Plenary perspective: the complexity of constitutive and inducible gene expression in mononuclear phagocytes

CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages

An intense, nonresolving airway inflammatory response leads to destructive lung disease in cystic fibrosis (CF). Dysregulation of macrophage immune function may be a key facet governing the progression of CF lung disease, but the underlying mechanisms are not fully understood. We used 5' end centered transcriptome sequencing to profile P. aeruginosa LPS-activated human CF macrophages, showing that CF and non-CF macrophages deploy substantially distinct transcriptional programs at baseline and following activation. This includes a significantly blunted type I IFN signaling response in activated patient cells relative to healthy controls that was reversible upon in vitro treatment with CFTR modulators in patient cells and by CRISPR-Cas9 gene editing to correct the F508del mutation in patient-derived iPSC macrophages. These findings illustrate a previously unidentified immune defect in human CF macrophages that is CFTR dependent and reversible with CFTR modulators, thus providing new avenues in the search for effective anti-inflammatory interventions in CF.

A simplified method for separating renal MPCs using SLAMF9

Mononuclear phagocytes comprise an array of tissue-resident and monocyte-derived cells with important roles in tissue homeostasis and resistance to infection. Their diverse phenotypes make functional characterization within tissues challenging, because multiple surface markers are typically required for subset identification and isolation by cell sorting methods. Analysis of SLAMF9 expression within renal mononuclear phagocyte populations by multi-parametric flow cytometry indicates that SLAMF9 is a specific marker for identification of kidney-resident CD45⁺ CD11c⁺  MHC-II⁺ cells corresponding to prominent tissue-resident MPC populations derived from dendritic cell progenitors in adult mice. High SLAMF9 expression was sufficient to identify and sort these cells from disaggregated tissue using a user-operated cell sorter. The population can be further subdivided according to expression of CD11b and CD14 to identify IRF8^high cDC1 cells and cleanly separate the CD11b^high F4/80^low and CD11b^int F4/80^high CD11c⁺ MPC subsets. Therefore, SLAMF9 expression allows for the identification and sorting of kidney-resident CD11b⁺ CD11c⁺ CD64⁺ F4/80⁺ CX₃ CR1⁺ MHC-II⁺ MPCs without the need for complex antibody panels or reporter mice, simplifying isolation of these cells for study ex vivo.

Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity

Macrophages are ubiquitous custodians of tissues, which play decisive role in maintaining cellular homeostasis through regulatory immune responses. Within tissues, macrophage exhibit extremely heterogeneous population with varying functions orchestrated through regulatory response, which can be further exacerbated in diverse genetic backgrounds. Gene regulatory networks (GRNs) offer comprehensive understanding of cellular regulatory behavior by unfolding the transcription factors (TFs) and regulated target genes. RNA-Seq coupled with ATAC-Seq has revolutionized the regulome landscape influenced by gene expression modeling. Here, we employ an integrative multi-omics systems biology-based analysis and generated GRNs derived from the unstimulated bone marrow-derived macrophages of five inbred genetically defined murine strains, which are reported to be linked with most of the population-wide human genetic variants. Our probabilistic modeling of a basal hemostasis pan regulatory repertoire in diverse macrophages discovered 96 TFs targeting 6279 genes representing 468,291 interactions across five inbred murine strains. Subsequently, we identify core and distinctive GRN sub-networks in unstimulated macrophages to describe the system-wide conservation and dissimilarities, respectively across five murine strains. Our study concludes that discrepancies in unstimulated macrophage-specific regulatory networks not only drives the basal functional plasticity within genetic backgrounds, additionally aid in understanding the complexity of racial disparity among the human population during stress.

Quantifying Heterogeneity According to Deformation of the U937 Monocytes and U937-Differentiated Macrophages Using 3D Carbon Dielectrophoresis in Microfluidics

A variety of force fields have thus far been demonstrated to investigate electromechanical properties of cells in a microfluidic platform which, however, are mostly based on fluid shear stress and may potentially cause irreversible cell damage. This work presents dielectric movement and deformation measurements of U937 monocytes and U937-differentiated macrophages in a low conductive medium inside a 3D carbon electrode array. Here, monocytes exhibited a crossover frequency around 150 kHz and presented maximum deformation index at 400 kHz and minimum deformation index at 1 MHz frequencies at 20 V_peak-peak. Although macrophages were differentiated from monocytes, their crossover frequency was lower than 50 kHz at 10 V_peak-peak. The change of the deformation index for macrophages was more constant and lower than the monocyte cells. Both dielectric mobility and deformation spectra revealed significant differences between the dielectric responses of U937 monocytes and U937-differentiated macrophages, which share the same origin. This method can be used for label-free, specific, and sensitive single-cell characterization. Besides, damage of the cells by aggressive shear forces can, hence, be eliminated and cells can be used for downstream analysis. Our results showed that dielectric mobility and deformation have a great potential as an electromechanical biomarker to reliably characterize and distinguish differentiated cell populations from their progenitors.

Pharmacological plasticity-How do you hit a moving target?

Paul Ehrlich's concept of the magic bullet, by which a single drug induces pharmacological effects by interacting with a single receptor has been a strong driving force in pharmacology for a century. It is continually thwarted, though, by the fact that the treated organism is highly dynamic and the target molecule(s) is (are) never static. In this article, we address some of the factors that modify and cause the mobility and plasticity of drug targets and their interactions with ligands and discuss how these can lead to unexpected (lack of) effects of drugs. These factors include genetic, epigenetic, and phenotypic variability, cellular plasticity, chronobiological rhythms, time, age and disease resolution, sex, drug metabolism, and distribution. We emphasize four existing approaches that can be taken, either singly or in combination, to try to minimize effects of pharmacological plasticity. These are firstly, to enhance specificity using target conditions close to those in diseases, secondly, by simultaneously or thirdly, sequentially aiming at multiple targets, and fourthly, in synchronization with concurrent dietary, psychological, training, and biorhythm-synchronizing procedures to optimize drug therapy.

Dual role of macrophage in tumor immunity

Macrophages are significant in immune responses, assuming a defensive role. In contrast, macrophages often cause undesirable changes. These reactions are processes by which macrophages express different functional programs in response to microenvironmental signals, defined as M1/M2 polarization. Tumor immunity has been acknowledged for contributing to the elucidation of the mechanism and clinical application in cancer therapy. One of the mechanisms for the refractoriness to cancer immunotherapy is the production of inhibitory cytokines by tumor cells or macrophages. Therefore, therapeutic strategy targeting macrophage or macrophage-derived cytokines may be effective and attractive. This review aims to investigate macrophage-associated pathophysiology and biological behavior in cancers, especially related to microenvironment, such as hypoxia, and current topics regarding some therapies involving macrophages.

A novel myeloid cell in murine spleen defined through gene profiling

A novel myeloid antigen presenting cell can be generated through in vitro haematopoiesis in long‐term splenic stromal cocultures. The in vivo equivalent subset was recently identified as phenotypically and functionally distinct from the spleen subsets of macrophages, conventional (c) dendritic cells (DC), resident monocytes, inflammatory monocytes and eosinophils. This novel subset which is myeloid on the basis of cell surface phenotype, but dendritic‐like on the basis of cell surface marker expression and antigen presenting function, has been tentatively labelled “L‐DC.” Transcriptome analysis has now been employed to determine the lineage relationship of this cell type with known splenic cDC and monocyte subsets. Principal components analysis showed separation of “L‐DC” and monocytes from cDC subsets in the second principal component. Hierarchical clustering then indicated a close lineage relationship between this novel subset, resident monocytes and inflammatory monocytes. Resident monocytes were the most closely aligned, with no genes specifically expressed by the novel subset. This subset, however, showed upregulation of genes reflecting both dendritic and myeloid lineages, with strong upregulation of several genes, particularly CD300e. While resident monocytes were found to be dependent on Toll‐like receptor signalling for development and were reduced in number in Myd88‐/‐ and Trif‐/‐ mutant mice, both the novel subset and inflammatory monocytes were unaffected. Here, we describe a novel myeloid cell type closely aligned with resident monocytes in terms of lineage but distinct in terms of development and functional capacity.

Macrophages mediate corticotomy-accelerated orthodontic tooth movement

Clinical evidence has suggested that surgical corticotomy of the alveolar bone can accelerate local orthodontic tooth movement (OTM), but the underlying cell and molecular mechanisms remain largely unclear. The present study examined the role of macrophages played in corticotomy-assisted OTM. Orthodontic nickel-titanium springs were applied to the left maxillary first molars of rats or mice to induce OTM with or without corticotomy. Corticotomy enhanced OTM distance by accelerating movement through induction of local osteoclastogenesis and macrophage infiltration during OTM. Further analysis showed that macrophages were polarized toward an M1-like phenotype immediately after corticotomy and then switched to an M2-like phenotype during OTM. The microenvironment of corticotomy induced macrophage infiltration and polarization through the production of TNF-α. More importantly, the amount of OTM induced by corticotomy was significantly decreased after mice were depleted of monocyte/macrophages by injection of liposome-encapsulated clodronate. Further experiments by incubating cultured macrophages with fresh tissue suspension obtained from post-corticotomy gingiva switched the cells to an M1 phenotype through activation of the nuclear factor-κB (NF-κB) signaling pathway, and to an M2 phenotype through activation of the JAK/STAT3 signaling pathway. Our results suggest that corticotomy induces macrophage polarization first by activating the NF-κB signaling pathway and later by activating the JAK/STAT3 signaling pathway, and that these processes contribute to OTM by triggering production of inflammatory cytokines and osteoclastogenesis.

MicroRNA-150 targets PU.1 and regulates macrophage differentiation and function in experimental autoimmune encephalomyelitis

PU.1 is a transcription factor which is expressed in myeloid cells. Herein, we investigated the expression of PU.1 and its potentially targeting miRNAs in the central nervous system (CNS) of mice with experimental autoimmune encephalitis (EAE) and in cultured primary macrophages. PU.1 levels where highly induced in EAE spinal cords and in activated macrophages; this was associated with a significant reduction in miR-150-5p levels at chronic phase of disease and in activated cells. Luciferase assays confirmed the PU.1-miR-150-5p interaction. Overexpression of miR-150-5p in macrophages decreased the expression of proinflammatory cytokines and shifted the polarization of macrophages away from the M1-like phenotype.

Transcriptional mechanisms that control expression of the macrophage colony-stimulating factor receptor locus

The proliferation, differentiation, and survival of cells of the macrophage lineage depends upon signals from the macrophage colony-stimulating factor (CSF) receptor (CSF1R). CSF1R is expressed by embryonic macrophages and induced early in adult hematopoiesis, upon commitment of multipotent progenitors to the myeloid lineage. Transcriptional activation of CSF1R requires interaction between members of the E26 transformation-specific family of transcription factors (Ets) (notably PU.1), C/EBP, RUNX, AP-1/ATF, interferon regulatory factor (IRF), STAT, KLF, REL, FUS/TLS (fused in sarcoma/ranslocated in liposarcoma) families, and conserved regulatory elements within the mouse and human CSF1R locus. One element, the Fms-intronic regulatory element (FIRE), within intron 2, is conserved functionally across all the amniotes. Lineage commitment in multipotent progenitors also requires down-regulation of specific transcription factors such as MYB, FLI1, basic leucine zipper transcriptional factor ATF-like (BATF3), GATA-1, and PAX5 that contribute to differentiation of alternative lineages and repress CSF1R transcription. Many of these transcription factors regulate each other, interact at the protein level, and are themselves downstream targets of CSF1R signaling. Control of CSF1R transcription involves feed–forward and feedback signaling in which CSF1R is both a target and a participant; and dysregulation of CSF1R expression and/or function is associated with numerous pathological conditions. In this review, we describe the regulatory network behind CSF1R expression during differentiation and development of cells of the mononuclear phagocyte system.

Contributions to the dynamics of cervix remodeling prior to term and preterm birth

Major clinical challenges for obstetricians and neonatologists result from early cervix remodeling and preterm birth. Complications related to cervix remodeling or delivery account for significant morbidity in newborns and peripartum mothers. Understanding morphology and structure of the cervix in pregnant women is limited mostly to the period soon before and after birth. However, evidence in rodent models supports a working hypothesis that a convergence of factors promotes a physiological inflammatory process that degrades the extracellular collagen matrix and enhances biomechanical distensibility of the cervix well before the uterus develops the contractile capabilities for labor. Contributing factors to this remodeling process include innervation, mechanical stretch, hypoxia, and proinflammatory mediators. Importantly, the softening and shift to ripening occurs while progesterone is near peak concentrations in circulation across species. Since progesterone is required to maintain pregnancy, the premise of this review is that loss of responsiveness to progesterone constitutes a common final mechanism for remodeling the mammalian cervix in preparation for birth at term. Various inputs are suggested to promote signaling between stromal cells and resident macrophages to drive proinflammatory processes that advance the soft cervix into ripening. With infection, pathophysiological processes may prematurely drive components of this remodeling mechanism and lead to preterm birth. Identification of critical molecules and pathways from studies in various rodent models hold promise for novel endpoints to assess risk and provide innovative approaches to treat preterm birth or promote the progress of ripening at term.

Immune surveillance of the lung by migrating tissue monocytes

Monocytes are phagocytic effector cells in the blood and precursors of resident and inflammatory tissue macrophages. The aim of the current study was to analyse and compare their contribution to innate immune surveillance of the lung in the steady state with macrophage and dendritic cells (DC). ECFP and EGFP transgenic reporters based upon Csf1r and Cx3cr1 distinguish monocytes from resident mononuclear phagocytes. We used these transgenes to study the migratory properties of monocytes and macrophages by functional imaging on explanted lungs. Migratory monocytes were found to be either patrolling within large vessels of the lung or locating at the interface between lung capillaries and alveoli. This spatial organisation gives to monocytes the property to capture fluorescent particles derived from both vascular and airway routes. We conclude that monocytes participate in steady-state surveillance of the lung, in a way that is complementary to resident macrophages and DC, without differentiating into macrophages.

DOI:http://dx.doi.org/10.7554/eLife.07847.001

White blood cells form part of the immune system, which protects the body against infectious diseases and other harmful agents. Some of these cells, including ‘mononuclear phagocytes’, can reside within different tissues of the body, such as the lungs. Other less specialized cells, called monocytes, circulate in the bloodstream. It had long been thought that once these monocytes had taken up residence in a tissue, they could only develop into tissue-resident phagocytes. Several researchers, however, recently reported that monocytes can also reside within tissues without becoming more specialized. Nevertheless, it remained unclear what these cells did when they were in these tissues.

Rodero, Poupel, Loyher et al. investigated the activities of tissue-resident monocytes found in the lungs of mice. First, mice were genetically engineered to produce fluorescent markers that meant that their monocytes could be easily distinguished from the mononuclear phagocytes in their lungs when viewed under a microscope. Rodero, Poupel, Loyher et al. then showed that the monocytes and the other mononuclear phagocytes localized to different regions of the lung. Further experiments showed that these two groups of cells also moved around the lungs in different ways. The tissue-resident monocytes surveyed both the blood vessels and airways, while the other tissue-resident mononuclear phagocytes only surveyed the airways.

These findings show that lung-resident monocytes perform a different role to those found in the bloodstream. The findings also open the way to improving our understanding of what tissue-resident monocytes do in other organs, and in healthy or diseased animals.

DOI:http://dx.doi.org/10.7554/eLife.07847.002

Transcriptomic analysis of mononuclear phagocyte differentiation and activation

Monocytes and macrophages differentiate from progenitor cells under the influence of colony-stimulating factors. Genome-scale data have enabled the identification of the sets of genes that are associated with specific functions and the mechanisms by which thousands of genes are regulated in response to pathogen challenge. In large datasets, it is possible to identify large sets of genes that are coregulated with the transcription factors that regulate them. They include macrophage-specific genes, interferon-responsive genes, early inflammatory genes, and those associated with endocytosis. Such analyses can also extract macrophage-associated signatures from large cancer tissue datasets. However, cluster analysis provides no support for a signature that distinguishes macrophages from antigen-presenting dendritic cells, nor the classification of macrophage activation states as classical versus alternative, or M1 versus M2. Although there has been a focus on a small subset of lineage-enriched transcription factors, such as PU.1, more than half of the transcription factors in the genome can be expressed in macrophage lineage cells under some state of activation, and they interact in a complex network. The network architecture is conserved across species, but many of the target genes evolve rapidly and differ between mouse and human. The data and publication deluge related to macrophage biology require the development of new analytical tools and ways of presenting information in an accessible form.

A transcriptional perspective on human macrophage biology

Macrophages are a major cell type in tissue homeostasis and contribute to both pathology and resolution in all acute and chronic inflammatory diseases ranging from infections, cancer, obesity, atherosclerosis, autoimmune disorders to neurodegenerative diseases such as Alzheimer's disease. The cellular and functional diversity of macrophages depends upon tightly regulated transcription. The innate immune system is under profound evolutionary selection. There is increasing recognition that human macrophage biology differs very significantly from that of commonly studied animal models, which therefore can have a limited predictive value. Here we report on the newest findings on transcriptional control of macrophage activation, and how we envision integrating studies on transcriptional and epigenetic regulation, and more classical approaches in murine models. Moreover, we provide new insights into how we can learn about transcriptional regulation in the human system from larger efforts such as the FANTOM (Functional Annotation of the Mammalian Genome) consortium.

Dendritic cells and macrophages in the kidney: a spectrum of good and evil

Renal dendritic cells (DCs) and macrophages represent a constitutive, extensive and contiguous network of innate immune cells that provide sentinel and immune-intelligence activity; they induce and regulate inflammatory responses to freely filtered antigenic material and protect the kidney from infection. Tissue-resident or infiltrating DCs and macrophages are key factors in the initiation and propagation of renal disease, as well as essential contributors to subsequent tissue regeneration, regardless of the aetiological and pathogenetic mechanisms. The identification, and functional and phenotypic distinction of these cell types is complex and incompletely understood, and the same is true of their interplay and relationships with effector and regulatory cells of the adaptive immune system. In this Review, we discuss the common and distinct characteristics of DCs and macrophages, as well as key advances that have identified the renal-specific functions of these important phagocytic, antigen-presenting cells, and their roles in potentiating or mitigating intrinsic kidney disease. We also identify remaining issues that are of priority for further investigation, and highlight the prospects for translational and therapeutic application of the knowledge acquired.

From Monocytes to M1/M2 Macrophages: Phenotypical vs. Functional Differentiation

Studies on monocyte and macrophage biology and differentiation have revealed the pleiotropic activities of these cells. Macrophages are tissue sentinels that maintain tissue integrity by eliminating/repairing damaged cells and matrices. In this M2-like mode, they can also promote tumor growth. Conversely, M1-like macrophages are key effector cells for the elimination of pathogens, virally infected, and cancer cells. Macrophage differentiation from monocytes occurs in the tissue in concomitance with the acquisition of a functional phenotype that depends on microenvironmental signals, thereby accounting for the many and apparently opposed macrophage functions. Many questions arise. When monocytes differentiate into macrophages in a tissue (concomitantly adopting a specific functional program, M1 or M2), do they all die during the inflammatory reaction, or do some of them survive? Do those that survive become quiescent tissue macrophages, able to react as naïve cells to a new challenge? Or, do monocyte-derived tissue macrophages conserve a “memory” of their past inflammatory activation? This review will address some of these important questions under the general framework of the role of monocytes and macrophages in the initiation, development, resolution, and chronicization of inflammation.

Homeostasis in the mononuclear phagocyte system

The mononuclear phagocyte system (MPS) is a family of functionally related cells including bone marrow precursors, blood monocytes, and tissue macrophages. We review the evidence that macrophages and dendritic cells (DCs) are separate lineages and functional entities, and examine whether the traditional view that monocytes are the immediate precursors of tissue macrophages needs to be refined based upon evidence that macrophages can extensively self-renew and can be seeded from yolk sac/foetal liver progenitors with little input from monocytes thereafter. We review the role of the growth factor colony-stimulating factor (CSF)1, and present a model consistent with the concept of the MPS in which local proliferation and monocyte recruitment are connected to ensure macrophages occupy their well-defined niche in most tissues.

Transcriptional switching in macrophages associated with the peritoneal foreign body response

We previously demonstrated that myeloid cells are the source of fibrotic tissue induced by foreign material implanted in the peritoneal cavity. This study utilised the MacGreen mouse, in which the Csf1r promoter directs myeloid-specific enhanced green fluorescent protein (EGFP) expression, to determine the temporal gene expression profile of myeloid subpopulations recruited to the peritoneal cavity to encapsulate implanted foreign material (cubes of boiled egg white). Cells with high EGFP expression (EGFP(hi)) were purified from exudate and encapsulating tissue at different times during the foreign body response, gene expression profiles determined using cDNA microarrays, and data clustered using the network analysis tool, Biolayout Express(3D). EGFP(hi) cells from all time points expressed high levels of Csf1r, Emr1 (encoding F4/80), Cd14 and Itgam (encoding Mac-1) providing internal validation of their myeloid nature. Exudate macrophages (days 4-7) expressed a large cluster of cell cycle genes; these were switched off in capsule cells. Early in capsule formation, Csf1r-EGFP(hi) cells expressed genes associated with tissue turnover, but later expressed both pro- and anti-inflammatory genes alongside a subset of mesenchyme-associated genes, a pattern of gene expression that adds weight to the concept of a continuum of macrophage phenotypes rather than distinct M1/M2 subsets. Moreover, rather than transdifferentiating to myofibroblasts, macrophages contributing to later stages of the peritoneal foreign body response warrant their own classification as 'fibroblastoid' macrophages.

An expression atlas of human primary cells: inference of gene function from coexpression networks

BACKGROUND

The specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed. Here we have combined a large number of publically available microarray datasets derived from human primary cells and analysed large correlation graphs of these data.

RESULTS

Using the network analysis tool BioLayout Express3D we identify robust co-associations of genes expressed in a wide variety of cell lineages. We discuss the biological significance of a number of these associations, in particular the coexpression of key transcription factors with the genes that they are likely to control.

CONCLUSIONS

We consider the regulation of genes in human primary cells and specifically in the human mononuclear phagocyte system. Of particular note is the fact that these data do not support the identity of putative markers of antigen-presenting dendritic cells, nor classification of M1 and M2 activation states, a current subject of debate within immunological field. We have provided this data resource on the BioGPS web site (http://biogps.org/dataset/2429/primary-cell-atlas/) and on macrophages.com (http://www.macrophages.com/hu-cell-atlas).

Macrophage biology in development, homeostasis and disease

Macrophages, the most plastic cells of the haematopoietic system, are found in all tissues and show great functional diversity. They have roles in development, homeostasis, tissue repair and immunity. Although tissue macrophages are anatomically distinct from one another, and have different transcriptional profiles and functional capabilities, they are all required for the maintenance of homeostasis. However, these reparative and homeostatic functions can be subverted by chronic insults, resulting in a causal association of macrophages with disease states. In this Review, we discuss how macrophages regulate normal physiology and development, and provide several examples of their pathophysiological roles in disease. We define the 'hallmarks' of macrophages according to the states that they adopt during the performance of their various roles, taking into account new insights into the diversity of their lineages, identities and regulation. It is essential to understand this diversity because macrophages have emerged as important therapeutic targets in many human diseases.