Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease

Integrated analysis of multimodal single-cell data

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Comprehensive Integration of Single-Cell Data

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UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

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Scenic: single-cell regulatory network inference and clustering.

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Dimensionality reduction for visualizing single-cell data using UMAP

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Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages

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Full-length RNA-seq from single cells using Smart-seq2

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Blood Monocytes Consist of Two Principal Subsets with Distinct Migratory Properties

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Tumour-educated macrophages promote tumour progression and metastasis

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M-1/M-2 Macrophages and the Th1/Th2 Paradigm

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Lactation-associated macrophages exist in murine mammary tissue and human milk

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Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma

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Cancer cell-derived type I interferons instruct tumor monocyte polarization

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Inflammatory and immune etiology of type 2 diabetes

Blériot, C., Dalmas, É., Ginhoux, F., & Venteclef, N. (2023) · Trends in Immunology · doi:10.1016/j.it.2022.12.004 · Cited by 53

Intercellular interaction between FAP+ fibroblasts and CD150+ inflammatory monocytes mediates fibrostenosis in Crohn’s disease

Ke, B.-J., Abdurahiman, S., Biscu, F., Zanella, G., Dragoni, G., Santhosh, S., Simone, V. D., Zouzaf, A., van Baarle, L., Stakenborg, M., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci173835 · Cited by 56

Single-Cell RNA Sequencing Reveals a Distinct Immune Landscape of Myeloid Cells in Coronary Culprit Plaques Causing Acute Coronary Syndrome

Emoto, T., Yamamoto, H., Yamashita, T., Takaya, T., Sawada, T., Takeda, S., Taniguchi, M., Sasaki, N., Yoshida, N., Saito, Y., et al. (2022) · Circulation · doi:10.1161/circulationaha.121.058414 · Cited by 51

High-Resolution Analysis of Mononuclear Phagocytes Reveals GPNMB as a Prognostic Marker in Human Colorectal Liver Metastasis

Cortese, N., Carriero, R., Barbagallo, M., Putignano, A. R., Costa, G., Giavazzi, F., Grizzi, F., Pasqualini, F., Peano, C., Basso, G., et al. (2023) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-22-0462 · Cited by 56

Macrophage and monocyte subsets as new therapeutic targets in cancer immunotherapy

Fendl, B., Berghoff, A. S., Preusser, M., & Maier, B. (2023) · ESMO Open · doi:10.1016/j.esmoop.2022.100776 · Cited by 49

Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours

Hegde, S., Giotti, B., Soong, B. Y., Halász, L., Bérichel, J. L., Schaefer, M. M., Kloeckner, B., Mattiuz, R., Park, M. D., Magen, A., et al. (2025) · Nature · doi:10.1038/s41586-025-09493-y · Cited by 52

Immunosuppressive landscape in hepatocellular carcinoma revealed by single-cell sequencing

Bai, Y., Chen, D., Cheng, C., Li, Z., Chi, H., Zhang, Y., Zhang, X., Tang, S., Zhao, Q., Zhang, Y., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.950536 · Cited by 52

Single-cell and spatially resolved transcriptomics for liver biology

Lin, P., Yan, X., Jing, S., Wu, Y., Shan, Y., Guo, W., Gu, J., Li, Y., Zhang, H., & Li, H. (2023) · Hepatology · doi:10.1097/hep.0000000000000387 · Cited by 56

Targeting metabolic-epigenetic-immune axis in cancer: molecular mechanisms and therapeutic implications

Wang, X., Luo, X., Xiao, R., Liu, X., Zhou, F., Jiang, D., Bai, J., Cui, M., You, L., & Yupei, Z. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-025-02334-4 · Cited by 59

Macrophage states: there's a method in the madness

Katkar, G. D., & Ghosh, P. (2023) · Trends in Immunology · doi:10.1016/j.it.2023.10.006 · Cited by 52

At the Interface of Tumor-Associated Macrophages and Fibroblasts: Immune-Suppressive Networks and Emerging Exploitable Targets

Timperi, E., Croizer, H., Khantakova, D., Rana, M., Molgora, M., Guerriero, J. L., Mechta-Grigoriou, F., & Romano, E. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-24-1690 · Cited by 49

Neuronal CaMKK2 promotes immunosuppression and checkpoint blockade resistance in glioblastoma

Tomaszewski, W. H., Polania, J. W., Chakraborty, M. A., Perera, J., Ratiu, J. J., Hoyt-Miggelbrink, A. M., McDonnell, D. P., Khasraw, M., Ashley, D. M., Fecci, P. E., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34175-y · Cited by 48

Microglia and macrophages in glioblastoma: landscapes and treatment directions

Solomou, G., Young, A. M. H., & Bulstrode, H. J. C. J. (2024) · Molecular Oncology · doi:10.1002/1878-0261.13657 · Cited by 54

Neoadjuvant Therapy Induces a Potent Immune Response to Sarcoma, Dominated by Myeloid and B Cells

Goff, P. H., Riolobos, L., LaFleur, B., Spraker, M. B., Seo, Y. D., Smythe, K. S., Campbell, J. S., Pierce, R. H., Zhang, Y., He, Q., et al. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-4239 · Cited by 49

NF-κB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironment

de la Calle‐Fabregat, C., Calafell-Segura, J., Gardet, M., Dunsmore, G., Mulder, K., Ciudad, L., Silvin, A., Moreno‐Càceres, J., Corbí, A. L., Muñoz‐Pinedo, C., et al. (2024) · Science Advances · doi:10.1126/sciadv.adq5226 · Cited by 48

A Population of TIM4+FOLR2+ Macrophages Localized in Tertiary Lymphoid Structures Correlates to an Active Immune Infiltrate Across Several Cancer Types

Bugatti, M., Bergamini, M., Missale, F., Monti, M., Ardighieri, L., Pezzali, I., Picinoli, S., Caronni, N., Missolo-Koussou, Y., Helft, J., et al. (2022) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-22-0271 · Cited by 45

Vax-Innate: improving therapeutic cancer vaccines by modulating T cells and the tumour microenvironment

Baharom, F., Hermans, D., Delamarre, L., & Seder, R. A. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01091-9 · Cited by 47

ZEB2 is a master switch controlling the tumor-associated macrophage program

Sheban, F., Phan, T. S., Xie, K., Ingelfinger, F., Gur, C., Itai, Y. S., Blecher‐Gonen, R., Yu, C., Avellino, R., Chalan, P., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.03.021 · Cited by 50

Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census

Wei, C., Ma, Y., Wang, M., Wang, S., Yu, W., Dong, S., Deng, W., Bie, L., Zhang, C., Shen, W., et al. (2024) · npj Precision Oncology · doi:10.1038/s41698-024-00660-4 · Cited by 55

Immunogenomic cancer evolution: A framework to understand cancer immunosuppression

Kumagai, S., Momoi, Y., & Nishikawa, H. (2025) · Science Immunology · doi:10.1126/sciimmunol.abo5570 · Cited by 46

A single-cell pan-cancer analysis to show the variability of tumor-infiltrating myeloid cells in immune checkpoint blockade

Li, W., Pan, L., Hong, W., Ginhoux, F., Zhang, X., Xiao, C., & Li, X. (2024) · Nature Communications · doi:10.1038/s41467-024-50478-8 · Cited by 46

Knee Alignment Correction by High Tibial Osteotomy Reduces Symptoms and Synovial Inflammation in Knee Osteoarthritis Accompanied by Macrophage Phenotypic Change From M1 to M2

Yoshida, S., Nishitani, K., Yoshitomi, H., Kuriyama, S., Nakamura, S., Fujii, T., Saito, M., Kobori, Y., Murakami, A., Murata, K., et al. (2022) · Arthritis & Rheumatology · doi:10.1002/art.42424 · Cited by 41

The multifaceted role of macrophages in homeostatic and injured skeletal muscle

Wang, X., & Zhou, L. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1274816 · Cited by 45

CSF1R-dependent macrophages in the salivary gland are essential for epithelial regeneration after radiation-induced injury

McKendrick, J. G., Jones, G., Elder, S. S., Watson, E. E., T’Jonck, W., Mercer, E., Pinto, M. M., Rocchi, C., Hegarty, L. M., Johnson, A. L., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.add4374 · Cited by 45

Advanced insights on tumor-associated macrophages revealed by single-cell RNA sequencing: The intratumor heterogeneity, functional phenotypes, and cellular interactions

Yang, S., Wang, M., Hua, Y., Li, J., Zheng, H., Cui, M., Huang, N., Liu, Q., & Liao, Q. (2024) · Cancer Letters · doi:10.1016/j.canlet.2024.216610 · Cited by 43

TREM2 is associated with tumor immunity and implies poor prognosis in glioma

Yu, M., Chang, Y., Zhai, Y., Pang, B., Wang, P., Li, G., Jiang, T., & Zeng, F. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1089266 · Cited by 40

Spatial dimension of macrophage heterogeneity in liver diseases

Guillot, A., & Tacke, F. (2023) · eGastroenterology · doi:10.1136/egastro-2023-000003 · Cited by 40

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

Heimberg, G., Kuo, T., DePianto, D., Heigl, T., Diamant, N., Salem, O., Scalia, G., Biancalani, T., Turley, S., Rock, J., et al. (2023) · doi:10.1101/2023.07.18.549537 · Cited by 40

Blockade of purine metabolism reverses macrophage immunosuppression and enhances anti-tumor immunity in non-small cell lung cancer

Yang, L., Li, A., Yu, W., Wang, H., Zhang, L., Wang, Y., Wang, Y., Zhang, R., Lei, Q., Liu, Z., et al. (2024) · Drug Resistance Updates · doi:10.1016/j.drup.2024.101175 · Cited by 40

Spatial and molecular profiling of the mononuclear phagocyte network in Classic Hodgkin lymphoma

Stewart, B. J., Fergie, M., Young, M. D., Jones, C., Sachdeva, A., Blain, A. E., Bacon, C. M., Rand, V., Ferdinand, J. R., James, K. R., et al. (2023) · Blood · doi:10.1182/blood.2022015575 · Cited by 39

Dynamic CD8+ T Cell Cooperation with Macrophages and Monocytes for Successful Cancer Immunotherapy

Vermare, A., Guérin, M. V., Peranzoni, E., & Bercovici, N. (2022) · Cancers · doi:10.3390/cancers14143546 · Cited by 42

Metabolism in type 2 immune responses

Kabat, A. M., Pearce, E. L., & Pearce, E. J. (2023) · Immunity · doi:10.1016/j.immuni.2023.03.007 · Cited by 37

Immune cell networking in solid tumors: focus on macrophages and neutrophils

Ceglie, I. D., Carnevale, S., Rigatelli, A., Grieco, G., Molisso, P., & Jaillon, S. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1341390 · Cited by 38

New insight into arginine and tryptophan metabolism in macrophage activation during tuberculosis

Zhang, K., Mishra, A., & Jagannath, C. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1363938 · Cited by 40

SPP1 macrophages in colorectal cancer: Markers of malignancy and promising therapeutic targets

Xie, Z., Zheng, G., Niu, L., Du, K., Li, R., Dan, H., Duan, L., Wu, H., Ren, G., Dou, X., et al. (2024) · Genes & Diseases · doi:10.1016/j.gendis.2024.101340 · Cited by 37

Single-cell transcriptional atlas of tumor-associated macrophages in breast cancer

Zhang, Y., Zhong, F., & Liu, L. (2024) · Breast Cancer Research · doi:10.1186/s13058-024-01887-6 · Cited by 43

A pancreatic cancer organoid incorporating macrophages reveals the correlation between the diversity of tumor-associated macrophages and cancer cell survival

Tabe, S., Takeuchi, K., Aoshima, K., Okumura, A., Yamamoto, Y., Yanagisawa, K., Eto, R., Matsuo, M., Ueno, Y., Konishi, T., et al. (2024) · Biomaterials · doi:10.1016/j.biomaterials.2024.122838 · Cited by 37

Tumor-associated macrophages: Prognostic and therapeutic targets for cancer in humans and dogs

Brady, R. V., & Thamm, D. H. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1176807 · Cited by 35

Asiaticoside promoted ferroptosis and suppressed immune escape in gastric cancer cells by downregulating the Wnt/β-catenin pathway

Ye, C., Yao, Z., Wang, Y., & Zhang, C. (2024) · International Immunopharmacology · doi:10.1016/j.intimp.2024.112175 · Cited by 35

NK Cell Anti-Tumor Surveillance in a Myeloid Cell-Shaped Environment

Russo, E., Laffranchi, M., Tomaipitinca, L., Prete, A. D., Santoni, A., Sozzani, S., & Bernardini, G. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.787116 · Cited by 36

Approaches for studying human macrophages

Bao, Y., Wang, G., & Li, H. (2024) · Trends in Immunology · doi:10.1016/j.it.2024.02.007 · Cited by 38

Integrated metabolic-transcriptomic network identifies immunometabolic modulations in human macrophages

Chen, H., Sévin, D. C., Griffith, G. R., Vappiani, J., Booty, L. M., van Roomen, C. P. A. A., Kuiper, J., den Dunnen, J., de Jonge, W. J., Prinjha, R. K., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114741 · Cited by 35

IL-1β+ macrophages and the control of pathogenic inflammation in cancer

Caronni, N., Terza, F. L., Frosio, L., & Ostuni, R. (2025) · Trends in Immunology · doi:10.1016/j.it.2025.03.001 · Cited by 36

Intrahepatic inflammatory IgA + PD-L1 high monocytes in hepatocellular carcinoma development and immunotherapy

Sung, P. S., Park, D. J., Roh, P. R., Mun, K. D., Cho, S. W., Lee, G. W., Jung, E. S., Lee, S. H., Jang, J. W., Bae, S. H., et al. (2022) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2021-003618 · Cited by 33

Dynamic polarization of tumor-associated macrophages and their interaction with intratumoral T cells in an inflamed tumor microenvironment: from mechanistic insights to therapeutic opportunities

Han, J., Dong, L., Wu, M., & Ma, F. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1160340 · Cited by 36

The lifespan and kinetics of human dendritic cell subsets and their precursors in health and inflammation

Lubin, R., Patel, A. A., Mackerodt, J., Zhang, Y., Gvili, R., Mulder, K., Dutertre, C., Jalali, P., Glanville, J., Hazan, I., et al. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20220867 · Cited by 32

Immune Microenvironment and the Effect of Vascular Endothelial Growth Factor Inhibition in Hepatocellular Carcinoma

Oura, K., Morishita, A., Tadokoro, T., Fujita, K., Tani, J., & Kobara, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252413590 · Cited by 35

Spatiotemporal analyses of the pan-cancer single-cell landscape reveal widespread profibrotic ecotypes associated with tumor immunity

Han, Y., Zhang, L., Sun, D., Cao, G., Wang, Y., Yue, J., Hu, J., Dong, Z., Li, F., Li, T., et al. (2025) · Nature Cancer · doi:10.1038/s43018-025-01039-5 · Cited by 40

Functional diversity of disorder-specific macrophages involved in various diseases

Mitsui, Y., & Satoh, T. (2025) · Inflammation and Regeneration · doi:10.1186/s41232-025-00390-5 · Cited by 37

Heterogeneity of glioblastoma stem cells in the context of the immune microenvironment and geospatial organization

Silver, A., Feier, D., Ghosh, T., Rahman, M., Huang, J., Sarkisian, M. R., & Deleyrolle, L. P. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.1022716 · Cited by 36

Indoleamine 2,3-dioxygenase 1 in circumventing checkpoint inhibitor responses: Updated

Charehjoo, A., Majidpoor, J., & Mortezaee, K. (2023) · International Immunopharmacology · doi:10.1016/j.intimp.2023.110032 · Cited by 33

Regulation of tumor angiogenesis by the crosstalk between innate immunity and endothelial cells

Ebeling, S., Kowalczyk, A., Pérez-Vázquez, D., & Mattiola, I. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1171794 · Cited by 34

Targeting amino acid-metabolizing enzymes for cancer immunotherapy

Grobben, Y. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1440269 · Cited by 35

Spatial architecture of development and disease

Lázár, E., & Lundeberg, J. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00892-5 · Cited by 38

Differential regulation of TNFα and IL-6 expression contributes to immune evasion in prostate cancer

Deichaite, I., Sears, T. J., Sutton, L., Rebibo, D., Morgan, K. M., Nelson, T. J., Rose, B. S., Tamayo, P., Ferrara, N., Asimakopoulos, F. A., et al. (2022) · Journal of Translational Medicine · doi:10.1186/s12967-022-03731-x · Cited by 33

Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea

Cortese, R., Adams, T. S., Cataldo, K., Hummel, J. J., Kaminski, N., Gozal, D., & Gozal, D. (2022) · European Respiratory Journal · doi:10.1183/13993003.01465-2022 · Cited by 31

Batf3+ DCs and the 4-1BB/4-1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy

Ziblat, A., Horton, B. L., Higgs, E. F., Hatogai, K., Martinez, A., Shapiro, J. W., Kim, D. E., Zha, Y., Sweis, R. F., & Gajewski, T. F. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114141 · Cited by 31

Lipid-associated macrophages for osimertinib resistance and leptomeningeal metastases in NSCLC

Li, Y.-S., Lai, W., Yin, K., Zheng, M.-M., Tu, H., Guo, W., Li, L., Lin, S., Wang, Z., Zeng, L., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114613 · Cited by 34

Single-cell RNA sequencing highlights the immunosuppression of IDO1+ macrophages in the malignant transformation of oral leukoplakia

Zhang, Y., Zhang, J., Zhao, S., Xu, Y., Huang, Y., Liu, S., Su, P., Wang, C., Li, Y., Li, H., et al. (2024) · Theranostics · doi:10.7150/thno.99112 · Cited by 32

Embryonic macrophages support endocrine commitment during human pancreatic differentiation

Migliorini, A., Ge, S., Atkins, M. H., Oakie, A., Sambathkumar, R., Kent, G., Huang, H., Sing, A., Chua, C., Gehring, A. J., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.09.011 · Cited by 36

Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF

Kvedaraite, E., Lourda, M., Mouratidou, N., Düking, T., Padhi, A., Moll, K., Czarnewski, P., Sinha, I., Xagoraris, I., Kokkinou, E., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46076-3 · Cited by 30

Rebuilding the microenvironment of primary tumors in humans: a focus on stroma

Mun, S., Lee, H. J., & Kim, P. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01191-5 · Cited by 31

Phenotypic heterogeneity and plasticity in colorectal cancer metastasis

Ogden, S., Metic, N., Leylek, O., Smith, E. A., Berner, A., Baker, A., Uddin, I., Buzzetti, M., Gerlinger, M., Graham, T. A., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100881 · Cited by 36

Integrated transcriptional analysis reveals macrophage heterogeneity and macrophage-tumor cell interactions in the progression of pancreatic ductal adenocarcinoma

Yang, K., Yang, T., Yu, J. C., Li, F., & Zhao, X. (2023) · BMC Cancer · doi:10.1186/s12885-023-10675-y · Cited by 31

Beyond the Complement Cascade: Insights into Systemic Immunosenescence and Inflammaging in Age-Related Macular Degeneration and Current Barriers to Treatment

Khan, A. H., Chowers, I., & Lotery, A. J. (2023) · Cells · doi:10.3390/cells12131708 · Cited by 31

Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritisPreprint

Zhang, F., Jonsson, A. H., Nathan, A., Wei, K., Millard, N., Xiao, Q., Gutiérrez‐Arcelus, M., Apruzzese, W. A., Watts, G. F. M., Weisenfeld, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.25.481990 · Cited by 30

Pro-Fibrotic Macrophage Subtypes: SPP1+ Macrophages as a Key Player and Therapeutic Target in Cardiac Fibrosis?

Uhlig, M., Billig, S., Wienhold, J., & Schumacher, D. (2025) · Cells · doi:10.3390/cells14050345 · Cited by 29

Macrophage Cx43 Is Necessary for Fibroblast Cytosolic Calcium and Lung Fibrosis After Injury

Bhattacharyya, A., Torre, P., Yadav, P., Boostanpour, K., Chen, T. Y., Tsukui, T., Sheppard, D., Muramatsu, R., Seed, R., Nishimura, S. L., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.880887 · Cited by 30

Leveraging macrophage metabolism for anticancer therapy: opportunities and pitfalls

Saha, P., Ettel, P., & Weichhart, T. (2024) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2024.02.005 · Cited by 33

Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn’s disease

Levantovsky, R. M., Tastad, C., Zhang, J., Gettler, K., Sabic, K., Werner, R., Chasteau, C., Korie, U. M., Paguay, D., Bao, M., et al. (2024) · Med · doi:10.1016/j.medj.2024.03.021 · Cited by 30

CSF1R+ myeloid-monocytic cells drive CAR-T cell resistance in aggressive B cell lymphoma

Stahl, D. J., Gödel, P., Balke‐Want, H., Gholamipoorfard, R., Segbers, P., Tetenborg, L., Koker, M., Dörr, J., Gregor, L., Bachurski, D., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.05.013 · Cited by 37

Spatially resolved C1QC+ macrophage-CD4+ T cell niche in colorectal cancer microenvironment: implications for immunotherapy response

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ABC portal: a single-cell database and web server for blood cells

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