Highlights d 51 cell subsets in colon mucosa of 18 ulcerative colitis and 12 healthy individuals d M-like cells, inflammatory monocytes and fibroblasts, and CD8 + IL-17 + T cells expand in disease d Oncostatin M circuit in inflammatory monocytes and fibroblasts may affect drug response d Co-expression of genes within cells allows inference of causal genes across risk loci

The current paradigm in macrophage biology is that some tissues mainly contain macrophages from embryonic origin, such as microglia in the brain, whereas other tissues contain postnatal-derived macrophages, such as the gut. However, in the lung and in other organs, such as the skin, there are both embryonic and postnatal-derived macrophages. In this study, we demonstrate in the steady-state lung that the mononuclear phagocyte system is comprised of three newly identified interstitial macrophages (IMs), alveolar macrophages, dendritic cells, and few extravascular monocytes. We focused on similarities and differences between the three IM subtypes, specifically, their phenotype, location, transcriptional signature, phagocytic capacity, turnover, and lack of survival dependency on fractalkine receptor, CXCR1. Pulmonary IMs were located in the bronchial interstitium but not the alveolar interstitium. At the transcriptional level, all three IMs displayed a macrophage signature and phenotype. All IMs expressed MER proto-oncogene, tyrosine kinase, CD64, CD11b, and CXCR1, and were further distinguished by differences in cell surface protein expression of CD206, Lyve-1, CD11c, CCR2, and MHC class II, along with the absence of Ly6C, Ly6G, and Siglec F. Most intriguingly, in addition to the lung, similar phenotypic populations of IMs were observed in other nonlymphoid organs, perhaps highlighting conserved functions throughout the body. These findings promote future research to track four distinct pulmonary macrophages and decipher the division of labor that exists between them.

CD103-expressing dendritic cells in the lungs preferentially take up and cross-present antigen from apoptotic cells.

Rationale: The pulmonary mononuclear phagocyte system is a critical host defense mechanism composed of macrophages, monocytes, monocyte-derived cells, and dendritic cells. However, our current characterization of these cells is limited because it is derived largely from animal studies and analysis of human mononuclear phagocytes from blood and small tissue resections around tumors.Objectives: Phenotypic and morphologic characterization of mononuclear phagocytes that potentially access inhaled antigens in human lungs.Methods: We acquired and analyzed pulmonary mononuclear phagocytes from fully intact nondiseased human lungs (including the major blood vessels and draining lymph nodes) obtained en bloc from 72 individual donors. Differential labeling of hematopoietic cells via intrabronchial and intravenous administration of antibodies within the same lobe was used to identify extravascular tissue-resident mononuclear phagocytes and exclude cells within the vascular lumen. Multiparameter flow cytometry was used to identify mononuclear phagocyte populations among cells labeled by each route of antibody delivery. Measurements and Main Results:We performed a phenotypic analysis of pulmonary mononuclear phagocytes isolated from whole nondiseased human lungs and lung-draining lymph nodes. Five pulmonary mononuclear phagocytes were observed, including macrophages, monocyte-derived cells, and dendritic cells that were phenotypically distinct from cell populations found in blood.Conclusions: Different mononuclear phagocytes, particularly dendritic cells, were labeled by intravascular and intrabronchial antibody delivery, countering the notion that tissue and blood mononuclear phagocytes are equivalent systems. Phenotypic descriptions of the mononuclear phagocytes in nondiseased lungs provide a precedent for comparative studies in diseased lungs and potential targets for therapeutics. Correspondence and requests for reprints should be addressed to Claudia V. Jakubzick, Ph.D., Department of Pediatrics and Immunology, National Jewish Health, 1400 Jackson Street, Denver, CO 80206. E-mail: jakubzickc@njhealth.org This article has an online supplement, which is accessible from this issue's table of contents at www.atsjournals.org The human respiratory tract has a branching structure that terminates in millions of alveoli, whose luminal surface covers an approximate area of 50 to 100 m 2 . In comparison to other barrier surfaces, such as the skin (2 m 2 ) and the gut (10 m 2 ), this surface area is massive, and therefore, comprises the body's largest interface with the ambient environment. Because of normal respiratory function, the average human exchanges 7,000 to 9,000 L of gas each day and inhales billions of particles, allergens, and microbes. Accordingly, the human lung constitutes a major site for the innate and adaptive immune responses. In this context, cells in the mononuclear phagocyte system (MPS), which consists of macrophages, monocytes, monocytederived cells, and dendritic cells (DCs), play critical roles. T...

• Of the 30 000 genes, there are ;0.1% genes whose expression is linked to the origin of the cell rather than the environment.• Marco was most conserved by embryonic origin and not altered by the environment, whereas C1qb and Plbd1 were most conserved by adult origin.Alveolar macrophages (AMs) reside on the luminal surfaces of the airways and alveoli where they maintain host defense and promote alveolar homeostasis by ingesting inhaled particulates and regulating inflammatory responses. Recent studies have demonstrated that AMs populate the lungs during embryogenesis and self-renew throughout life with minimal replacement by circulating monocytes, except under extreme conditions of depletion or radiation injury. Here we demonstrate that on a global scale, environment appears to dictate AM development and function. Indeed, transcriptome analysis of embryonic host-derived and postnatal donor-derived AMs coexisting within the same mouse demonstrated >98% correlation and overall functional analyses were similar. However, we also identified several genes whose expression was dictated by origin rather than environment. The most differentially expressed gene not altered by environment was Marco, a gene recently demonstrated to have enhancer activity in embryonic-derived but not postnatal-derived tissue macrophages. Overall, we show that under homeostatic conditions, the environment largely dictates the programming and function of AMs, whereas the expression of a small number of genes remains linked to the origin of the cell. (Blood. 2015;126(11):1357-1366 Introduction Alveolar macrophages (AMs) reside on the luminal surfaces of the airways and airspaces where they serve critical roles in host defense and alveolar homeostasis, ingesting particulates and microbes that are constantly encountered in the lungs. Importantly, under most circumstances the phagocytosis of inhaled foreign agents is silent, such that inflammatory responses are activated only under circumstances when host defenses become overwhelmed.1 Indeed, compared with macrophages from other sites, AMs are relatively ineffective at initiating immune responses.2,3 Furthermore, compared with other tissue macrophages, they display a unique repertoire of cell surface molecules and have a distinct transcriptome profile. [4][5][6] AMs are now known to derive primarily from fetal liver monocytes and self-renew throughout life with minimal replenishment from circulating monocytes. [7][8][9][10][11][12][13][14][15] This self-renewal is not only maintained under steady-state conditions, but also during acute and chronic inflammation.16 These concepts were illustrated in lung-protected bone marrow (BM) chimera studies in which lead shields were used to protect AMs during radiation. Eight weeks after BM transplantation, the lungs of these chimeras contained AMs of host origin, whereas circulating monocytes were donor-derived. 16 In these chimeric mice, we showed that during inflammation (lipopolysaccharide or influenza A infection), BM donor-derived monocytes were rapidly...

Dendritic cells (DCs) are required for the induction of cytotoxic T cells (CTL). In most tissues, including the lung, the resident DCs fall into two types, respectively expressing the integrin markers, CD103 and CD11b. The current supposition is that DC function is predetermined by lineage, designating the CD103+ DC as the major cross-presenting DC able to induce CTL. Here we show that Poly I:C (TLR3 agonist) or R848 (TLR7 agonist) do not activate all endogenous DCs. CD11b+ DCs can orchestrate a CTL response in vivo in the presence of TLR7 agonist but not TLR3 agonist, whereas CD103+ DCsrequire ligation of TLR3 for this purpose. This selectivity does not extend to antigen cross-presentation for T cell proliferation but is required for induction of cytotoxicity. Thus, we demonstrate that the ability of DCsto induce functional CTLs isspecific to the nature of the pathogen associated molecular pattern (PAMP) encountered by endogenous DC.

Polymorphisms in C1orf106 are associated with increased risk of inflammatory bowel disease (IBD). However, the function of C1orf106 and the consequences of disease-associated polymorphisms are unknown. Here we demonstrate that C1orf106 regulates adherens junction stability by regulating the degradation of cytohesin-1, a guanine nucleotide exchange factor that controls activation of ARF6. By limiting cytohesin-1–dependent ARF6 activation, C1orf106 stabilizes adherens junctions. Consistent with this model, C1orf106−/− mice exhibit defects in the intestinal epithelial cell barrier, a phenotype observed in IBD patients that confers increased susceptibility to intestinal pathogens. Furthermore, the IBD risk variant increases C1orf106 ubiquitination and turnover with consequent functional impairments. These findings delineate a mechanism by which a genetic polymorphism fine-tunes intestinal epithelial barrier integrity and elucidate a fundamental mechanism of cellular junctional control.

Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10−7, odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain.