ReviewA transcriptional perspective on human macrophage biology
Introduction
Macrophages are an important cell of the innate immune system. They mediate their actions in two ways; through endocytosis and phagocytosis, to remove and destroy components of their extracellular environment such as damaged tissue and pathogens and through exocytosis and secretion of bioactive molecules to regulate the function of other cells. Macrophages are a significant resident cellular component of most tissues, occupying precise anatomical niches especially proximal to the vasculature and epithelia [1], [2], [3]. In homeostasis, resident macrophages are actively involved in tissue integrity, through the removal of dead cells and debris and regeneration [4], and in physiological processes such angiogenesis [5], [6], lipid homeostasis [7], [8], [9], [10], or iron homeostasis [10], [11], [12], [13]. Their numbers increase significantly through recruitment and extravasation in response to chemoattractants secreted locally in response to a wide range of pro-inflammatory sterile and non-sterile stressors. The initiation of inflammation involves the recognition of pathogen-associated molecular patterns (PAMPs) [14], [15] associated with invading microbes or damage-associated molecular patterns (DAMPs) [16]. Macrophages are equipped with a large number of receptors that can recognize PAMPs or DAMPs. Signaling systems activated by these receptors are integrated in the context of tissue-derived signals, and resident and recruited macrophages quickly generate appropriate effector programs to eliminate the stressor and repair the damage. The nature of the effector mechanism must be appropriate to the challenge, and may change with time as a lesion progresses from initiation to resolution. A simplistic view of macrophage activation states is based upon a binary divide between pro-inflammatory or an anti-inflammatory state. The pro-inflammatory program has also been termed classical or M1 polarization while the anti-inflammatory program is described as alternative or M2 polarization, to parallel the concept of Th1 and Th2 states of T cell activation. M1 macrophages have been linked to stimulation by IFNγ, a cytokine secreted by Th1 cells while M2 macrophages were associated with IL-4, a classical Th2 cytokine [17], [18], [19], [20], [21], [22]. Given the fact that macrophages possess regulatory receptors for a bewildering array of growth factors, cytokines, chemokines, prostanoids, etc. [4], [23], this binary divide is intrinsically unlikely. A more sustainable view sees macrophage polarization more in the nature of a color wheel [24], [25] and recent work clearly suggests a much broader multi-dimensional model [23]. The regulation of macrophage function and the balance between inflammation and resolution is arguably the key event in most disease processes. Dysregulated macrophage function contributes to almost all chronic inflammatory conditions including obesity [10], [19], [26], [27], [28], [29], atherosclerosis [30], [31], [32], [33], cancer [18], [34], [35], [36], [37], [38], [39], [40], [41], chronic obstructive pulmonary diseases [42], [43], [44], chronic infections [17], [45], [46], and even Alzheimer's [47], [48], [49], [50].
Resident tissue macrophages in the mouse respond to the local tissue environment and differ substantially from each other in terms of function and gene expression [51], [52], [53]. In the mouse, fate mapping and labeling studies suggested that murine tissue macrophages are derived from yolk sac during embryogenesis [54], [55], [56], [57], [58]. Moreover, most tissue macrophage populations can be maintained in the absence of monocytic recruitment through local proliferation [59], [60]. This seems to be in contrast to earlier findings, clearly showing that tissue macrophages are replaced ultimately by blood monocytes produced from the bone marrow [1], [3]. In fact, several recent reports have already indicated that yolk sac derived murine tissue macrophages are replaced by monocyte-derived macrophages in some organs including the gut [61], the heart [62] and the skin [63] even under homeostatic conditions. Whether these findings of macrophage origin in mice can ever be translated to humans and whether this will be important for human disease, therapy or diagnosis remains to be seen. Clearly, tissue macrophage populations depend upon continued signaling from the key growth factor, macrophage colony-stimulating factor (CSF1) [64], [65], and the circulating level of CSF1 is itself controlled by monocytes [58]. So, there is an intrinsic homeostasis regulating tissue macrophage numbers. During an inflammatory response, recruited monocytes differentiate to macrophages and contribute to the pool of macrophages involved in local tissue inflammation [66]. Ongoing studies are addressing the contribution of both types of macrophages during inflammation [67]. Not unexpectedly, there is little known about the origin of macrophages in humans or any other non-rodent species, and there is a need to extend our understanding of human macrophage heterogeneity and origins.
However, genome-wide assessment of transcriptional regulation in murine and human macrophages in their resting and activated states has created doubt about the validity of easily translating findings from murine to human macrophages [68]. For example, mouse macrophages induce the set of genes required to transport and metabolize arginine to produce nitric oxide, whereas human macrophages induce the set of genes required to metabolize tryptophan through indoleamine 2,3-dioxygenase to kynurenine metabolites [68], [69], [70]. In fact, some of us have provided evidence that the domestic pig provides a much better approximation of the human macrophage response [71]. We also believe that further work is necessary to build reliable databases for conservation of expression between macrophages derived from humans and other species after a set of different stimuli.
Clearly, there is no perfect substitute for data from humans. With the advent of genome-wide assessment of gene transcription, epigenetic regulation, or translational control completely new approaches for research in human macrophage biology have been introduced over the last decade. Combined with sophisticated biostatistics, biomathematics, bioinformatics and systems approaches, a complementary or even alternative to more conventional or classical animal model system based approaches has evolved. We will give an overview of genome-wide approaches applied to human macrophage biology during the last decade, introduce novel concepts of human macrophage activation, suggest workflows to integrate genome-wide approaches with animal models and other more gene-centered strategies, and give an overview on recent international activities to better understand macrophage biology in the context of other cell types.
Section snippets
Existing data on global transcriptional programming of human macrophages
Macrophages respond to exogenous stimuli such as PAMPS with massive changes in gene expression [23], [72], [73], [74]. The earliest changes can be detected within minutes, and involve the activation of transcriptional elongation from preexisting poised RNAPolII complexes [75]. Thereafter, there is a cascade of transcriptional activation, involving many regulated transcription factors and chromatin reorganization, as macrophage cells transition toward a new steady state over around 24 h.
From bipolarity to a multi-dimensional model of macrophage activation
A PubMed search in May 2014 for the keywords ((“M1” or “M2”) and “macrophage”) revealed more than 3400 original papers and 218 reviews indicating that a bipolar macrophage activation model has been widely adopted by the scientific community. The implication of the M1/M2 model is that there are two distinct transcriptional states in macrophages. If those states exist as a kind of “regulon”, there should be two distinct sets of co-expressed transcripts that cluster together in a network graph. At
Switching transcriptional programs in macrophages: the HDL example
Although human and murine macrophages differ significantly in their transcriptional regulation upon particular input signals such as LPS [68], it is still valid to study macrophage biology in the murine model provided that a similar regulation is first identified in humans. Using one of our previous findings as an example we highlight, how genome-wide transcriptional profiling can lead to the identification of novel mechanisms of macrophage biology. When stimulating human macrophages with TLR
Distinguishing macrophages from other cells
While macrophages are easily to be distinguished from granulocytes even based on morphology, the delineation between macrophages and dendritic cells is still an area of some debate [52]. “Dendritic cells (DC) are the antigen presenting cells that initiate and direct adaptive immune responses, capable of inducing protective adaptive immune responses and tolerance”. This statement by Mellman [91] has become a dogma in the literature, but it is intrinsically circular. It relies upon the ability to
Human macrophages within FANTOM5
Additional evidence for the requirement of studying macrophage biology directly in humans comes from a large international effort known as FANTOM5 (Functional Annotation of the Mammalian Genome) [84], [96]. In this large effort, 573 primary human cells also including samples of monocyte-derived macrophages, 152 human tissues, 250 human cell lines, 128 murine primary cells and 271 murine tissues were profiled by cap analysis of gene expression (CAGE) to generate genome-wide maps of transcription
Outlook
Macrophages play a very important role for many aspects of tissue homeostasis and are similarly important during many acute inflammatory reactions as a response of the host to endogenous or exogenous stress signals. Moreover, their impact in many of the common diseases of our societies including obesity, atherosclerosis, autoimmune disorders, cancer, and even Alzheimer's disease is still underappreciated. Chronic inflammation is often driven by myeloid cells and macrophages are probably the
Concluding remarks
On transcriptional level, most recent work has clearly shown that macrophages are well equipped to compute input signals in a very specific fashion thereby generating similarly unique output programs. Old observation from more classical approaches and more recent work utilizing genome-wide gene expression profiling clearly supports a multi-dimensional model of macrophage activation rather than the simple two-armed polarization model favored for more than a decade. Recent work from FANTOM5
Acknowledgements
J.L.S and E.L. are members of the Excellence Cluster ImmunoSensation. This work was supported by Sonderforschungsbereiche SFB704 and SFB645 to J.L.S. and E.L. T.C.F. and D.A.H. are funded by an Institute Strategic Grant from the Biotechnology and Biological Sciences Research Council [grant number BB/JO1446X/1].
References (98)
Differentiation and heterogeneity in the mononuclear phagocyte system
Mucosal Immunol.
(2008)The mononuclear phagocyte system
Curr. Opin. Immunol.
(2006)- et al.
Apoptotic cell removal in development and tissue homeostasis
Trends Immunol.
(2006) - et al.
Role of macrophage polarization in tumor angiogenesis and vessel normalization: implications for new anticancer therapies
Int. Rev. Cell Mol. Biol.
(2013) - et al.
Proresolving lipid mediators and mechanisms in the resolution of acute inflammation
Immunity
(2014) - et al.
Diet, metabolites, and western-lifestyle inflammatory diseases
Immunity
(2014) - et al.
Orchestration of metabolism by macrophages
Cell Metab.
(2012) - et al.
Macrophage polarization comes of age
Immunity
(2005) - et al.
Transcriptome-based network analysis reveals a spectrum model of human macrophage activation
Immunity
(2014) - et al.
Macrophages, immunity, and metabolic disease
Immunity
(2014)
Hypoxia in murine atherosclerotic plaques and its adverse effects on macrophages
Trends Cardiovasc. Med.
Tumor-associated macrophages: from mechanisms to therapy
Immunity
MicroRNA-mediated control of macrophages and its implications for cancer
Trends Immunol.
Macrophage regulation of tumor responses to anticancer therapies
Cancer Cell.
Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment
Cell
Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis
Immunity
Homeostasis in the mononuclear phagocyte system
Trends Immunol.
Intestinal macrophages: well educated exceptions from the rule
Trends Immunol.
An antibody against the colony-stimulating factor 1 receptor depletes the resident subset of monocytes and tissue- and tumor-associated macrophages but does not inhibit inflammation
Blood
Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct
Blood
Macrophage activation: glancing into diversity
Immunity
Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations
Immunobiology
Harnessing dendritic cells for immunotherapy
Semin. Immunol.
A prescription for human immunology
Immunity
Macrophage biology in development, homeostasis and disease
Nature
Role of tumor associated macrophages in tumor angiogenesis and lymphangiogenesis
Front. Physiol.
Macrophages preventing lipid overload
Nat. Rev. Immunol.
A decade of progress in adipose tissue macrophage biology
Immunol. Rev.
The role of iron metabolism as a mediator of macrophage inflammation and lipid handling in atherosclerosis
Front. Pharmacol.
Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis
Nature
Macrophage iron homeostasis and polarization in the context of cancer
Immunobiology
Toll-like receptors: critical proteins linking innate and acquired immunity
Nat. Immunol.
Pathogen recognition by the innate immune system
Int. Rev. Immunol.
Sterile inflammation: sensing and reacting to damage
Nat. Rev. Immunol.
Macrophage plasticity and polarization: in vivo veritas
J. Clin. Investig.
Macrophage plasticity and interaction with lymphocyte subsets: cancer as a paradigm
Nat. Immunol.
Macrophage activation and polarization
Front. Biosci.
Alternative activation of macrophages
Nat. Rev. Immunol.
Exploring the full spectrum of macrophage activation
Nat. Rev. Immunol.
Plenary perspective: the complexity of constitutive and inducible gene expression in mononuclear phagocytes
J. Leukoc. Biol.
Macrophage polarization in obesity and type 2 diabetes: weighing down our understanding of macrophage function?
Front. Immunol.
Changes in adipose tissue macrophages and T cells during aging
Crit. Rev. Immunol.
Protective and pathogenic functions of macrophage subsets
Nat. Rev. Immunol.
Imaging macrophage development and fate in atherosclerosis and myocardial infarction
Immunol. Cell Biol.
Macrophages in atherosclerosis: a dynamic balance
Nat. Rev. Immunol.
Phenotypic polarization of macrophages in atherosclerosis
Arterioscler. Thromb. Vasc. Biol.
Mechanisms driving macrophage diversity and specialization in distinct tumor microenvironments and parallelisms with other tissues
Front. Immunol.
Functional relationship between tumor-associated macrophages and macrophage colony-stimulating factor as contributors to cancer progression
Front. Immunol.
The cellular and molecular origin of tumor-associated macrophages
Science
Cited by (30)
Artificial M2 macrophages for disease-modifying osteoarthritis therapeutics
2021, BiomaterialsCitation Excerpt :Interestingly,the density signal of IL-1β and IL-6 in the GC and ChS@GC groups through quantitative analysis was higher than AM2M group and ChS@GC@EM group (Fig. 6B). Several studies reported that macrophages could secrete large amounts of pro-inflammatory cytokines (IL-1β, IL-6 and so on) through immune activation in the microenvironment of OA [59–61]. Thus, this result demonstrated that membrane-cloaking groups enhanced the anti-inflammatory efficacy of ChS through the membrane coating which shielded immunostimulatory effects of ChS on macrophages.
The number and phenotype of myocardial and adipose tissue CD68+ cells is associated with cardiovascular and metabolic disease in heart surgery patients
2019, Nutrition, Metabolism and Cardiovascular DiseasesCitation Excerpt :In addition, we found that EAT had in general higher CD68+ cell number when compared to SAT and that CLS-positive adipose tissue samples contained numerous pro-inflammatory CD11c+ macrophages in contrast to non-CLS adipose tissue samples. Despite some recent controversies regarding markers of pro- and anti-inflammatory macrophages and slightly simplified phenotypic classification of macrophages into these two groups [18], the finding of CD11c+ macrophages participating in an obviously inflammatory process is in line with their pro-inflammatory activation. Furthermore, CD11c+ macrophages in CLS found in SAT were already demonstrated in one previous paper [19].
Chromatin Remodeling in Monocyte and Macrophage Activation
2017, Advances in Protein Chemistry and Structural BiologyCitation Excerpt :There was no evidence that monocytes or macrophages follow an activation model simply described by being either pro- or antiinflammatory (Xue et al., 2014). This led us to define the new multidimensional model of macrophage activation (Ginhoux et al., 2016; Schultze, 2015; Schultze et al., 2015; Schultze & Schmidt, 2015). In principle, monocytes and macrophages are never in a resting state, since they always integrate signals from their microenvironment.
Modulation of Macrophage Activation
2016, Immune Rebalancing: The Future of ImmunosuppressionEditorial
2015, Seminars in ImmunologyEffect of exosomes derived from Echinococcus multilocularis on macrophage polarization:A preliminary study
2023, Journal of Clinical Hepatology