Orecchioni, M., Ghosheh, Y., Pramod, A. B. & Ley, K. Macrophage polarization: different gene signatures in M1(LPS+) vs. classically and M2(LPS−) vs. alternatively activated macrophages. Front. Immunol. 10, 1084 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Van Dyken, S. J. & Locksley, R. M. Interleukin-4- and interleukin-13-mediated alternatively activated macrophages: roles in homeostasis and disease. Annu. Rev. Immunol. 31, 317–343 (2013).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Wynn, T. A. & Vannella, K. M. Macrophages in tissue repair, regeneration, and fibrosis. Immunity 44, 450–462 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Murray, P. J. et al. Macrophage activation and polarization: nomenclature and experimental guidelines. Immunity 41, 14–20 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Xue, J. et al. Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity 40, 274–288 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Blériot, C., Chakarov, S. & Ginhoux, F. Determinants of resident tissue macrophage identity and function. Immunity 52, 957–970 (2020).

PubMed  Article  CAS  Google Scholar 

Ginhoux, F. & Guilliams, M. Tissue-resident macrophage ontogeny and homeostasis. Immunity 44, 439–449 (2016).

CAS  PubMed  Article  Google Scholar 

Mass, E. et al. Specification of tissue-resident macrophages during organogenesis. Science 353, aaf4238 (2016).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Lacerda Mariano, L. et al. Functionally distinct resident macrophage subsets differentially shape responses to infection in the bladder. Sci. Adv. 6, eabc5739 (2020).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Owusu-Boaitey, N., Bauckman, K. A., Zhang, T. & Mysorekar, I. U. Macrophagic control of the response to uropathogenic E. coli infection by regulation of iron retention in an IL-6-dependent manner. Immun. Inflamm. Dis. 4, 413–426 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Fu, C. L., Odegaard, J. I. & Hsieh, M. H. Macrophages are required for host survival in experimental urogenital schistosomiasis. Faseb J. 29, 193–207 (2015).

CAS  PubMed  Article  Google Scholar 

Ligon, M. M. et al. Single cell and tissue-transcriptomic analysis of murine bladders reveals age- and TNFα-dependent but microbiota-independent tertiary lymphoid tissue formation. Mucosal Immunol. 13, 908–918 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mould, K. J., Jackson, N. D., Henson, P. M., Seibold, M. & Janssen, W. J. Single cell RNA sequencing identifies unique inflammatory airspace macrophage subsets. JCI Insight 4, e126556 (2019).

PubMed Central  Article  Google Scholar 

Zimmerman, K. A. et al. Single-Cell RNA sequencing identifies candidate renal resident macrophage gene expression signatures across species. J. Am. Soc. Nephrol. 30, 767–781 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Guilliams, M. et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell 185, 379–396 (2022).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Schulz, C. et al. A lineage of myeloid cells independent of Myb and hematopoietic stem cells. Science 336, 86–90 (2012).

CAS  PubMed  Article  Google Scholar 

Hoeffel, G. et al. C-Myb(+) erythro-myeloid progenitor-derived fetal monocytes give rise to adult tissue-resident macrophages. Immunity 42, 665–678 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Gomez Perdiguero, E. et al. Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors. Nature 518, 547–551 (2015).

PubMed  Article  CAS  Google Scholar 

Gentek, R. et al. Hemogenic endothelial fate mapping reveals dual developmental origin of mast cells. Immunity 48, 1160–1171 (2018).

CAS  PubMed  Article  Google Scholar 

Boyer, S. W., Schroeder, A. V., Smith-Berdan, S. & Forsberg, E. C. All hematopoietic cells develop from hematopoietic stem cells through Flk2/Flt3-positive progenitor cells. Cell Stem Cell 9, 64–73 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Arandjelovic, S. & Ravichandran, K. S. Phagocytosis of apoptotic cells in homeostasis. Nat. Immunol. 16, 907–917 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Henson, P. M. & Hume, D. A. Apoptotic cell removal in development and tissue homeostasis. Trends Immunol. 27, 244–250 (2006).

CAS  PubMed  Article  Google Scholar 

A-Gonzalez, N. et al. Phagocytosis imprints heterogeneity in tissue-resident macrophages. J. Exp. Med. 214, 1281–1296 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

A-Gonzalez, N. et al. Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR. Immunity 31, 45–258 (2009).

Article  CAS  Google Scholar 

Fadok, V. A. et al. Macrophages that have ingested apoptotic cells in vitro inhibit proinflammatory cytokine production through autocrine/paracrine mechanisms involving TGF-beta, PGE2, and PAF. J. Clin. Investig. 101, 890–898 (1998).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Joseph, D. B. et al. In vivo replacement of damaged bladder urothelium by Wolffian duct epithelial cells. Proc. Natl Acad. Sci. U.S.A. 115, 8394–8399 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bottek, J. et al. Spatial proteomics revealed a CX(3)CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder. Mucosal Immunol. 13, 702–714 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Munro, D. A. D. & Hughes, J. The origins and functions of tissue-resident macrophages in kidney development. Front. Physiol. 8, 837 (2017).

PubMed  PubMed Central  Article  Google Scholar 

Puranik, A. S. et al. Kidney-resident macrophages promote a proangiogenic environment in the normal and chronically ischemic mouse kidney. Sci. Rep. 8, 13948 (2018).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Dong, Y. et al. CD44 loss disrupts lung lipid surfactant homeostasis and exacerbates oxidized lipid-induced lung inflammation. Front. Immunol. 11, 29 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Taylor, P. R. et al. Macrophage receptors and immune recognition. Annu. Rev. Immunol. 23, 901–944 (2005).

CAS  PubMed  Article  Google Scholar 

Akira, S., Takeda, K. & Kaisho, T. Toll-like receptors: critical proteins linking innate and acquired immunity. Nat. Immunol. 2, 675–680 (2001).

CAS  PubMed  Article  Google Scholar 

Inohara, N. & Nuñez, G. NODs: intracellular proteins involved in inflammation and apoptosis. Nat. Rev. Immunol. 3, 371–382 (2003).

CAS  PubMed  Article  Google Scholar 

Schilling, J. D., Martin, S. M., Hung, C. S., Lorenz, R. G. & Hultgren, S. J. Toll-like receptor 4 on stromal and hematopoietic cells mediates innate resistance to uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA 100, 4203–4208 (2003).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Carey, A. J. et al. Uropathogenic Escherichia coli engages CD14-dependent signaling to enable bladder-macrophage-dependent control of acute urinary tract infection. J. Infect. Dis. 213, 659–668 (2016).

CAS  PubMed  Article  Google Scholar 

Mossman, K. L. et al. Cutting edge: FimH adhesin of type 1 fimbriae is a novel TLR4 ligand. J. Immunol. 181, 6702–6706 (2008).

CAS  PubMed  Article  Google Scholar 

Ching, C. B. et al. Interleukin-6/Stat3 signaling has an essential role in the host antimicrobial response to urinary tract infection. Kidney Int. 93, 1320–1329 (2018).

CAS  PubMed  PubMed Central  Article