The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
Open accessAbstract
We assessed gene expression in tissue macrophages from various mouse organs. The diversity in gene expression among different populations of macrophages was considerable. Only a few hundred mRNA transcripts were selectively expressed by macrophages rather than dendritic cells, and many of these were not present in all macrophages. Nonetheless, well-characterized surface markers, including MerTK and FcγR1 (CD64), along with a cluster of previously unidentified transcripts, were distinctly and universally associated with mature tissue macrophages. TCEF3, C/EBP-α, Bach1 and CREG-1 were among the transcriptional regulators predicted to regulate these core macrophage-associated genes. The mRNA encoding other transcription factors, such as Gata6, was associated with single macrophage populations. We further identified how these transcripts and the proteins they encode facilitated distinguishing macrophages from dendritic cells.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Microglia also express hundreds of genes at higher levels than other macrophage subsets (24–26) that may be influenced by factors present in the CNS microenvironment (25, 27), suggesting mechanisms by which the brain environment influences the activity and functions of one of its primary support cells.”
From An environment-dependent transcriptional network specifies human microglia identity (2017) · cites this paper as [24]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Recent work demonstrated that all tissue resident macrophages are different to an extent yet cluster together when compared to monocytes and DCs and that spleen red pulp macrophages were closely associated with microglia14.”
From Identification of a unique TGF-β–dependent molecular and functional signature in microglia (2014) · cites this paper as [14]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“We also found that organ-resident macrophages in the gut and liver are “microglia-like” as they express Gas6 and Mertk and these genes may have a role in maintaining tissue homeostasis which is consistent with a recent transcriptional profiling of murine tissue macrophages14.”
From Identification of a unique TGF-β–dependent molecular and functional signature in microglia (2014) · cites this paper as [14]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“FFAR2-deficient mice displayed microglia reminiscent of those found in GF mice (103).”
From The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication (2020) · cites this paper as [103]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“we found increased microglial expression of C1q, Csfr1 and Cd34 genes, which are known to be expressed on tissue resident macrophages14.”
From Identification of a unique TGF-β–dependent molecular and functional signature in microglia (2014) · cites this paper as [14]
Experimental — accuracy not yet measured
In the citing paper
“Because macrophages and dendritic cells have similar transcriptomic profiles23–25, we repeated SingleR analysis using published RNA-seq datasets of mouse lung macrophages and dendritic cells26,27 to isolate the macrophages”
From Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage (2019) · cites this paper as [25]
In the citing paper
“microglia — but not peripheral myeloid cells — were shown to express P2Y purinoceptor 12 (P2ry12), transmembrane protein 119 (Tmem119), sialic acid binding Ig-like lectin H (Siglech), probable G protein coupled receptor 34 (Gpr34), suppressor of cytokine signalling 3 (Socs3), β-hexosaminidase subunit β (Hexb), olfactomedin-like protein 3 (Olfml3) and Fc receptor-like S, scavenger receptor (Fcrls).”
From Microglial signatures and their role in health and disease (2018) · cites this paper as [29]
In the citing paper
“In the healthy brain, they exhibit a unique molecular homeostatic ‘signature’, consisting of a specific transcriptional profile and surface protein expression pattern, which differs from that of tissue macrophages.”
From Microglial signatures and their role in health and disease (2018) · cites this paper as [29]
In the citing paper
“Tissue micro-environmental factors activate cascades resulting in co-operative binding of certain transcription factors with PU.1, leading to a unique enhancer profile enabling microglial dynamic response to its surrounding micro-environment [24, 72].”
From Transcriptional and Epigenetic Regulation of Microglia in Health and Disease (2019) · cites this paper as [72]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Exploring the full spectrum of macrophage activation
Mosser, D. M., & Edwards, J. P. (2008) · Nature Reviews Immunology · doi:10.1038/nri2448 · Cited by 9,144
Monocyte and macrophage heterogeneity
Gordon, S., & Taylor, P. R. (2005) · Nature Reviews Immunology · doi:10.1038/nri1733 · Cited by 5,190
Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages
Ginhoux, F., Greter, M., Leboeuf, M., Nandi, S., See, P., Gokhan, S., Mehler, M. F., Conway, S. J., Ng, L. G., Stanley, E. R., et al. (2010) · Science · doi:10.1126/science.1194637 · Cited by 5,175
Self-citationA Lineage of Myeloid Cells Independent of Myb and Hematopoietic Stem Cells
Schulz, C., Perdiguero, E. G., Chorro, L., Szabo-Rogers, H., Cagnard, N., Kierdorf, K., Prinz, M., Wu, B., Jacobsen, S. E. W., Pollard, J. W., et al. (2012) · Science · doi:10.1126/science.1219179 · Cited by 2,578
Nahrendorf, M., Swirski, F. K., Aikawa, E., Stangenberg, L., Wurdinger, T., Figueiredo, J.-L., Libby, P., Weissleder, R., & Pittet, M. J. (2007) · The Journal of Experimental Medicine · doi:10.1084/jem.20070885 · Cited by 2,300
Batf3 Deficiency Reveals a Critical Role for CD8α + Dendritic Cells in Cytotoxic T Cell Immunity
Hildner, K., Edelson, B. T., Purtha, W. E., Diamond, M., Matsushita, H., Kohyama, M., Calderon, B., Schraml, B. U., Unanue, E. R., Diamond, M. S., et al. (2008) · Science · doi:10.1126/science.1164206 · Cited by 2,081
The Immunological Genome Project: networks of gene expression in immune cells
The Immunological Genome Project Consortium, Heng, T. S. P., Painter, M. W., Elpek, K., Lukacs-Kornek, V., Mauermann, N., Turley, S. J., Koller, D., Kim, F. S., Wagers, A. J., et al. (2008) · Nature Immunology · doi:10.1038/ni1008-1091 · Cited by 1,864
Self-citationGenetic regulation of osteoclast development and function
Teitelbaum, S. L., & Ross, F. P. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1122 · Cited by 1,720
CCR7 governs skin dendritic cell migration under inflammatory and steady-state conditions
Ohl, L., Mohaupt, M., Czeloth, N., Hintzen, G., Kiafard, Z., Zwirner, J., Blankenstein, T., Henning, G., & Förster, R. (2004) · Immunity · doi:10.1016/j.immuni.2004.06.014 · Cited by 1,086
A Clonogenic Bone Marrow Progenitor Specific for Macrophages and Dendritic Cells
Fogg, D. K., Sibon, C., Miled, C., Jung, S., Aucouturier, P., Littman, D. R., Cumano, A., & Geissmann, F. (2005) · Science · doi:10.1126/science.1117729 · Cited by 1,050
Flagged first, then by citations
Cited by
Sorted by citations
Items 401–500 of 1,008
Zhang, M., Cheng, Q., Zheng, Z., Qian, F., Wang, Y., Thu, P. M., Zhang, X., Zhou, Y., Tu, L., Liu, Q., et al. (2018) · Theranostics · doi:10.7150/thno.26164 · Cited by 148
“In the CNS, Tyro3 is abundant in neurons [68], whereas Mer and Axl are present in microglia [69-71].”
BackgroundThe Skin-Resident Immune Network
Tay, S. S., Roediger, B., Tong, P. L., Tikoo, S., & Weninger, W. (2014) · Current Dermatology Reports · doi:10.1007/s13671-013-0063-9 · Cited by 147
Microglia Participate in Neurogenic Regulation of Hypertension
Shen, X. Z., Li, Y., Li, L., Shah, K. H., Bernstein, K. E., Lyden, P. D., & Shi, P. D. (2015) · Hypertension · doi:10.1161/hypertensionaha.115.05333 · Cited by 148
“Recent transcriptome analyses revealed that microglia have a distinct phenotype from macrophages in other tissues, suggesting unique characteristics of microglia.(11,12) As surveillance cells, microglia are highly sensitive to pathological disturbance in the brain and play major roles in the progressive pathology of n…”
BackgroundHagemeyer, N., Kierdorf, K., Frenzel, K., Xue, J., Ringelhan, M., Abdullah, Z., Godin, I., Wieghofer, P., Jordão, M. J. C., Ulas, T., et al. (2016) · The EMBO Journal · doi:10.15252/embj.201693801 · Cited by 144
“However, a core gene signature of all macrophages could be detected (Gautier et al , 2012).”
A novel real time imaging platform to quantify macrophage phagocytosis
Kapellos, T. S., Taylor, L., Lee, H., Cowley, S. A., James, W. S., Iqbal, A. J., & Greaves, D. R. (2016) · Biochemical Pharmacology · doi:10.1016/j.bcp.2016.07.011 · Cited by 148
Pavlou, S., Wang, L., Xu, H., et al. (2017) · Journal of Inflammation · doi:10.1186/s12950-017-0151-x · Cited by 145
Transcriptional profiling of microglia; current state of the art and future perspectives
Gerrits, E., Heng, Y., Boddeke, E. W. G. M., & Eggen, B. J. L. (2020) · Glia · doi:10.1002/glia.23767 · Cited by 140
“For mouse microglia, the first core microglia signature was generated in 2012 using microarrays in the Immunological Genome (ImmGen) project (Gautier et al., 2012).”
MethodMacrophages are metabolically heterogeneous within the tumor microenvironment
Geeraerts, X., Fernández-García, J., Hartmann, F. J., de Goede, K. E., Martens, L., Elkrim, Y., Debraekeleer, A., Stijlemans, B., Vandekeere, A., Rinaldi, G., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110171 · Cited by 151
“Mature TAMs (clusters 2–7 and 10) were defined based on the absence of Ly6C expression and an enhanced macrophage marker expression (CD64, F4/80, CD206, SRA) (Gautier et al., 2012; Zilionis et al., 2019) (Figures 7B and 7C).”
BackgroundRole of microglia in ischemic focal stroke and recovery: focus on Toll-like receptors
Anttila, J. E., Whitaker, K. W., Wires, E. S., Harvey, B. K., & Airavaara, M. (2016) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2016.07.003 · Cited by 148
“Microglia are a distinct subtype of mononuclear macrophages, which is a class that also includes peripheral tissue macrophages, dendritic cells and monocyte-derived cells (Butovsky et al., 2012; Gautier et al., 2012; Prinz and Priller, 2014).”
Louwe, P. A., Gomez, L. B., Webster, H. C., Perona‐Wright, G., Bain, C. C., Forbes, S. J., & Jenkins, S. J. (2021) · Nature Communications · doi:10.1038/s41467-021-21778-0 · Cited by 148
Sorrentino, F. S., Allkabes, M., Salsini, G., Bonifazzi, C., & Perri, P. (2016) · Life Sciences · doi:10.1016/j.lfs.2016.08.001 · Cited by 150
Myeloid cell–synthesized coagulation factor X dampens antitumor immunity
Graf, C., Wilgenbus, P., Pagel, S., Pott, J., Marini, F., Reyda, S., Kitano, M., Macher-Göppinger, S., Weiler-Guettler, H., & Ruf, W. (2019) · Science Immunology · doi:10.1126/sciimmunol.aaw8405 · Cited by 145
Metformin targets mitochondrial electron transport to reduce air-pollution-induced thrombosis
Soberanes, S., Misharin, A. V., Jairaman, A., Morales-Nebreda, L., McQuattie-Pimentel, A. C., Cho, T., Hamanaka, R. B., Meliton, A. Y., Reyfman, P. A., Walter, J. M., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2018.09.019 · Cited by 131
Wermuth, P. J., & Jiménez, S. A. (2015) · Clinical and Translational Medicine · doi:10.1186/s40169-015-0047-4 · Cited by 141
Macrophages with regulatory functions, a possible new therapeutic perspective in autoimmune diseases
Benedetto, P. D., Ruscitti, P., Vadasz, Z., Toubi, E., & Giacomelli, R. (2019) · Autoimmunity Reviews · doi:10.1016/j.autrev.2019.102369 · Cited by 140
Macrophage Biology, Classification, and Phenotype in Cardiovascular Disease
Williams, J. W., Giannarelli, C., Rahman, A. H., Randolph, G. J., & Kovacic, J. C. (2018) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2018.08.2148 · Cited by 149
Self-citationRegulation of myelopoiesis by the transcription factor IRF8
Tamura, T., Kurotaki, D., & Koizumi, S.-I. (2015) · International Journal of Hematology · doi:10.1007/s12185-015-1761-9 · Cited by 139
“Monocytes are IRF8, and most types of macrophages (Mφs)—including Langerhans cells (LCs) and microglia—are IRF8 [15].”
BackgroundRetinoid X receptors in macrophage biology
Rőszer, T., Menéndez-Gutiérrez, M. P., Cedenilla, M., & Ricote, M. (2013) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2013.04.004 · Cited by 137
Arnold, I. C., Mathisen, S., Schulthess, J., Danne, C., Hegazy, A. N., & Powrie, F. M. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.65 · Cited by 138
Konishi, H., Kobayashi, M., Kunisawa, T., Imai, K., Sayo, A., MALISSEN, B., Crocker, P. R., Sato, K., & Kiyama, H. (2017) · Glia · doi:10.1002/glia.23204 · Cited by 141
“…in the identification of molecules that are highly expressed by microglia but not by other myeloid cells (Bedard, Tremblay, Chernomoretz, & Vallieres, 2007); Butovsky et al., 2014; Chiu et al., 2013; Gautier et al., 2012; Hickman et al., 2013; Wes, Holtman, Boddeke, Moller, & Eggen, 2016).”
BackgroundResultInfluentialSchleicher, U., Paduch, K., Debus, A., Obermeyer, S., König, T., Kling, J. C., Ribechini, E., Dudziak, D., Mougiakakos, D., Murray, P. J., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.001 · Cited by 136
ZEBs: Novel Players in Immune Cell Development and Function
Scott, C. L., & Omilusik, K. D. (2019) · Trends in Immunology · doi:10.1016/j.it.2019.03.001 · Cited by 141
Macrophages Subvert Adaptive Immunity to Urinary Tract Infection
Mora-Bau, G., Platt, A. M., van Rooijen, N., Randolph, G., Albert, M., & Ingersoll, M. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005044 · Cited by 134
“Macrophages, delineated by CD64 [26,27] and F4/ 80 co-expression, were by far the largest APC population (~40% of CD45 cells) (Fig 2B and 2E).”
BackgroundInfluentialSelf-citationPridans, C., Raper, A., Davis, G. M., Alves, J., Sauter, K. A. D., Lefèvre, L., Regan, T. W., Meek, S. E., Sutherland, L., Thomson, A. J., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1701783 · Cited by 139
Transcriptional and Epigenetic Regulation of Microglia in Health and Disease
Yeh, H., & Ikezu, T. (2019) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2018.11.004 · Cited by 135
“1, leading to a unique enhancer profile enabling microglial dynamic response to its surrounding micro-environment [24, 72].”
BackgroundA signalling cascade of IL-33 to IL-13 regulates metaplasia in the mouse stomach
Petersen, C. P., Meyer, A. R., Salvo, C. D., Choi, E.-Y. K., Schlegel, C. E., Petersen, A., Engevik, A. C., Prasad, N., Levy, S., Peebles, R. S., et al. (2017) · Gut · doi:10.1136/gutjnl-2016-312779 · Cited by 139
Human and Mouse Mononuclear Phagocyte Networks: A Tale of Two Species?
Reynolds, G., & Haniffa, M. A. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00330 · Cited by 138
“Microarray transcriptome analysis has identified several thousand transcripts with greater than twofold difference in expression between macrophages from different sites in mice (219), supporting unique local microenvironment-related characteristics.”
BackgroundKIT oncogene inhibition drives intratumoral macrophage M2 polarization
Cavnar, M. J., Zeng, S., Kim, T. S., Sorenson, E. C., Ocuin, L. M., Balachandran, V. P., Seifert, A. M., Greer, J. B., Popow, R., Crawley, M. H., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20130875 · Cited by 140
The endocytic pathway in microglia during health, aging and Alzheimer’s disease
Solé-Domènech, S., Cruz, D. L., Capetillo-Zarate, E., & Maxfield, F. R. (2016) · Ageing Research Reviews · doi:10.1016/j.arr.2016.07.002 · Cited by 133
Synovial tissue macrophages: friend or foe?
Kurowska‐Stolarska, M., & Alivernini, S. (2017) · RMD Open · doi:10.1136/rmdopen-2017-000527 · Cited by 140
“These cooperate with macrophage lineage master regulator transcription factors such as PU.1 induced by macrophage colony-stimulating factor (M-CSF)/IL-34 that maintain universal macrophage-specific gene expression.”
BackgroundHow to reprogram microglia toward beneficial functions
Fumagalli, M., Lombardi, M., Gressèns, P., & Verderio, C. (2018) · Glia · doi:10.1002/glia.23484 · Cited by 134
Alveolar and lung interstitial macrophages: Definitions, functions, and roles in lung fibrosis
Shi, T., Denney, L., An, H., Ho, L., & Zheng, Y. (2020) · Journal of Leukocyte Biology · doi:10.1002/jlb.3ru0720-418r · Cited by 146
Wieghofer, P., Hagemeyer, N., Sankowski, R., Schlecht, A., Staszewski, O., Amann, L., Gruber, M., Koch, J., Hausmann, A., Zhang, P., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2020105123 · Cited by 130
“The clusters 4 and 5 were characterized by a high expression of previously reported microglia signature genes, such as Hexb, C1qa, and Sparc (Gautier et al , 2012; Butovsky et al , 2014; Fig 7H and I).”
CD11b immunophenotyping identifies inflammatory profiles in the mouse and human lungs
Duan, M., Steinfort, D., Smallwood, D., Hew, M. J., Chen, W., Ernst, M., Irving, L. B., Anderson, G. P., & Hibbs, M. L. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.84 · Cited by 135
“30, [33] [34] [35] This unbiased and systematic approach may generate new disease-specific MF markers for further evaluation and renders the discovery of systematic human MF profiling methods an even more critical objective.”
BackgroundPalis, J. (2016) · FEBS Letters · doi:10.1002/1873-3468.12459 · Cited by 143
Expression of factor V by resident macrophages boosts host defense in the peritoneal cavity
Zhang, N., Czepielewski, R. S., Jarjour, N. N., Erlich, E. C., Esaulova, E., Saunders, B. T., Grover, S. P., Cleuren, A. C. A., Broze, G., Edelson, B. T., et al. (2019) · The Journal of Experimental Medicine · doi:10.1084/jem.20182024 · Cited by 132
Self-citationPlanas, A. M. (2024) · Glia · doi:10.1002/glia.24501 · Cited by 144
“However, they acquire distinct functions tailored to their unique living environment, akin to other tissue-resident macrophages (Gautier et al., 2012; Lavin et al., 2014; Wculek et al., 2022).”
BackgroundDistinct development and functions of resident and recruited liver Kupffer cells/macrophages
Ikarashi, M., Nakashima, H., Kinoshita, M., Sato, A., Nakashima, M., Miyazaki, H., Nishiyama, K., Yamamoto, J., & Seki, S. (2013) · Journal of Leukocyte Biology · doi:10.1189/jlb.0313144 · Cited by 132
“Therefore, consistent with a recent study [27], although some F4/80 CD68 Kupffer cells express CD11c, MerTK and CD64 could be useful markers to distinguish F4/80 CD68 Kupffer cells from F4/80 CD11c DCs in the steady-state liver.”
ResultJohnson, A. R., Qin, Y., Cozzo, A. J., Freemerman, A. J., Huang, M. J., Zhao, L., Sampey, B. P., Milner, J. J., Beck, M. A., Damania, B., et al. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.04.005 · Cited by 130
The Axl receptor tyrosine kinase is a discriminator of macrophage function in the inflamed lung
Fujimori, T., Grabiec, A. M., Kaur, M., Bell, T. J., Fujino, N., Cook, P. C., Svedberg, F. R., MacDonald, A. S., Maciewicz, R. A., Singh, D., et al. (2015) · Mucosal Immunology · doi:10.1038/mi.2014.129 · Cited by 132
Innate and Adaptive Immune Functions of Peyer’s Patch Monocyte-Derived Cells
Bonnardel, J., Silva, C. D., Henri, S., Tamoutounour, S., Chasson, L., Montañana-Sanchis, F., Gorvel, J., & Lelouard, H. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.067 · Cited by 136
“FcgrI (encoding CD64, the Fc Gamma receptor I), expressed virtually by all monocyte and macrophage populations (Gautier et al., 2012; Tamoutounour et al., 2012), was not expressed by LysoMacs (Figure S4).”
BackgroundIRF5 Is a Specific Marker of Inflammatory MacrophagesIn Vivo
Weiss, M., Blazek, K. D., Byrne, A. J., Perocheau, D. P. B., & Udalova, I. A. (2013) · Mediators of Inflammation · doi:10.1155/2013/245804 · Cited by 132
“This probably reflects the extent of macrophage plasticity and the wide spectrum of in vivo macrophage subtypes [32].”
BackgroundThe Bach Family of Transcription Factors: A Comprehensive Review
Zhou, Y. X., Wu, H., Zhao, M., Chang, C., & Lu, Q. (2016) · Clinical Reviews in Allergy & Immunology · doi:10.1007/s12016-016-8538-7 · Cited by 126
Phosphatidylserine Is the Signal for TAM Receptors and Their Ligands
Lemke, G. (2017) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2017.06.004 · Cited by 133
“These red pulp macrophages express the highest known levels of both Mertk and Axl mRNA [62].”
BackgroundChronic exposure to TGFβ1 regulates myeloid cell inflammatory response in an IRF7-dependent manner
Cohen, M., Matcovitch, O., David, E., Barnett‐Itzhaki, Z., Keren‐Shaul, H., Blecher‐Gonen, R., Jaitin, D. A., Sica, A., Amit, I., & Schwartz, M. (2014) · The EMBO Journal · doi:10.15252/embj.201489293 · Cited by 142
“…healing or pathogen removal, monocytes infiltrate the damaged tissue, leading to a transient inflammatory response (M1) that is resolved either via local conversion to M2-like macrophages or through additional recruitment of anti-inflammatory cells (Auffray et al , 2007; Geissmann et al , 2008).”
Shen, K., Reichelt, M., Kyauk, R. V., Ngu, H., Shen, Y.-A. A., Foreman, O., Modrusan, Z., Friedman, B. A., Sheng, M., & Yuen, T. J. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108835 · Cited by 138
A Close Encounter of the Third Kind
Mildner, A., Yona, S., & Jung, S. (2013) · Advances in immunology · doi:10.1016/b978-0-12-417028-5.00003-x · Cited by 136
T Cell Zone Resident Macrophages Silently Dispose of Apoptotic Cells in the Lymph Node
Baratin, M., Simon, L., Jorquera, A., Ghigo, C., Dembélé, D., Nowak, J., Gentek, R., Wienert, S., Klauschen, F., MALISSEN, B., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.07.019 · Cited by 136
“We examined the expression pattern of previously described core macrophages versus DC gene signatures (Carpentier et al., 2016; Gautier et al., 2012; Miller et al., 2012; Vu Manh and Dalod, 2016).”
MethodManaging Inflammation after Spinal Cord Injury through Manipulation of Macrophage Function
Ren, Y., & Young, W. (2013) · Neural Plasticity · doi:10.1155/2013/945034 · Cited by 135
“Detailed analysis of macrophage transcriptome revealed the heterogeneity in the gene expression pattern of different tissue-resident macrophages [14].”
McClean, C. M., & Tobin, D. M. (2016) · Pathogens and Disease · doi:10.1093/femspd/ftw068 · Cited by 135
Macrophages and Cardiovascular Health
Frodermann, V., & Nahrendorf, M. (2018) · Physiological Reviews · doi:10.1152/physrev.00068.2017 · Cited by 128
Sinclair, C., Bommakanti, G., Gardinassi, L., Loebbermann, J., Johnson, M. J., Hakimpour, P., Hagan, T., Benitez, L., Todor, A., Machiah, D., et al. (2017) · Science · doi:10.1126/science.aaj2155 · Cited by 126
“Previous studies have identified core sets of lineage-specifying genes, enriched in either CD11b+ lung APCs or AMs, relative to other APC subsets (21, 22).”
Shaked, I., Hanna, R. N., Shaked, H., Chodaczek, G., Nowyhed, H. N., Tweet, G., Tacke, R., Basat, A. B., Mikulski, Z., Togher, S., et al. (2015) · Nature Immunology · doi:10.1038/ni.3321 · Cited by 128
Self-citationMicroglia: unique and common features with other tissue macrophages
Prinz, M., Tay, T. L., Wolf, Y., & Jung, S. (2014) · Acta Neuropathologica · doi:10.1007/s00401-014-1267-1 · Cited by 126
“Genome-wide expression profiling of multiple immune cell subsets by the Immunological Genome Consortium has established that microglia stand out with a unique transcriptome among other tissue macrophages, such as the ones in the splenic red pulp, peritoneum or lung alveolar space [32].”
BackgroundAlternative pathways of osteoclastogenesis in inflammatory arthritis
Adamopoulos, I. E., & Mellins, E. (2014) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2014.198 · Cited by 130
“12 Similarly, high dimen sional cytometric analysis of human bone marrow shows a large number of distinct monocyte/macrophage phenotypes.”
BackgroundInnate Immune Cells in Inflammation and Cancer
Nowarski, R., Gagliani, N., Huber, S., & Flavell, R. A. (2013) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-13-0081 · Cited by 129
The Gut-Microglia Connection: Implications for Central Nervous System Diseases
Wang, Y., Wang, Z., Wang, Y., Li, F., Jia, J., Song, X., Qin, S., Wang, R., Jin, F., Kitazato, K., et al. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02325 · Cited by 130
Human mononuclear phagocyte system reunited
Haniffa, M. A., Bigley, V., & Collin, M. P. (2015) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2015.05.004 · Cited by 133
MafB-restricted local monocyte proliferation precedes lung interstitial macrophage differentiation
Vanneste, D., Bai, Q., Hasan, S., Peng, W., Pirottin, D., Schyns, J., Maréchal, P., Ruscitti, C., Meunier, M., Liu, Z., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01468-3 · Cited by 111
Mer receptor tyrosine kinase mediates both tethering and phagocytosis of apoptotic cells
Dransfield, I., Zagórska, A., Lew, E. D., Michail, K., & Lemke, G. (2015) · Cell Death and Disease · doi:10.1038/cddis.2015.18 · Cited by 125
“Although peritoneal macrophages are widely used for functional analyses, they represent an unusual population of cells associated with immunity at serosal surfaces.56 In contrast, there are many phagocytic tissue macrophage populations in vivo, for example, the microglia of the central nervous system, that are, like G…”
BackgroundSinger, K., Maley, N., Mergian, T. A., DelProposto, J. L., Cho, K. W., Zamarron, B. F., Martinez-Santibañez, G., Geletka, L. M., Muir, L. A., Wachowiak, P., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.634568 · Cited by 129
“ATMs were defined using CD64, a recently identified specific marker for murine macrophages (26).”
MethodDifferential contribution of microglia and monocytes in neurodegenerative diseases
Baufeld, C., O'Loughlin, E. K., Calcagno, N., Madore, C., & Butovsky, O. (2017) · Journal of Neural Transmission · doi:10.1007/s00702-017-1795-7 · Cited by 128
“…such as transcrip- tomic profiles, proteomic signatures, and surface markers, to reduce the observation of artifacts arising from other myeloid cells (Gautier et al. 2012; Chiu et al. 2013; Goldmann et al. 2013; Parkhurst et al. 2013; Yona et al. 2013; Butovsky et al. 2014; Bennett et al. 2016).”
BackgroundBok, E., Chung, Y. C., Kim, K., Baik, H. H., Shin, W.-H., & Jin, B. K. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0111-4 · Cited by 125
Exploring the complex role of chemokines and chemoattractants in vivo on leukocyte dynamics
David, B. A., & Kubes, P. (2019) · Immunological Reviews · doi:10.1111/imr.12757 · Cited by 128
Xia, H., Li, S., Li, X., Wang, W., Bian, Y., Wei, S., Grove, S., Wang, W., Vatan, L., Liu, J. R., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.141115 · Cited by 127
“Interestingly, Tim-4+ and Tim-4– TAMs are respectively enriched in F4/80hiMHC-IIlo and F4/80loMHC-IIhi cells (31, 32).”
Guilliams, M., & van de Laar, L. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00406 · Cited by 135
“manuscript in preparation) and we expect that given the striking heterogeneity of tissue-resident MΦs (104, 105) many of these MΦ-specific markers will be found.”
BackgroundMicroglial diversity by responses and responders
Gertig, U., & Hanisch, U.-K. (2014) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2014.00101 · Cited by 123
“In series of seminal studies, the ontogenetic origin and the maintenance of a stable microglia population have been dissected, identifying sources, critical transcription factors and steps of microgliogenesis (Naito et al., 1996; Ginhoux et al., 2010; Gautier et al., 2012; Gomez Perdiguero et al., 2013; Schulz et al.,…”
BackgroundInfluentialImmune surveillance of the lung by migrating tissue monocytes
Rodero, M. P., Poupel, L., Loyher, P.-L., Hamon, P., Licata, F., Pessel, C., Hume, D. A., Combadière, C., & Boissonnas, A. (2015) · eLife · doi:10.7554/elife.07847 · Cited by 131
“Macrophages isolated from different organs have distinct expression profiles which can be distinguished further if the cells are separated according to their surface markers (Gautier et al., 2013).”
BackgroundMacrophages and Dendritic Cells
Cybulsky, M. I., Cheong, C., & Robbins, C. S. (2016) · Circulation Research · doi:10.1161/circresaha.115.306542 · Cited by 130
Buscher, K., Ehinger, E., Gupta, P. P., Pramod, A. B., Wolf, D., Tweet, G., Pan, C., Mills, C. D., Lusis, A. J., & Ley, K. F. (2017) · Nature Communications · doi:10.1038/ncomms16041 · Cited by 123
Luk, B., Engevik, M. A., Ganesh, B. P., Lackey, E. P., Lin, T., Balderas, M. A., Major, A. M., Runge, J. K., Luna, R. A., Sillitoe, R. V., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-64173-3 · Cited by 128
A short field guide to fibroblast function in immunity
Buechler, M. B., & Turley, S. J. (2018) · Seminars in Immunology · doi:10.1016/j.smim.2017.11.001 · Cited by 121
Self-citationKuan, E. L., Ivanov, S., Bridenbaugh, E. A., Victora, G. D., Wang, W., Childs, E. W., Platt, A. M., Jakubzick, C., Mason, R. J., Gashev, A. A., et al. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1500221 · Cited by 121
“Cells with the highest levels of EYFP were DCs, not macrophages, since few adipose macrophages, identified as CD64+ MERTK+ cells (17) were fluorescent, in contrast to CD64-MERTK-CD11c+ MHC II+ DCs (Fig.”
Self-citationMcCubbrey, A. L., Allison, K. C., Lee-Sherick, A. B., Jakubzick, C. V., & Janssen, W. J. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01618 · Cited by 114
“4), Siglec-F (BD/ E50-2440), CD11c (eBioscience/N418), CD11b (eBioscience/ M1/70), CD103 (eBioscience/2E7), CD115 (eBioscience/ AFS98), CD64 (Biolegend/X54-5/7.1), MerTK (R&D/BAF591), CD3 (Biolegend/17A2), CD19 (eBioscience/eBio1D3), NK1.”
BackgroundInfluentialSelf-citationInvestigating Evolutionary Conservation of Dendritic Cell Subset Identity and Functions
Manh, T. V., Bertho, N., Hosmalin, A., Schwartz-Cornil, I., & Dalod, M. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00260 · Cited by 139
“Gene expression profiling also allowed aligning subsets of mononuclear cells across tissues (6, 8, 9, 40, 55, 99), establishing cell type homologies across species (5, 39, 50, 76, 83–85, 88, 89, 100), and rigorously examining the proximity of in vitro-derived subsets of mononuclear cells with those naturally existing…”
BackgroundThe Role of FcRn in Antigen Presentation
Baker, K., Räth, T., Pyzik, M., & Blumberg, R. S. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00408 · Cited by 123
Wu, X., Briseño, C. G., Durai, V., Albring, J. C., Haldar, M., Bagadia, P., Kim, K.-W., Randolph, G. J., Murphy, T. L., & MURPHY, K. M. M. (2016) · The Journal of Experimental Medicine · doi:10.1084/jem.20160600 · Cited by 116
“We surmise that the short half-life (∼20 h at steady state) of Ly-6Chi monocytes (Ginhoux and Jung, 2014) accounts for the lack of extensive lineage-tracing activity.”
BackgroundSelf-citationFrom infection to immunotherapy: host immune responses to bacteria at the bladder mucosa
Ingersoll, M. A., & Albert, M. L. (2013) · Mucosal Immunology · doi:10.1038/mi.2013.72 · Cited by 122
Lee, S. H., Charmoy, M., Romano, A., Paun, A., Chaves, M. M., Cope, F. O., Ralph, D. A., & Sacks, D. L. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20171389 · Cited by 120
“Recent studies have emphasized the plasticity of tissue macrophages with regard to their activation states and have suggested that their ontogeny and tissue-derived signals shape their functional specialization (Gautier et al., 2012; Lavin et al., 2014).”
BackgroundRole of bone marrow macrophages in controlling homeostasis and repair in bone and bone marrow niches
Kaur, S., Raggatt, L. J., Batoon, L., Hume, D. A., Lévesque, J.-P., & Pettit, A. R. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.08.009 · Cited by 123
“Macrophages, first described by Élie Metchnikoff, form a heterogeneous population of cells with diverse and adaptive transcriptomes [5, 6].”
BackgroundMicroglia: Brain cells on the move
Smolders, S., Kessels, S., Vangansewinkel, T., Rigo, J., Legendre, P., & Brône, B. (2019) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2019.04.001 · Cited by 126
Lymphatic Endothelial Cells Are Essential Components of the Subcapsular Sinus Macrophage Niche
Mondor, I., Baratin, M., Lagueyrie, M., Saro, L., Henri, S., Gentek, R., Suerinck, D., Kastenmüller, W., Jiang, J. X., & Bajénoff, M. (2019) · Immunity · doi:10.1016/j.immuni.2019.04.002 · Cited by 125
Gut-resident CX3CR1 hi macrophages induce tertiary lymphoid structures and IgA response in situ
Koscsó, B., Kurapati, S., Rodrigues, R. R., Nedjic, J., Gowda, K., Shin, C., Soni, C., Ashraf, A. Z., Purushothaman, I., Palisoc, M., et al. (2020) · Science Immunology · doi:10.1126/sciimmunol.aax0062 · Cited by 112
“We next compared the expression of the established cDC and M signature genes defined by the ImmGen Consortium (10, 11) among MP subsets and controls (SB cDC2 and peritoneal Ms).”
BackgroundMethodResultInfluentialSUMMERS, K. M., Bush, S. J., & Hume, D. A. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000859 · Cited by 114
Grassivaro, F., Menon, R., Acquaviva, M., Ottoboni, L., Ruffini, F., Bergamaschi, A., Muzio, L., Farina, C., & Martino, G. (2020) · The Journal of Neuroscience · doi:10.1523/jneurosci.1523-19.2019 · Cited by 127
“…among the top expressed genes the E14 and P1 microglia-specific lists contained well known microglia markers such as Olfml3, Crybb1, Gpr34, Siglech (Gautier et al., 2012; Chiu et al., 2013; Hickman et al., 2013; Butovsky et al., 2014; Zhang et al., 2014; Crotti and Ransohoff, 2016; Wolf et al.,…”
BackgroundInfluentialBlood vessel control of macrophage maturation promotes arteriogenesis in ischemia
Krishnasamy, K., Limbourg, A., Kapanadze, T. G., Gamrekelashvili, J., Beger, C., Häger, C., Lozanovski, V. J., Falk, C. S., Napp, L. C., Bauersachs, J. K., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00953-2 · Cited by 121
Studying tissue macrophages in vitro: are iPSC-derived cells the answer?
Lee, C., Kozaki, T., & Ginhoux, F. (2018) · Nature reviews. Immunology · doi:10.1038/s41577-018-0054-y · Cited by 124
Isolation and Culture of Microglia
Bohlen, C. J., Bennett, F. C., & Bennett, M. L. (2018) · Current Protocols in Immunology · doi:10.1002/cpim.70 · Cited by 118
“In part due to their unusual ontogeny and in part due to cues from the central nervous system (CNS) environment, microglia possess features that distinguish them from other tissue-resident macrophages (Bennett et al., 2018; Gautier et al., 2012; Gosselin et al., 2014; Lavin et al., 2014).”
BackgroundGut microbiota–driven brain Aβ amyloidosis in mice requires microglia
Dodiya, H. B., Lutz, H. L., Weigle, I. Q., Patel, P., Michalkiewicz, J., Roman-Santiago, C. J., Zhang, C. M., Liang, Y., Srinath, A., Zhang, X., et al. (2022) · Journal of Experimental Medicine · doi:10.1084/jem.20200895 · Cited by 120
Origin, development, and homeostasis of tissue‐resident macrophages
Haldar, M., & MURPHY, K. M. M. (2014) · Immunological Reviews · doi:10.1111/imr.12215 · Cited by 125
“RPMs and BMM degrade heme and release the heme-associated iron back into the circulation.”
BackgroundInfluentialInoue, T., Tanaka, M., Masuda, S., Ohue‐Kitano, R., Yamakage, H., Muranaka, K., Wada, H., Kusakabe, T., Shimatsu, A., Hasegawa, K., et al. (2017) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2017.02.010 · Cited by 117
Microglial Corpse Clearance: Lessons From Macrophages
Márquez-Ropero, M., Benito, E., Plaza‐Zabala, A., & Sierra, A. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00506 · Cited by 115
“Macrophages share a common core transcriptional identity, but each tissue-specific population expresses a unique set of transcripts that is organ-specific (45, 46).”
BackgroundFunctional Immune Anatomy of the Liver—As an Allograft
Demetris, A. J., Bellamy, C. O. C., Gandhi, C. R., Prost, S., Nakanuma, Y., & Stolz, D. B. (2016) · American Journal of Transplantation · doi:10.1111/ajt.13749 · Cited by 117
“CD68 also marks plasmacytoid DC, while CD68, CD163 and other general resting macrophage markers such as CD64 and MERTK are expressed on some monocytes/monocytederived cells (339, 426-431).”
BackgroundInfluentialDiversity of transcriptomic microglial phenotypes in aging and Alzheimer's disease
Boche, D., & Gordon, M. N. (2021) · Alzheimer s & Dementia · doi:10.1002/alz.12389 · Cited by 122
Epigenetic regulation of innate immune memory in microglia
Zhang, X., Kracht, L., Lerário, A. M., Dubbelaar, M. L., Brouwer, N., Wesseling, E. M., Boddeke, E., Eggen, B. J. L., & Kooistra, S. M. (2022) · Journal of Neuroinflammation · doi:10.1186/s12974-022-02463-5 · Cited by 116
Yun, T. J., Lee, J. S., Machmach, K., Shim, D., Choi, J., Wi, Y. J., Jang, H. S., Jung, I.-H., Kim, K., Yoon, W. K., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.04.010 · Cited by 116
The islet-resident macrophage is in an inflammatory state and senses microbial products in blood
Ferris, S. T., Zakharov, P. N., Wan, X., Calderón, B., Artyomov, M. N., Unanue, E. R., & Carrero, J. A. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20170074 · Cited by 118
“…all the tissue macrophages share core gene transcripts, including the transcription factor Spi1 (PU.1) and cell surface receptors such as Mertk (Mer) and Fcgr1 (CD64), a comparison of different organs reveals substantial differences that may relate to a specific function (Gautier et al., 2012).”
BackgroundInfluentialAPOE genotype and sex affect microglial interactions with plaques in Alzheimer’s disease mice
Stephen, T. L., Cacciottolo, M., Balu, D., Morgan, T. E., LaDu, M. J., Finch, C. E., & Pike, C. J. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0729-z · Cited by 115
Development, Diversity, and Function of Dendritic Cells in Mouse and HumanPreprint
Anderson, D. A., MURPHY, K. M. M., & Briseño, C. G. (2017) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a028613 · Cited by 120
“Alternatively, the transcription factor MafB is expressed by cells of the monocyte and macrophage lineage (Aziz et al. 2009; Gautier et al. 2012).”
BackgroundGrabert, K., Sehgal, A., Irvine, K. M., Wollscheid-Lengeling, E., Ozdemir, D. D., Stables, J., Luke, G. A., Ryan, M. D., Adamson, A., Humphreys, N. E., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.2000835 · Cited by 114
Metadata
- Authors
- the Immunological Genome Consortium, Gautier, E. L., Shay, T., Miller, J., Greter, M., Jakubzick, C., Ivanov, S., Helft, J., Chow, A., Elpek, K. G., Gordonov, S., Mazloom, A. R., Ma'ayan, A., Chua, W.-J., Hansen, T. H., Turley, S. J., Merad, M., & Randolph, G. J.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- Broad Institute (US)
- Mount Sinai Hospital (US)
- Washington University in St. Louis (US)
- Harvard University (US)
- Corresponding author
- Randolph, Gwendalyn J
- ORCID
- Venue
- Nature Immunology
- Published
- 2012-09-30
- Volume
- 13
- Issue
- 11
- Pages
- 1118-1128
- ISSN
- 1529-2908 (ISSN-L)
- 1529-2916
- PMC
- PMC3558276
- OpenAlex
- W2136188258
- Cited by
- 1,972
- References
- 41
- Citations by year
- 2026: 71 · 2025: 88 · 2024: 104 · 2023: 113 · 2022: 152 · 2021: 174 · 2020: 177 · 2019: 155 · 2018: 183 · 2017: 190 · 2016: 159 · 2015: 170 · 2014: 140 · 2013: 90 · 2012: 4
- FWCI
- 56.29
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Immunology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute on Drug Abuse (T32DA007135)
- National Cancer Institute (R01CA154947)
- National Institute of General Medical Sciences (P50GM071558, R01GM098316)
- National Institute of Allergy and Infectious Diseases (R01AI049653, R01AI046553, R01AI061741, R24AI072073)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK08854, P30DK020579)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › Immune cells in cancer
- Life Sciences › Immunology and Microbiology › Immunology › Phagocytosis and Immune Regulation
- Life Sciences › Immunology and Microbiology › Immunology › Atherosclerosis and Cardiovascular Diseases
- Keywords
- tissue macrophages, macrophage heterogeneity, gene expression profiling, macrophage identity, dendritic cells, MERTK, C/EBPα, BACH1, GATA6, mouse organs
- MeSH terms
- Animals, Cell Differentiation, Dendritic Cells, Gene Expression Regulation, Liver, Lung, Macrophages, Organ Specificity, RNA, Messenger, Spleen, Transcription Factors, Transcription, Genetic, Genetic Variation, Antigens, CD, Microglia, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
