid tissues

    Blood

    (2012)
  • E. Klechevsky et al.

    Functional specializations of human epidermal Langerhans cells and CD14++ dermal dendritic cells

    Immunity

    (2008)
  • L. Chorro et al.

    Development and homeostasis of’ resident’ myeloid cells: the case of the Langerhans cell

    Trends Immunol.

    (2010)
  • T. Doebel et al.

    Langerhans cells- the macrophage in dendritic cell clothing

    Trends Immunol.

    (2017)
  • G. Hoeffel et al.

    C-myb(+) erythro-myeloid progenitor-derived fetal monocytes give rise to adult tissue-resident macrophages

    Immunity

    (2015)
  • S. Carpentier et al.

    Comparative genomics analysis of mononuclear phagocyte subsets confirms homology between lymphoid tissue-resident and dermal XCR1(+) DCs in mouse and human and distinguishes them from Langerhans cells

    J. Immunol. Methods

    (2016)
  • I.C. Macaulay et al.

    Single-cell multiomics: multiple measurements from single cells

    Trends Genet.

    (2017)
  • D. Grun et al.

    Design and analysis of single-cell sequencing experiments

    Cell

    (2015)
  • A.A. Kolodziejczyk et al.

    The technology and biology of single-cell RNA sequencing

    Mol. Cell

    (2015)
  • Y. Wang et al.

    Advances and applications of single-cell sequencing technologies

    Mol. Cell

    (2015)
  • J.L. Schultze et al.

    Myelopoiesis reloaded: single-cell transcriptomics leads the way

    Immunity

    (2016)
  • T. Granot et al.

    Dendritic cells display subset and tissue-specific maturation dynamics over human life

    Immunity

    (2017)
  • J. Cros et al.

    Human CD14dim monocytes patrol and sense nucleic acids and viruses via TLR7 and TLR8 receptors

    Immunity

    (2010)
  • M.A. Ingersoll et al.

    Comparison of gene expression profiles between human and mouse monocyte subsets

    Blood

    (2010)
  • J. Xue et al.

    Transcriptome-based network analysis reveals a spectrum model of human macrophage activation

    Immunity

    (2014)
  • E. Guttman-Yassky et al.

    Major differences in inflammatory dendritic cells and their products distinguish atopic dermatitis from psoriasis

    J. Allergy Clin. Immunol. Pract.

    (2007)
  • J. Sander et al.

    Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2

    Immunity

    (2017)
  • M. Guilliams et al.

    Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny

    Nat. Rev. Immunol.

    (2014)
  • R.M. Steinman et al.

    Identification of a novel cell type in peripheral lymphoid organs of mice. I. Morphology, quantitation, tissue distribution

    J. Exp. Med.

    (1973)
  • R.M. Steinman et al.

    Identification of a novel cell type in peripheral lymphoid organs of mice. II. Functional properties in vitro

    J. Exp. Med.

    (1974)
  • R.M. Steinman et al.

    Identification of a novel cell type in peripheral lymphoid organs of mice. 3. Functional properties in vivo

    J. Exp. Med.

    (1974)
  • R.M. Steinman et al.

    Lymphoid dendritic cells are potent stimulators of the primary mixed leukocyte reaction in mice

    Proc. Natl. Acad. Sci. U. S. A.

    (1978)
  • M. Merad et al.

    The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting

    Annu. Rev. Immunol.

    (2013)
  • F. Ginhoux et al.

    Monocytes and macrophages: developmental pathways and tissue homeostasis

    Nat. Rev. Immunol.

    (2014)
  • F. Geissmann et al.

    Unravelling mononuclear phagocyte heterogeneity

    Nat. Rev. Immunol.

    (2010)
  • D.A. Hume

    Applications of myeloid-specific promoters in transgenic mice support in vivo imaging and functional genomics but do not support the concept of distinct macrophage and dendritic cell lineages or roles in immunity

    J. Leukoc. Biol.

    (2011)
  • A. Schlitzer 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)
  • P. See et al.

    Mapping the human DC lineage through the integration of high-dimensional techniques

    Science

    (2017)
  • R. van Furth et al.

    Mononuclear phagocytic system: new classification of macrophages, monocytes and of their cell line

    Bull. World Health Organ.

    (1972)
  • F. Sallusto et al.

    Efficient presentation of soluble antigen by cultured human dendritic cells is maintained by granulocyte/macrophage colony-stimulating factor plus interleukin 4 and downregulated by tumor necrosis factor alpha

    J. Exp. Med.

    (1994)
  • P. Chomarat et al.

    IL-6 switches the differentiation of monocytes from dendritic cells to macrophages

    Nat. Immunol.

    (2000)
  • W. Kastenmuller et al.

    Dendritic cell-targeted vaccines–hope or hype?

    Nat. Rev. Immunol.

    (2014)
  • D.A. Jaitin et al.

    Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

    Science

    (2014)
  • A.K. Shalek et al.

    Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

    Nature

    (2014)
  • A. Dixit et al.

    Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens

    Cell

    (2016)
  • Cited by (15)

    • The Whole Body as the System in Systems Immunology

      2020, iScience
      Citation Excerpt :

      Since the introduction of scRNA-seq in 2009 (Tang et al., 2009), new technological advances in scRNA-seq methods including plate-based approaches and the 10X Genomics approach employing microdroplet-based systems enable rapid and efficient capture of high transcript numbers per cell (Bush et al., 2017; Hwang et al., 2018; Jaitin et al., 2014). Recent studies using scRNA-seq approaches have led to identification of cell types and progenitors, developmental processes, activation trajectories, and functional signatures for diverse immune cell lineages (Papalexi and Satija, 2018; Paul et al., 2015; Popescu et al., 2019; Schultze and Aschenbrenner, 2019; See et al., 2017; Stewart et al., 2019, 2020; Szabo et al., 2019a; Villani et al., 2017; Yu et al., 2016). T and B cells exhibit an additional level of genomic complexity in their expression of uniquely rearranged antigen receptor genes.

    • Emerging Principles in Myelopoiesis at Homeostasis and during Infection and Inflammation

      2019, Immunity
      Citation Excerpt :

      Only if we understand these system-wide regulatory circuits and feedback loops will we be in a position to develop novel diagnostic and therapeutic targets for many of the major chronic diseases that are characterized by an inflammatory condition including demand-adapted myelopoiesis. This will also require a multi-disciplinary approach that goes far beyond classical immunology integrating state-of-the-art omics technologies up to the single cell level and novel HDFC with genetic engineering and fate-mapping strategies (Davis et al., 2017; Schultze and Aschenbrenner, 2018). An important aspect will be to generate quantitative data that will allow computational and mathematical modeling of system-wide feedback loops including myelopoiesis, which subsequently can guide and prioritize further experimentation.

    View all citing articles on Scopus
    View full text