Roles of Macrophages in the Development and Treatment of Gut Inflammation

Abraham, 2009, Inflammatory bowel disease., N. Engl. J. Med., 361, 2066, 10.1056/NEJMra0804647

Ahluwalia, 2017, Mucosal immune system of the gastrointestinal tract: maintaining balance between the good and the bad., Scand. J. Gastroenterol., 52, 1185, 10.1080/00365521.2017.1349173

Ahluwalia, 2018, Immunopathogenesis of inflammatory bowel disease and mechanisms of biological therapies., Scand. J. Gastroenterol., 53, 379, 10.1080/00365521.2018.1447597

Ananthakrishnan, 2018, Environmental triggers in IBD: a review of progress and evidence., Nat. Rev. Gastroenterol. Hepatol., 15, 39, 10.1038/nrgastro.2017.136

Bain, 2011, Intestinal macrophages - specialised adaptation to a unique environment., Eur. J. Immunol., 41, 2494, 10.1002/eji.201141714

Bain, 2014, Macrophages in intestinal homeostasis and inflammation., Immunol. Rev., 260, 102, 10.1111/imr.12192

Bain, 2018, Origin, differentiation, and function of intestinal macrophages., Front. Immunol., 9, 10.3389/fimmu.2018.02733

Bain, 2013, Resident and pro-inflammatory macrophages in the colon represent alternative context-dependent fates of the same Ly6Chi monocyte precursors., Mucosal. Immunol., 6, 498, 10.1038/mi.2012.89

Barman, 2016, Identification of a human intestinal myeloid cell subset that regulates gut homeostasis., Int. Immunol., 28, 533, 10.1093/intimm/dxw034

Baumgart, 2007, Inflammatory bowel disease: cause and immunobiology., Lancet, 369, 1627, 10.1016/s0140-6736(07)60750-8

Becker, 2016, A critical role for monocytes/macrophages during intestinal inflammation-associated Lymphangiogenesis., Inflamm. Bowel. Dis., 22, 1326, 10.1097/mib.0000000000000731

Belkaid, 2014, Role of the microbiota in immunity and inflammation., Cell, 157, 121, 10.1016/j.cell.2014.03.011

Belkaid, 2017, Homeostatic immunity and the microbiota., Immunity, 46, 562, 10.1016/j.immuni.2017.04.008

Bernardo, 2018, Human intestinal pro-inflammatory CD11c(high)CCR2(+)CX3CR1(+) macrophages, but not their tolerogenic CD11c(-)CCR2(-)CX3CR1(-) counterparts, are expanded in inflammatory bowel disease., Mucosal. Immunol., 11, 1114, 10.1038/s41385-018-0030-7

Best, 2013, Transcriptional insights into the CD8(+) T cell response to infection and memory T cell formation., Nat. Immunol., 14, 404, 10.1038/ni.2536

Bettenworth, 2017, Pathogenesis of intestinal fibrosis in inflammatory bowel disease and perspectives for therapeutic implication., Dig. Dis., 35, 25, 10.1159/000449079

Bezman, 2012, Molecular definition of the identity and activation of natural killer cells., Nat. Immunol., 13, 1000, 10.1038/ni.2395

Biagioli, 2017, The bile acid receptor GPBAR1 regulates the M1/M2 phenotype of intestinal macrophages and activation of GPBAR1 rescues mice from murine colitis., J. Immunol., 199, 718, 10.4049/jimmunol.1700183

Bian, 2020, Deciphering human macrophage development at single-cell resolution., Nature, 582, 571, 10.1038/s41586-020-2316-7

Bouma, 2003, The immunological and genetic basis of inflammatory bowel disease., Nat. Rev. Immunol., 3, 521, 10.1038/nri1132

Brynjolfsson, 2016, An antibody against triggering receptor expressed on myeloid cells 1 (TREM-1) dampens proinflammatory cytokine secretion by lamina propria cells from patients with IBD., Inflamm. Bowel. Dis., 22, 1803, 10.1097/mib.0000000000000822

Buettner, 2016, Development and function of secondary and tertiary lymphoid organs in the small intestine and the colon., Front. Immunol., 7, 10.3389/fimmu.2016.00342

Bujko, 2018, Transcriptional and functional profiling defines human small intestinal macrophage subsets., J. Exp. Med., 215, 441, 10.1084/jem.20170057

Caër, 2020, Human intestinal mononuclear phagocytes in health and inflammatory bowel disease., Front. Immunol., 11, 10.3389/fimmu.2020.00410

Carlin, 2013, Nr4a1-dependent Ly6C(low) monocytes monitor endothelial cells and orchestrate their disposal., Cell, 153, 362, 10.1016/j.cell.2013.03.010

Carlsen, 2006, The proportion of CD40+ mucosal macrophages is increased in inflammatory bowel disease whereas CD40 ligand (CD154)+ T cells are relatively decreased, suggesting differential modulation of these costimulatory molecules in human gut lamina propria., Inflamm. Bowel. Dis., 12, 1013, 10.1097/01.mib.0000234135.43336.72

Castro-Dopico, 2019, IgG and Fcγ receptors in intestinal immunity and inflammation., Front. Immunol., 10, 10.3389/fimmu.2019.00805

Cerovic, 2014, Intestinal macrophages and dendritic cells: what’s the difference?, Trends Immunol., 35, 270, 10.1016/j.it.2014.04.003

Chapuy, 2020, IL-12 and Mucosal CD14+ monocyte-like cells induce IL-8 in colonic memory CD4+ T cells of patients with ulcerative colitis but not crohn’s disease., J. Crohns. Colitis, 14, 79, 10.1093/ecco-jcc/jjz115

Chapuy, 2019, Two distinct colonic CD14(+) subsets characterized by single-cell RNA profiling in Crohn’s disease., Mucosal. Immunol., 12, 703, 10.1038/s41385-018-0126-0

Chelakkot, 2018, Mechanisms regulating intestinal barrier integrity and its pathological implications., Exp. Mol. Med., 50, 10.1038/s12276-018-0126-x

Chinthrajah, 2016, Molecular and cellular mechanisms of food allergy and food tolerance., J. Allergy Clin. Immunol., 137, 984, 10.1016/j.jaci.2016.02.004

Clevers, 2013, Paneth cells: maestros of the small intestinal crypts., Annu. Rev. Physiol., 75, 289, 10.1146/annurev-physiol-030212-183744

Colgan, 2016, Hypoxia and mucosal inflammation., Annu. Rev. Pathol., 11, 77, 10.1146/annurev-pathol-012615-044231

Cosín-Roger, 2016, The activation of Wnt signaling by a STAT6-dependent macrophage phenotype promotes mucosal repair in murine IBD., Mucosal. Immunol., 9, 986, 10.1038/mi.2015.123

Cummings, 2016, Different tissue phagocytes sample apoptotic cells to direct distinct homeostasis programs., Nature, 539, 565, 10.1038/nature20138

Da Silva, 2017, The peyer’s patch mononuclear phagocyte system at steady state and during infection., Front. Immunol., 8, 10.3389/fimmu.2017.01254

Danese, 2015, Biologic agents for IBD: practical insights., Nat. Rev. Gastroenterol. Hepatol., 12, 537, 10.1038/nrgastro.2015.135

de Souza, 2016, Immunopathogenesis of IBD: current state of the art., Nat. Rev. Gastroenterol. Hepatol., 13, 13, 10.1038/nrgastro.2015.186

Denning, 2011, Functional specializations of intestinal dendritic cell and macrophage subsets that control Th17 and regulatory T cell responses are dependent on the T cell/APC ratio, source of mouse strain, and regional localization., J. Immunol., 187, 733, 10.4049/jimmunol.1002701

Ding, , Lactobacillus brevis Alleviates DSS-induced colitis by reprograming intestinal microbiota and influencing serum metabolome in murine model., Front. Physiol., 10, 10.3389/fphys.2019.01152

Ding, , Modulatory mechanisms of the NLRP3 inflammasomes in diabetes., Biomolecules, 9, 10.3390/biom9120850

Dionne, 2017, The influence of vitamin D on M1 and M2 macrophages in patients with Crohn’s disease., Innate. Immun., 23, 557, 10.1177/1753425917721965

Eissa, 2017, Chromofungin ameliorates the progression of colitis by regulating alternatively activated macrophages., Front. Immunol., 8, 10.3389/fimmu.2017.01131

Epelman, 2014, Embryonic and adult-derived resident cardiac macrophages are maintained through distinct mechanisms at steady state and during inflammation., Immunity, 40, 91, 10.1016/j.immuni.2013.11.019

Esterházy, 2016, Classical dendritic cells are required for dietary antigen-mediated induction of peripheral T(reg) cells and tolerance., Nat. Immunol., 17, 545, 10.1038/ni.3408

Fassarella, 2020, Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health., Gut, 70, 595, 10.1136/gutjnl-2020-321747

Festuccia, 2014, Myeloid-specific Rictor deletion induces M1 macrophage polarization and potentiates in vivo pro-inflammatory response to lipopolysaccharide., PLoS One, 9, 10.1371/journal.pone.0095432

Frank, 2007, Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases., Proc. Natl. Acad. Sci. U.S.A., 104, 13780, 10.1073/pnas.0706625104

Franzosa, 2019, Gut microbiome structure and metabolic activity in inflammatory bowel disease., Nat. Microbiol., 4, 293, 10.1038/s41564-018-0306-4

Friedrich, 2019, Cytokine networks in the pathophysiology of inflammatory bowel disease., Immunity, 50, 992, 10.1016/j.immuni.2019.03.017

Gabanyi, 2016, Neuro-immune interactions drive tissue programming in intestinal macrophages., Cell, 164, 378, 10.1016/j.cell.2015.12.023

Garcia-Carbonell, 2018, Elevated A20 promotes TNF-induced and RIPK1-dependent intestinal epithelial cell death., Proc. Natl. Acad. Sci. U.S.A., 115, E9192, 10.1073/pnas.1810584115

Gaudino, 2019, Cross-talk between antigen presenting cells and t cells impacts intestinal homeostasis, bacterial infections, and tumorigenesis., Front. Immunol., 10, 10.3389/fimmu.2019.00360

Geissmann, 2003, Blood monocytes consist of two principal subsets with distinct migratory properties., Immunity, 19, 71, 10.1016/s1074-7613(03)00174-2

Geremia, 2017, Innate lymphoid cells in intestinal inflammation., Front. Immunol., 8, 10.3389/fimmu.2017.01296

Geremia, 2014, Innate and adaptive immunity in inflammatory bowel disease., Autoimmun. Rev., 13, 3, 10.1016/j.autrev.2013.06.004

Gevers, 2014, The treatment-naive microbiome in new-onset Crohn’s disease., Cell Host. Microbe., 15, 382, 10.1016/j.chom.2014.02.005

Grainger, 2017, Macrophages in gastrointestinal homeostasis and inflammation., Pflugers Arch., 469, 527, 10.1007/s00424-017-1958-2

Grainger, 2013, Inflammatory monocytes regulate pathologic responses to commensals during acute gastrointestinal infection., Nat. Med., 19, 713, 10.1038/nm.3189

Gren, 2016, Role of monocytes and intestinal macrophages in crohn’s disease and ulcerative colitis., Inflamm. Bowel. Dis., 22, 1992, 10.1097/mib.0000000000000824

Guan, 2019, Macleaya cordata extract alleviated oxidative stress and altered innate immune response in mice challenged with enterotoxigenic Escherichia coli., Sci. China Life Sci., 62, 1019, 10.1007/s11427-018-9494-6

Guo, 2018, Human intestinal epithelial cells release antiviral factors that inhibit HIV infection of macrophages., Front. Immunol., 9, 10.3389/fimmu.2018.00247

Hadis, 2011, Intestinal tolerance requires gut homing and expansion of FoxP3+ regulatory T cells in the lamina propria., Immunity, 34, 237, 10.1016/j.immuni.2011.01.016

Hashimoto, 2013, Tissue-resident macrophages self-maintain locally throughout adult life with minimal contribution from circulating monocytes., Immunity, 38, 792, 10.1016/j.immuni.2013.04.004

Hewison, 2012, An update on vitamin D and human immunity., Clin. Endocrinol. (Oxf), 76, 315, 10.1111/j.1365-2265.2011.04261.x

Hidalgo-Garcia, 2018, Can a conversation between mesenchymal stromal cells and macrophages solve the crisis in the inflamed intestine?, Front. Pharmacol., 9, 10.3389/fphar.2018.00179

Hill, 2010, Intestinal bacteria and the regulation of immune cell homeostasis., Annu. Rev. Immunol., 28, 623, 10.1146/annurev-immunol-030409-101330

Hosomi, 2015, Role of endoplasmic reticulum stress and autophagy as interlinking pathways in the pathogenesis of inflammatory bowel disease., Curr. Opin. Gastroenterol., 31, 81, 10.1097/mog.0000000000000144

Huang, 2017, Gut REG3γ-associated lactobacillus induces anti-inflammatory macrophages to maintain adipose tissue homeostasis., Front. Immunol., 8, 10.3389/fimmu.2017.01063

Hundertmark, 2018, Adapted immune responses of myeloid-derived cells in fatty liver disease., Front. Immunol., 9, 10.3389/fimmu.2018.02418

Isidro, 2016, Colonic macrophage polarization in homeostasis, inflammation, and cancer., Am. J. Physiol. Gastrointest Liver Physiol., 311, G59, 10.1152/ajpgi.00123.2016

Italiani, 2014, From monocytes to M1/M2 macrophages: phenotypical vs. functional differentiation., Front. Immunol., 5, 10.3389/fimmu.2014.00514

Jain, 2019, Mechanobiology of macrophages: how physical factors coregulate macrophage plasticity and phagocytosis., Annu. Rev. Biomed. Eng., 21, 267, 10.1146/annurev-bioeng-062117-121224

Joeris, 2017, Diversity and functions of intestinal mononuclear phagocytes., Mucosal. Immunol., 10, 845, 10.1038/mi.2017.22

Johansson, 2016, Immunological aspects of intestinal mucus and mucins., Nat. Rev. Immunol., 16, 639, 10.1038/nri.2016.88

Johansson, 2013, The gastrointestinal mucus system in health and disease., Nat. Rev. Gastroenterol. Hepatol., 10, 352, 10.1038/nrgastro.2013.35

Jones, 2018, Dynamics of colon monocyte and macrophage activation during colitis., Front. Immunol., 9, 10.3389/fimmu.2018.02764

Kamada, 2009, Human CD14+ macrophages in intestinal lamina propria exhibit potent antigen-presenting ability., J. Immunol., 183, 1724, 10.4049/jimmunol.0804369

Kamada, 2008, Unique CD14 intestinal macrophages contribute to the pathogenesis of Crohn disease via IL-23/IFN-gamma axis., J. Clin. Invest., 118, 2269, 10.1172/jci34610

Kaneda, 2016, PI3Kγ is a molecular switch that controls immune suppression., Nature, 539, 437, 10.1038/nature19834

Karin, 2016, Reparative inflammation takes charge of tissue regeneration., Nature, 529, 307, 10.1038/nature17039

Khor, 2011, Genetics and pathogenesis of inflammatory bowel disease., Nature, 474, 307, 10.1038/nature10209

Kim, 2018, Critical role for the microbiota in CX(3)CR1(+) intestinal mononuclear phagocyte regulation of intestinal t cell responses., Immunity, 49, 151, 10.1016/j.immuni.2018.05.009

Kostic, 2014, The microbiome in inflammatory bowel disease: current status and the future ahead., Gastroenterology, 146, 1489, 10.1053/j.gastro.2014.02.009

Lee, 2017, Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn’s disease., Nat. Genet., 49, 262, 10.1038/ng.3755

Lee, 1985, Quantitative analysis of total macrophage content in adult mouse tissues. Immunochemical studies with monoclonal antibody F4/80., J. Exp. Med., 161, 475, 10.1084/jem.161.3.475

Leonardi, 2018, CX3CR1(+) mononuclear phagocytes control immunity to intestinal fungi., Science, 359, 232, 10.1126/science.aao1503

Lepage, 2011, Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis., Gastroenterology, 141, 227, 10.1053/j.gastro.2011.04.011

Ley, 2016, How mouse macrophages sense what is going on., Front. Immunol., 7, 10.3389/fimmu.2016.00204

Li, 2018, Critical role of alternative M2 Skewing in miR-155 deletion-mediated protection of colitis., Front. Immunol., 9, 10.3389/fimmu.2018.00904

Li, 2010, Oxidized low-density lipoprotein-induced proinflammatory cytokine response in macrophages are suppressed by CD4CD25(+)Foxp3(+) regulatory T cells through downregulating toll like receptor 2-mediated activation of NF-kappaB., Cell Physiol. Biochem., 25, 649, 10.1159/000315084

Liang, 2018, Risk factors for postoperative infection after gastrointestinal surgery among adult patients with inflammatory bowel disease: findings from a large observational US cohort study., JGH Open, 2, 182, 10.1002/jgh3.12072

Linkermann, 2014, Necroptosis., N. Engl. J. Med., 370, 455, 10.1056/NEJMra1310050

Lissner, 2015, Monocyte and M1 macrophage-induced barrier defect contributes to chronic intestinal inflammation in IBD., Inflamm. Bowel. Dis., 21, 1297, 10.1097/mib.0000000000000384

Litinskiy, 2002, DCs induce CD40-independent immunoglobulin class switching through BLyS and APRIL., Nat. Immunol., 3, 822, 10.1038/ni829

Liu, 2016, Genetics and pathogenesis of inflammatory bowel disease., Annu. Rev. Pathol., 11, 127, 10.1146/annurev-pathol-012615-044152

Lloyd-Price, 2019, Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases., Nature, 569, 655, 10.1038/s41586-019-1237-9

Loschko, 2016, Absence of MHC class II on cDCs results in microbial-dependent intestinal inflammation., J. Exp. Med., 213, 517, 10.1084/jem.20160062

Lu, 2018, Toll-like receptors and inflammatory bowel disease., Front. Immunol., 9, 10.3389/fimmu.2018.00072

Luu, 2017, Functional heterogeneity of gut-resident regulatory T cells., Clin. Transl. Immunol., 6, 10.1038/cti.2017.39

Ma, , Dietary polyphenols in lipid metabolism: a role of gut microbiome., Anim. Nutr., 6, 404, 10.1016/j.aninu.2020.08.002

Ma, , Lactobacillus pentosus increases the abundance of akkermansia and affects the serum metabolome to alleviate DSS-induced colitis in a murine model., Front. Cell Dev. Biol., 8, 10.3389/fcell.2020.591408

Macpherson, 2018, IgA function in relation to the intestinal microbiota., Annu. Rev. Immunol., 36, 359, 10.1146/annurev-immunol-042617-053238

Magnusson, 2016, Macrophage and dendritic cell subsets in IBD: ALDH+ cells are reduced in colon tissue of patients with ulcerative colitis regardless of inflammation., Mucosal. Immunol., 9, 171, 10.1038/mi.2015.48

Maloy, 2011, Intestinal homeostasis and its breakdown in inflammatory bowel disease., Nature, 474, 298, 10.1038/nature10208

Mantovani, 2004, The chemokine system in diverse forms of macrophage activation and polarization., Trends Immunol., 25, 677, 10.1016/j.it.2004.09.015

Martens, 2018, Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier., Nat. Rev. Microbiol., 16, 457, 10.1038/s41579-018-0036-x

Martin, 2019, Single-cell analysis of crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy., Cell, 178, 1493, 10.1016/j.cell.2019.08.008

Martinez, 2014, The M1 and M2 paradigm of macrophage activation: time for reassessment., F1000Prime Rep., 6, 10.12703/p6-13

Mills, 2000, M-1/M-2 macrophages and the Th1/Th2 paradigm., J. Immunol., 164, 6166, 10.4049/jimmunol.164.12.6166

Mosser, 2008, Exploring the full spectrum of macrophage activation., Nat. Rev. Immunol., 8, 958, 10.1038/nri2448

Mowat, 2018, To respond or not to respond - a personal perspective of intestinal tolerance., Nat. Rev. Immunol., 18, 405, 10.1038/s41577-018-0002-x

Mowat, 2011, Mucosal macrophages in intestinal homeostasis and inflammation., J. Innate. Immun., 3, 550, 10.1159/000329099

Muller, 2014, Crosstalk between muscularis macrophages and enteric neurons regulates gastrointestinal motility., Cell, 158, 300, 10.1016/j.cell.2014.04.050

Murray, 2017, Macrophage Polarization., Annu. Rev. Physiol., 79, 541, 10.1146/annurev-physiol-022516-034339

Murray, 2014, Macrophage activation and polarization: nomenclature and experimental guidelines., Immunity, 41, 14, 10.1016/j.immuni.2014.06.008

Murray, 2012, Restraint of inflammatory signaling by interdependent strata of negative regulatory pathways., Nat. Immunol., 13, 916, 10.1038/ni.2391

Nagashima, 1996, Lamina propria macrophages in the human gastrointestinal mucosa: their distribution, immunohistological phenotype, and function., J. Histochem. Cytochem., 44, 721, 10.1177/44.7.8675993

Ni, 2017, Gut microbiota and IBD: causation or correlation?, Nat. Rev. Gastroenterol. Hepatol., 14, 573, 10.1038/nrgastro.2017.88

Nutsch, 2016, Rapid and efficient generation of regulatory t cells to commensal antigens in the periphery., Cell Rep., 17, 206, 10.1016/j.celrep.2016.08.092

Odenwald, 2017, The intestinal epithelial barrier: a therapeutic target?, Nat. Rev. Gastroenterol. Hepatol., 14, 9, 10.1038/nrgastro.2016.169

Ogino, 2013, Increased Th17-inducing activity of CD14+ CD163 low myeloid cells in intestinal lamina propria of patients with Crohn’s disease., Gastroenterology, 145, 1380, 10.1053/j.gastro.2013.08.049

Okumura, 2017, Roles of intestinal epithelial cells in the maintenance of gut homeostasis., Exp. Mol. Med., 49, 10.1038/emm.2017.20

Ortega-Gómez, 2013, Resolution of inflammation: an integrated view., EMBO Mol. Med., 5, 661, 10.1002/emmm.201202382

Pabst, 2012, Oral tolerance to food protein., Mucosal. Immunol., 5, 232, 10.1038/mi.2012.4

Peterson, 2014, Intestinal epithelial cells: regulators of barrier function and immune homeostasis., Nat. Rev. Immunol., 14, 141, 10.1038/nri3608

Piacenza, 2019, Reactive species and pathogen antioxidant networks during phagocytosis., J. Exp. Med., 216, 501, 10.1084/jem.20181886

Platt, 2010, An independent subset of TLR expressing CCR2-dependent macrophages promotes colonic inflammation., J. Immunol., 184, 6843, 10.4049/jimmunol.0903987

Popov, 2008, Infection of myeloid dendritic cells with Listeria monocytogenes leads to the suppression of T cell function by multiple inhibitory mechanisms., J. Immunol., 181, 4976, 10.4049/jimmunol.181.7.4976

Pull, 2005, Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury., Proc. Natl. Acad. Sci. U.S.A., 102, 99, 10.1073/pnas.0405979102

Qin, 2014, Alterations of the human gut microbiome in liver cirrhosis., Nature, 513, 59, 10.1038/nature13568

Rabbi, 2017, Reactivation of intestinal inflammation is suppressed by catestatin in a murine model of colitis via M1 macrophages and not the gut microbiota., Front. Immunol., 8, 10.3389/fimmu.2017.00985

Ramachandran, 2013, Receptor interacting protein kinase 3 is a critical early mediator of acetaminophen-induced hepatocyte necrosis in mice., Hepatology, 58, 2099, 10.1002/hep.26547

Ramakrishnan, 2016, Role of intestinal HIF-2α in health and disease., Annu. Rev. Physiol., 78, 301, 10.1146/annurev-physiol-021115-105202

Ramesh, 2014, Pro-inflammatory human Th17 cells selectively express P-glycoprotein and are refractory to glucocorticoids., J. Exp. Med., 211, 89, 10.1084/jem.20130301

Rieder, 2009, Intestinal fibrosis in IBD–a dynamic, multifactorial process., Nat. Rev. Gastroenterol. Hepatol., 6, 228, 10.1038/nrgastro.2009.31

Rieder, 2017, Mechanisms, management, and treatment of fibrosis in patients with inflammatory bowel diseases., Gastroenterology, 152, 340, 10.1053/j.gastro.2016.09.047

Rivollier, 2012, Inflammation switches the differentiation program of Ly6Chi monocytes from antiinflammatory macrophages to inflammatory dendritic cells in the colon., J. Exp. Med., 209, 139, 10.1084/jem.20101387

Roychowdhury, 2013, Absence of receptor interacting protein kinase 3 prevents ethanol-induced liver injury., Hepatology, 57, 1773, 10.1002/hep.26200

Rugtveit, 1997, Differential distribution of B7.1 (CD80) and B7.2 (CD86) costimulatory molecules on mucosal macrophage subsets in human inflammatory bowel disease (IBD)., Clin. Exp. Immunol., 110, 104, 10.1046/j.1365-2249.1997.5071404.x

Salvador, 2018, CD16+ Macrophages mediate fibrosis in inflammatory bowel disease., J. Crohns. Colitis, 12, 589, 10.1093/ecco-jcc/jjx185

Samadder, 2019, Family History associates with increased risk of colorectal cancer in patients with inflammatory bowel diseases., Clin. Gastroenterol. Hepatol., 17, 1807, 10.1016/j.cgh.2018.09.038

Sanders, 2014, Increased production of retinoic acid by intestinal macrophages contributes to their inflammatory phenotype in patients with Crohn’s disease., Gastroenterology, 146, 1278, 10.1053/j.gastro.2014.01.057

Scharl, 2019, Malignancies in inflammatory bowel disease: frequency, incidence and risk factors-results from the swiss IBD cohort study., Am. J. Gastroenterol., 114, 116, 10.1038/s41395-018-0360-9

Scheibe, 2019, Inhibiting interleukin 36 receptor signaling reduces fibrosis in mice with chronic intestinal inflammation., Gastroenterology, 156, 1082, 10.1053/j.gastro.2018.11.029

Schenk, 2007, TREM-1–expressing intestinal macrophages crucially amplify chronic inflammation in experimental colitis and inflammatory bowel diseases., J. Clin. Invest., 117, 3097, 10.1172/jci30602

Schett, 2018, Resolution of chronic inflammatory disease: universal and tissue-specific concepts., Nat. Commun., 9, 10.1038/s41467-018-05800-6

Schierwagen, 2020, The role of macrophage-inducible C-Type lectin in different stages of chronic liver disease., Front. Immunol., 11, 10.3389/fimmu.2020.01352

Schippers, 2016, β7-Integrin exacerbates experimental DSS-induced colitis in mice by directing inflammatory monocytes into the colon., Mucosal. Immunol., 9, 527, 10.1038/mi.2015.82

Schridde, 2017, Tissue-specific differentiation of colonic macrophages requires TGFβ receptor-mediated signaling., Mucosal. Immunol., 10, 1387, 10.1038/mi.2016.142

Schulthess, 2012, Interleukin-15-dependent NKp46+ innate lymphoid cells control intestinal inflammation by recruiting inflammatory monocytes., Immunity, 37, 108, 10.1016/j.immuni.2012.05.013

Schulz, 2012, A lineage of myeloid cells independent of Myb and hematopoietic stem cells., Science, 336, 86, 10.1126/science.1219179

Schwerd, 2017, Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn’s disease., Gut, 66, 1060, 10.1136/gutjnl-2015-310382

Seo, 2015, Distinct commensals induce interleukin-1β via NLRP3 inflammasome in inflammatory monocytes to promote intestinal inflammation in response to injury., Immunity, 42, 744, 10.1016/j.immuni.2015.03.004

Sheng, 2015, Most tissue-resident macrophages except microglia are derived from fetal hematopoietic stem cells., Immunity, 43, 382, 10.1016/j.immuni.2015.07.016

Shkoda, 2007, Interleukin-10 blocked endoplasmic reticulum stress in intestinal epithelial cells: impact on chronic inflammation., Gastroenterology, 132, 190, 10.1053/j.gastro.2006.10.030

Smillie, 2019, Intra- and inter-cellular rewiring of the human colon during ulcerative colitis., Cell, 178, 714, 10.1016/j.cell.2019.06.029

Smith, 2009, Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn’s disease., J. Exp. Med., 206, 1883, 10.1084/jem.20091233

Smith, 2007, Infection with a helminth parasite prevents experimental colitis via a macrophage-mediated mechanism., J. Immunol., 178, 4557, 10.4049/jimmunol.178.7.4557

Stein, 1992, Interleukin 4 potently enhances murine macrophage mannose receptor activity: a marker of alternative immunologic macrophage activation., J. Exp. Med., 176, 287, 10.1084/jem.176.1.287

Strauss-Ayali, 2007, Monocyte subpopulations and their differentiation patterns during infection., J. Leukoc. Biol., 82, 244, 10.1189/jlb.0307191

Sugimoto, 2019, Mediators of the resolution of the inflammatory response., Trends Immunol., 40, 212, 10.1016/j.it.2019.01.007

Sun, 2015, Regulatory immune cells in regulation of intestinal inflammatory response to microbiota., Mucosal. Immunol., 8, 969, 10.1038/mi.2015.49

Tajima, 2012, EP2 and EP4 receptors on muscularis resident macrophages mediate LPS-induced intestinal dysmotility via iNOS upregulation through cAMP/ERK signals., Am. J. Physiol. Gastrointest Liver Physiol., 302, G524, 10.1152/ajpgi.00264.2011

Takada, 2010, Monocyte chemoattractant protein-1 contributes to gut homeostasis and intestinal inflammation by composition of IL-10-producing regulatory macrophage subset., J. Immunol., 184, 2671, 10.4049/jimmunol.0804012

Tamoutounour, 2012, CD64 distinguishes macrophages from dendritic cells in the gut and reveals the Th1-inducing role of mesenteric lymph node macrophages during colitis., Eur. J. Immunol., 42, 3150, 10.1002/eji.201242847

Tang, 2020, Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions., Cell Res., 30, 833, 10.1038/s41422-020-0338-1

Thiesen, 2014, CD14(hi)HLA-DR(dim) macrophages, with a resemblance to classical blood monocytes, dominate inflamed mucosa in Crohn’s disease., J. Leukoc. Biol., 95, 531, 10.1189/jlb.0113021

Thomas, 2014, “Of mice and men”: arginine metabolism in macrophages., Front. Immunol., 5, 10.3389/fimmu.2014.00479

Tordesillas, 2018, Mechanisms of oral tolerance., Clin. Rev. Allergy Immunol., 55, 107, 10.1007/s12016-018-8680-5

Torres, 2017, Crohn’s disease., Lancet, 389, 1741, 10.1016/s0140-6736(16)31711-1

Ungaro, 2017, Ulcerative colitis., Lancet, 389, 1756, 10.1016/s0140-6736(16)32126-2

Uno, 2010, Altered macrophage function contributes to colitis in mice defective in the phosphoinositide-3 kinase subunit p110δ., Gastroenterology, 139, 1642, 10.1053/j.gastro.2010.07.008

van Furth, 1968, The origin and kinetics of mononuclear phagocytes., J. Exp. Med., 128, 415, 10.1084/jem.128.3.415

van Furth, 1972, The mononuclear phagocyte system: a new classification of macrophages, monocytes, and their precursor cells., Bull. World Health Organ., 46, 845

VanDussen, 2018, Abnormal small intestinal epithelial microvilli in patients with crohn’s disease., Gastroenterology, 155, 815, 10.1053/j.gastro.2018.05.028

Vannella, 2017, Mechanisms of organ injury and repair by macrophages., Annu. Rev. Physiol., 79, 593, 10.1146/annurev-physiol-022516-034356

Varol, 2009, Intestinal lamina propria dendritic cell subsets have different origin and functions., Immunity, 31, 502, 10.1016/j.immuni.2009.06.025

Vigorito, 2013, miR-155: an ancient regulator of the immune system., Immunol. Rev., 253, 146, 10.1111/imr.12057

Vos, 2012, Regulatory macrophages induced by infliximab are involved in healing in vivo and in vitro., Inflamm. Bowel Dis., 18, 401, 10.1002/ibd.21818

Waddell, 2011, Colonic eosinophilic inflammation in experimental colitis is mediated by Ly6C(high) CCR2(+) inflammatory monocyte/macrophage-derived CCL11., J. Immunol., 186, 5993, 10.4049/jimmunol.1003844

Wallace, 2014, Immunopathology of inflammatory bowel disease., World J. Gastroenterol., 20, 6, 10.3748/wjg.v20.i1.6

Wang, 2013, RIG-I activation inhibits HIV replication in macrophages., J. Leukoc. Biol., 94, 337, 10.1189/jlb.0313158

Wang, 2019, Gab2 and Gab3 redundantly suppress colitis by modulating macrophage and CD8(+) T-Cell activation., Front. Immunol., 10, 10.3389/fimmu.2019.00486

Wawrzyniak, 2017, Role of regulatory cells in oral tolerance., Allergy Asthma. Immunol. Res., 9, 107, 10.4168/aair.2017.9.2.107

Weber, 2011, CX3CR1 defines functionally distinct intestinal mononuclear phagocyte subsets which maintain their respective functions during homeostatic and inflammatory conditions., Eur. J. Immunol., 41, 773, 10.1002/eji.201040965

Wei, 2019, RIP3 deficiency alleviates liver fibrosis by inhibiting ROCK1-TLR4-NF-κB pathway in macrophages., Faseb J., 33, 11180, 10.1096/fj.201900752R

Weiner, 2000, Oral tolerance, an active immunologic process mediated by multiple mechanisms., J. Clin. Invest., 106, 935, 10.1172/jci11348

Weinhage, 2015, Granulocyte macrophage colony-stimulating factor-activated CD39(+)/CD73(+) murine monocytes modulate intestinal inflammation via induction of regulatory t cells., Cell Mol. Gastroenterol. Hepatol., 1, 433, 10.1016/j.jcmgh.2015.04.005

West, 2017, Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease., Nat. Med., 23, 579, 10.1038/nm.4307

Woehlbier, 2011, Modulating stress responses by the UPRosome: a matter of life and death., Trends Biochem. Sci., 36, 329, 10.1016/j.tibs.2011.03.001

Wu, 2015, miR-10a inhibits dendritic cell activation and Th1/Th17 cell immune responses in IBD., Gut, 64, 1755, 10.1136/gutjnl-2014-307980

Xavier, 2007, Unravelling the pathogenesis of inflammatory bowel disease., Nature, 448, 427, 10.1038/nature06005

Xue, 2014, Transcriptome-based network analysis reveals a spectrum model of human macrophage activation., Immunity, 40, 274, 10.1016/j.immuni.2014.01.006

Yang, 2019, TREM-1-dependent M1 macrophage polarization restores intestinal epithelium damaged by DSS-induced colitis by activating IL-22-producing innate lymphoid cells., J. Biomed. Sci., 26, 10.1186/s12929-019-0539-4

Yona, 2013, Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis., Immunity, 38, 79, 10.1016/j.immuni.2012.12.001

Zeissig, 2004, Downregulation of epithelial apoptosis and barrier repair in active Crohn’s disease by tumour necrosis factor alpha antibody treatment., Gut, 53, 1295, 10.1136/gut.2003.036632

Zhang, 2009, Two chromogranin a-derived peptides induce calcium entry in human neutrophils by calmodulin-regulated calcium independent phospholipase A2., PLoS One, 4, 10.1371/journal.pone.0004501

Zhang, 2010, Intestinal flora imbalance results in altered bacterial translocation and liver function in rats with experimental cirrhosis., Eur. J. Gastroenterol. Hepatol., 22, 1481, 10.1097/MEG.0b013e32833eb8b0

Zhang, 2016, Silencing MicroRNA-155 attenuates cardiac injury and dysfunction in viral myocarditis via promotion of M2 phenotype polarization of macrophages., Sci. Rep., 6, 10.1038/srep22613

Zhou, 2019, YAP aggravates inflammatory bowel disease by regulating M1/M2 macrophage polarization and gut microbial homeostasis., Cell Rep., 27, 1176, 10.1016/j.celrep.2019.03.028

Zhou, 2013, TLR3 activation efficiency by high or low molecular mass poly I:C., Innate. Immun., 19, 184, 10.1177/1753425912459975

Zigmond, 2014, Macrophage-restricted interleukin-10 receptor deficiency, but not IL-10 deficiency, causes severe spontaneous colitis., Immunity, 40, 720, 10.1016/j.immuni.2014.03.012

Zigmond, 2012, Ly6C hi monocytes in the inflamed colon give rise to proinflammatory effector cells and migratory antigen-presenting cells., Immunity, 37, 1076, 10.1016/j.immuni.2012.08.026