[en] Tumor-associated macrophages (TAMs) are a heterogeneous population of cells whose phenotypes and functions are shaped by factors that are incompletely understood. Herein, we asked when and where TAMs arise from blood monocytes and how they evolve during tumor development. We initiated pancreatic ductal adenocarcinoma (PDAC) in inducible monocyte fate-mapping mice and combined single-cell transcriptomics and high-dimensional flow cytometry to profile the monocyte-to-TAM transition. We revealed that monocytes differentiate first into a transient intermediate population of TAMs that generates two longer-lived lineages of terminally differentiated TAMs with distinct gene expression profiles, phenotypes, and intratumoral localization. Transcriptome datasets and tumor samples from patients with PDAC evidenced parallel TAM populations in humans and their prognostic associations. These insights will support the design of new therapeutic strategies targeting TAMs in PDAC.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Dunsmore, Garett ; Université de Liège - ULiège > Département des sciences fonctionnelles (DSF) > Physiologie générale et des systèmes
Guo, Wei ; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
Li, Ziyi; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
Bejarano, David Alejandro ; Quantitative Systems Biology, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
Pai, Rhea; Curtin Medical School, Curtin University, Bentley, WA, Australia
De La Calle Fabregat, Carlos ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France
Yatim, Aline; Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
Bougouin, Antoine; Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC Université Paris Cité, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
Mulder, Kevin ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France ; Université Paris-Saclay, Ile-de-France, France
Thomas, Jake ; Quantitative Systems Biology, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
Villar, Javiera ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France
Bied, Mathilde; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France ; Université Paris-Saclay, Ile-de-France, France
Kloeckner, Benoit ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France ; Université Paris-Saclay, Ile-de-France, France
Dutertre, Charles-Antoine ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France
Gessain, Grégoire ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France
Chakarov, Svetoslav ; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
Liu, Zhaoyuan ; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
Scoazec, Jean-Yves ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France
Lennon-Dumenil, Ana-Maria ; Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
Marichal, Thomas ; Université de Liège - ULiège > GIGA > GIGA Immunobiology - Immunophysiology ; Walloon Excellence in Life Sciences and Biotechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
Sautès-Fridman, Catherine; Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC Université Paris Cité, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
Fridman, Wolf Herman ; Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC Université Paris Cité, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
Sharma, Ankur ; Curtin Medical School, Curtin University, Bentley, WA, Australia ; Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia ; Institute of Molecular and Cellular Biology, A*STAR, Singapore 138673, Singapore ; KK Research Centre, KK Women's and Children's Hospital, Singapore 229899, Singapore ; Translational Genomics Program, Garvan Institute of Medical Research and Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
Su, Bing ; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
Schlitzer, Andreas; Quantitative Systems Biology, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
Ng, Lai Guan ; Shanghai Immune Therapy Institute Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200010, China ; Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
Blériot, Camille ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France ; Institut Necker Enfants Malades (INEM), CNRS UMR 8253, INSERM U1151, 160 rue de Vaugirard, 75015 Paris, France
Ginhoux, Florent ; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France ; Université Paris-Saclay, Ile-de-France, France ; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China ; Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore ; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228 Singapore
We thank the W. S. Cheng laboratory for the use of the KPC pancreatic cancer model described here. We thank M. Lecuit laboratory for providing the Ccr2-KO mice. We thank the animal facilities in the Institute Gustave Roussy, Shanghai Jiao Tong University School of Medicine, and Singapore Immunology Network for ensuring that all protocols were performed within the appropriate ethical considerations. We thank the members of U1015 for helpful discussion. We thank L. Robinson for the invaluable input and editing of this manuscript. We thank the ARC Foundation (Recruiting International Leaders 2020) and Fondation Gustave Roussy for the financial support in this work. A.S. and D.A.B. were funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) under Germany\u2019s Excellence Strategy\u2013EXC2151\u2013390873048 (A.S. and D.A.B.) and the SFB 1454-P05-432325352 (A.S. and D.A.B.).Acknowledgments: We thank the W. S. cheng laboratory for the use of the KPc pancreatic cancer model described here. We thank m. lecuit laboratory for providing the ccr2-Ko mice. We thank the animal facilities in the institute gustave Roussy, Shanghai Jiao tong university School of medicine, and Singapore immunology network for ensuring that all protocols were performed within the appropriate ethical considerations. We thank the members of u1015 for helpful discussion. We thank l. Robinson for the invaluable input and editing of this manuscript. Funding: We thank the aRc Foundation (Recruiting international leaders 2020) and Fondation gustave Roussy for the financial support in this work. a.S. and D.a.B. were funded by the Deutsche Forschungsgemeinschaft (DFg; german Research Foundation) under germany\u2019s excellence Strategy\u2013eXc2151\u2013390873048 (a.S. and D.a.B.) and the SFB 1454-P05-432325352 (a.S. and D.a.B.). Author contributions: g.D., W.g., D.a.B., K.y., l.t., m.n., i.K., a.B., m.B., R.P., a.y., c.D.l.c.F., Z.l., S.c., and c.B. performed experimentation. g.D., Z.l., D.a.B., i.K., B.K., a.B., a.y., J.t., J.V., K.m., and c.B. performed formal analysis. Z.l., J.-y.S., and g.g. performed data curation. c.-a.D., S.c., Z.l., a.-m.l.-D., B.S., c.S.-F., W.h.F., a. Sharma, and a. Schlitzer provided invaluable advice. l.g.n., c.B., and F.g. supervised the project. c.B. and F.g. acquired funding for the project. g.D., c.B., and F.g. wrote the original draft of the paper. Competing interests: F.g. and c.B. are inventors on patent application (Pct/eP2024/060644) submitted by gustave Roussy hospital that covers detecting tams in pancreatic cancer. the other authors declare that they have no competing interests. Data and materials availability: all data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary materials. all generated scRna-seq data have been deposited in the ncBi gene expression omnibus under accession number gSe270793. tabulated data underlying the main figures are provided in data file S11. mouse models (Ms4a3Cre, Ms4a3CreERT2, and Trem2EGFP) are available upon request to F.g. after execution of a material transfer agreement with the Shanghai institute of immunology.
Y. Iwai, M. Ishida, Y. Tanaka, T. Okazaki, T. Honjo, N. Minato, Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade. Proc. Natl. Acad. Sci. U.S.A. 99, 12293–12297 (2002).
D. R. Leach, M. F. Krummel, J. P. Allison, Enhancement of antitumor immunity by CTLA-4 blockade. Science 271, 1734–1736 (1996).
C. Robert, G. V. Long, B. Brady, C. Dutriaux, M. Maio, L. Mortier, J. C. Hassel, P. Rutkowski, C. McNeil, E. Kalinka-Warzocha, K. J. Savage, M. M. Hernberg, C. Lebbé, J. Charles, C. Mihalcioiu, V. Chiarion-Sileni, C. Mauch, F. Cognetti, A. Arance, H. Schmidt, D. Schadendorf, H. Gogas, L. Lundgren-Eriksson, C. Horak, B. Sharkey, I. M. Waxman, V. Atkinson, P. A. Ascierto, Nivolumab in previously untreated melanoma without BRAF mutation. N. Engl. J. Med. 372, 320–330 (2015).
J. Bian, K. Almhanna, Pancreatic cancer and immune checkpoint inhibitors—still a long way to go. Transl. Gastroenterol. Hepatol. 6, 6 (2021).
M. D. Park, A. Silvin, F. Ginhoux, M. Merad, Macrophages in health and disease. Cell 185, 4259–4279 (2022).
A. Mantovani, F. Marchesi, A. Malesci, L. Laghi, P. Allavena, Tumour-associated macrophages as treatment targets in oncology. Nat. Rev. Clin. Oncol. 14, 399–416 (2017).
K. Mulder, A. A. Patel, W. T. Kong, C. Piot, E. Halitzki, G. Dunsmore, S. Khalilnezhad, S. E. Irac, A. Dubuisson, M. Chevrier, X. M. Zhang, J. K. C. Tam, T. K. H. Lim, R. M. M. Wong, R. Pai, A. I. S. Khalil, P. K. H. Chow, S. Z. Wu, G. al-Eryani, D. Roden, A. Swarbrick, J. K. Y. Chan, S. Albani, L. Derosa, L. Zitvogel, A. Sharma, J. Chen, A. Silvin, A. Bertoletti, C. Blériot, C. A. Dutertre, F. Ginhoux, Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease. Immunity 54, 1883–1900.e5 (2021).
S. Cheng, Z. Li, R. Gao, B. Xing, Y. Gao, Y. Yang, S. Qin, L. Zhang, H. Ouyang, P. du, L. Jiang, B. Zhang, Y. Yang, X. Wang, X. Ren, J. X. Bei, X. Hu, Z. Bu, J. Ji, Z. Zhang, A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells. Cell 184, 792–809.e23 (2021).
C. Bleriot, S. Chakarov, F. Ginhoux, Determinants of resident tissue macrophage identity and function. Immunity 52, 957–970 (2020).
F. Ginhoux, M. Guilliams, Tissue-resident macrophage ontogeny and homeostasis. Immunity 44, 439–449 (2016).
Y. Zhu, J. M. Herndon, D. K. Sojka, K. W. Kim, B. L. Knolhoff, C. Zuo, D. R. Cullinan, J. Luo, A. R. Bearden, K. J. Lavine, W. M. Yokoyama, W. G. Hawkins, R. C. Fields, G. J. Randolph, D. G. DeNardo, Tissue-resident macrophages in pancreatic ductal adenocarcinoma originate from embryonic hematopoiesis and promote tumor progression. Immunity 47, 323–338.e6 (2017).
M. Casanova-Acebes, E. Dalla, A. M. Leader, J. LeBerichel, J. Nikolic, B. M. Morales, M. Brown, C. Chang, L. Troncoso, S. T. Chen, A. Sastre-Perona, M. D. Park, A. Tabachnikova, M. Dhainaut, P. Hamon, B. Maier, C. M. Sawai, E. Agulló-Pascual, M. Schober, B. D. Brown, B. Reizis, T. Marron, E. Kenigsberg, C. Moussion, P. Benaroch, J. A. Aguirre-Ghiso, M. Merad, Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells. Nature 595, 578–584 (2021).
Z. Liu, Y. Gu, S. Chakarov, C. Bleriot, I. Kwok, X. Chen, A. Shin, W. Huang, R. J. Dress, C. A. Dutertre, A. Schlitzer, J. Chen, L. G. Ng, H. Wang, Z. Liu, B. Su, F. Ginhoux, Fate mapping via Ms4a3-expression history traces monocyte-derived cells. Cell 178, 1509–1525.e19 (2019).
R. Nalio Ramos, Y. Missolo-Koussou, Y. Gerber-Ferder, C. P. Bromley, M. Bugatti, N. G. Núñez, J. Tosello Boari, W. Richer, L. Menger, J. Denizeau, C. Sedlik, P. Caudana, F. Kotsias, L. L. Niborski, S. Viel, M. Bohec, S. Lameiras, S. Baulande, L. Lesage, A. Nicolas, D. Meseure, A. Vincent-Salomon, F. Reyal, C. A. Dutertre, F. Ginhoux, L. Vimeux, E. Donnadieu, B. Buttard, J. Galon, S. Zelenay, W. Vermi, P. Guermonprez, E. Piaggio, J. Helft, Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer. Cell 185, 1189–1207.e25 (2022).
A. Chow, S. Schad, M. D. Green, M. D. Hellmann, V. Allaj, N. Ceglia, G. Zago, N. S. Shah, S. K. Sharma, M. Mattar, J. Chan, H. Rizvi, H. Zhong, C. Liu, Y. Bykov, D. Zamarin, H. Shi, S. Budhu, C. Wohlhieter, F. Uddin, A. Gupta, I. Khodos, J. J. Waninger, A. Qin, G. J. Markowitz, V. Mittal, V. Balachandran, J. N. Durham, D. T. le, W. Zou, S. P. Shah, A. McPherson, K. Panageas, J. S. Lewis, J. S. A. Perry, E. de Stanchina, T. Sen, J. T. Poirier, J. D. Wolchok, C. M. Rudin, T. Merghoub, Tim-4+ cavity-resident macrophages impair anti-tumor CD8+ T cell immunity. Cancer Cell 39, 973–988.e9 (2021).
R. E. Menjivar, Z. C. Nwosu, W. du, K. L. Donahue, H. S. Hong, C. Espinoza, K. Brown, A. Velez-Delgado, W. Yan, F. Lima, A. Bischoff, P. Kadiyala, D. Salas-Escabillas, H. C. Crawford, F. Bednar, E. Carpenter, Y. Zhang, C. J. Halbrook, C. A. Lyssiotis, M. Pasca di Magliano, Arginase 1 is a key driver of immune suppression in pancreatic cancer. eLife 12, e80721 (2023).
L. Zhang, Z. Li, K. M. Skrzypczynska, Q. Fang, W. Zhang, S. A. O’Brien, Y. He, L. Wang, Q. Zhang, A. Kim, R. Gao, J. Orf, T. Wang, D. Sawant, J. Kang, D. Bhatt, D. Lu, C. M. Li, A. S. Rapaport, K. Perez, Y. Ye, S. Wang, X. Hu, X. Ren, W. Ouyang, Z. Shen, J. G. Egen, Z. Zhang, X. Yu, Single-cell analyses inform mechanisms of myeloid-targeted therapies in colon cancer. Cell 181, 442–459.e29 (2020).
E. Kerkelä, R. Ala-aho, P. Klemi, S. Grénman, S. D. Shapiro, V.-M. Kähäri, U. Saarialho-Kere, Metalloelastase (MMP-12) expression by tumour cells in squamous cell carcinoma of the vulva correlates with invasiveness, while that by macrophages predicts better outcome. J. Pathol. 198, 258–269 (2002).
E. Timperi, P. Gueguen, M. Molgora, I. Magagna, Y. Kieffer, S. Lopez-Lastra, P. Sirven, L. G. Baudrin, S. Baulande, A. Nicolas, G. Champenois, D. Meseure, A. Vincent-Salomon, A. Tardivon, E. Laas, V. Soumelis, M. Colonna, F. Mechta-Grigoriou, S. Amigorena, E. Romano, Lipid-associated macrophages are induced by cancer-associated fibroblasts and mediate immune suppression in breast cancer. Cancer Res. 82, 3291–3306 (2022).
D. A. Jaitin, L. Adlung, C. A. Thaiss, A. Weiner, B. Li, H. Descamps, P. Lundgren, C. Bleriot, Z. Liu, A. Deczkowska, H. Keren-Shaul, E. David, N. Zmora, S. M. Eldar, N. Lubezky, O. Shibolet, D. A. Hill, M. A. Lazar, M. Colonna, F. Ginhoux, H. Shapiro, E. Elinav, I. Amit, Lipid-associated macrophages control metabolic homeostasis in a Trem2-dependent manner. Cell 178, 686–698.e14 (2019).
V. Bergen, M. Lange, S. Peidli, F. A. Wolf, F. J. Theis, Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
K. Street, D. Risso, R. B. Fletcher, D. das, J. Ngai, N. Yosef, E. Purdom, S. Dudoit, Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
E. Becht, D. Tolstrup, C. A. Dutertre, P. A. Morawski, D. J. Campbell, F. Ginhoux, E. W. Newell, R. Gottardo, M. B. Headley, High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning. Sci. Adv. 7, eabg0505 (2021).
C. A. Dutertre, E. Becht, S. E. Irac, A. Khalilnezhad, V. Narang, S. Khalilnezhad, P. Y. Ng, L. L. van den Hoogen, J. Y. Leong, B. Lee, M. Chevrier, X. M. Zhang, P. J. A. Yong, G. Koh, J. Lum, S. W. Howland, E. Mok, J. Chen, A. Larbi, H. K. K. Tan, T. K. H. Lim, P. Karagianni, A. G. Tzioufas, B. Malleret, J. Brody, S. Albani, J. van Roon, T. Radstake, E. W. Newell, F. Ginhoux, Single-cell analysis of human mononuclear phagocytes reveals subset-defining markers and identifies circulating inflammatory dendritic cells. Immunity 51, 573–589.e8 (2019).
M. D. Park, I. Reyes-Torres, J. LeBerichel, P. Hamon, N. M. LaMarche, S. Hegde, M. Belabed, L. Troncoso, J. A. Grout, A. Magen, E. Humblin, A. Nair, M. Molgora, J. Hou, J. H. Newman, A. M. Farkas, A. M. Leader, T. Dawson, D. D’Souza, S. Hamel, A. R. Sanchez-Paulete, B. Maier, N. Bhardwaj, J. C. Martin, A. O. Kamphorst, E. Kenigsberg, M. Casanova-Acebes, A. Horowitz, B. D. Brown, L. F. de Andrade, M. Colonna, T. U. Marron, M. Merad, TREM2 macrophages drive NK cell paucity and dysfunction in lung cancer. Nat. Immunol. 24, 792–801 (2023).
M. Molgora, E. Esaulova, W. Vermi, J. Hou, Y. Chen, J. Luo, S. Brioschi, M. Bugatti, A. S. Omodei, B. Ricci, C. Fronick, S. K. Panda, Y. Takeuchi, M. M. Gubin, R. Faccio, M. Cella, S. Gilfillan, E. R. Unanue, M. N. Artyomov, R. D. Schreiber, M. Colonna, TREM2 modulation remodels the tumor myeloid landscape enhancing anti-PD-1 immunotherapy. Cell 182, 886–900.e17 (2020).
H. Keren-Shaul, A. Spinrad, A. Weiner, O. Matcovitch-Natan, R. Dvir-Szternfeld, T. K. Ulland, E. David, K. Baruch, D. Lara-Astaiso, B. Toth, S. Itzkovitz, M. Colonna, M. Schwartz, I. Amit, A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290.e17 (2017).
S. Aibar, C. B. González-Blas, T. Moerman, V. A. Huynh-Thu, H. Imrichova, G. Hulselmans, F. Rambow, J. C. Marine, P. Geurts, J. Aerts, J. van den Oord, Z. K. Atak, J. Wouters, S. Aerts, SCENIC: Single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
Y. Zhou, B. Zhou, L. Pache, M. Chang, A. H. Khodabakhshi, O. Tanaseichuk, C. Benner, S. K. Chanda, Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
S. Jin, C. F. Guerrero-Juarez, L. Zhang, I. Chang, R. Ramos, C. H. Kuan, P. Myung, M. V. Plikus, Q. Nie, Inference and analysis of cell-cell communication using CellChat. Nat. Commun. 12, 1088 (2021).
C. Baccin, J. al-Sabah, L. Velten, P. M. Helbling, F. Grünschläger, P. Hernández-Malmierca, C. Nombela-Arrieta, L. M. Steinmetz, A. Trumpp, S. Haas, Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization. Nat. Cell Biol. 22, 38–48 (2020).
M. S. F. Ng, I. Kwok, L. Tan, C. Shi, D. Cerezo-Wallis, Y. Tan, K. Leong, G. F. Calvo, K. Yang, Y. Zhang, J. Jin, K. H. Liong, D. Wu, R. He, D. Liu, Y. C. Teh, C. Bleriot, N. Caronni, Z. Liu, K. Duan, V. Narang, I. Ballesteros, F. Moalli, M. Li, J. Chen, Y. Liu, L. Liu, J. Qi, Y. Liu, L. Jiang, B. Shen, H. Cheng, T. Cheng, V. Angeli, A. Sharma, Y. H. Loh, H. L. Tey, S. Z. Chong, M. Iannacone, R. Ostuni, A. Hidalgo, F. Ginhoux, L. G. Ng, Deterministic reprogramming of neutrophils within tumors. Science 383, eadf6493 (2024).
E. Zhao, M. R. Stone, X. Ren, J. Guenthoer, K. S. Smythe, T. Pulliam, S. R. Williams, C. R. Uytingco, S. E. B. Taylor, P. Nghiem, J. H. Bielas, R. Gottardo, Spatial transcriptomics at subspot resolution with BayesSpace. Nat. Biotechnol. 39, 1375–1384 (2021).
Y. Goltsev, N. Samusik, J. Kennedy-Darling, S. Bhate, M. Hale, G. Vazquez, S. Black, G. P. Nolan, Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell 174, 968–981.e15 (2018).
W. L. Hwang, K. A. Jagadeesh, J. A. Guo, H. I. Hoffman, P. Yadollahpour, J. W. Reeves, R. Mohan, E. Drokhlyansky, N. van Wittenberghe, O. Ashenberg, S. L. Farhi, D. Schapiro, P. Divakar, E. Miller, D. R. Zollinger, G. Eng, J. M. Schenkel, J. Su, C. Shiau, P. Yu, W. A. Freed-Pastor, D. Abbondanza, A. Mehta, J. Gould, C. Lambden, C. B. M. Porter, A. Tsankov, D. Dionne, J. Waldman, M. S. Cuoco, L. Nguyen, T. Delorey, D. Phillips, J. L. Barth, M. Kem, C. Rodrigues, D. Ciprani, J. Roldan, P. Zelga, V. Jorgji, J. H. Chen, Z. Ely, D. Zhao, K. Fuhrman, R. Fropf, J. M. Beechem, J. S. Loeffler, D. P. Ryan, C. D. Weekes, C. R. Ferrone, M. Qadan, M. J. Aryee, R. K. Jain, D. S. Neuberg, J. Y. Wo, T. S. Hong, R. Xavier, A. J. Aguirre, O. Rozenblatt-Rosen, M. Mino-Kenudson, C. F. D. Castillo, A. S. Liss, D. T. Ting, T. Jacks, A. Regev, Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nat. Genet. 54, 1178–1191 (2022).
K. Chen, Y. Wang, Y. Hou, Q. Wang, D. Long, X. Liu, X. Tian, Y. Yang, Single cell RNA-seq reveals the CCL5/SDC1 receptor-ligand interaction between T cells and tumor cells in pancreatic cancer. Cancer Lett. 545, 215834 (2022).
N. G. Steele, E. S. Carpenter, S. B. Kemp, V. R. Sirihorachai, S. The, L. Delrosario, J. Lazarus, E. A. D. Amir, V. Gunchick, C. Espinoza, S. Bell, L. Harris, F. Lima, V. Irizarry-Negron, D. Paglia, J. Macchia, A. K. Y. Chu, H. Schofield, E. J. Wamsteker, R. Kwon, A. Schulman, A. Prabhu, R. Law, A. Sondhi, J. Yu, A. Patel, K. Donahue, H. Nathan, C. Cho, M. A. Anderson, V. Sahai, C. A. Lyssiotis, W. Zou, B. L. Allen, A. Rao, H. C. Crawford, F. Bednar, T. L. Frankel, M. Pasca di Magliano, Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer. Nat. Cancer 1, 1097–1112 (2020).
J. Peng, B. F. Sun, C. Y. Chen, J. Y. Zhou, Y. S. Chen, H. Chen, L. Liu, D. Huang, J. Jiang, G. S. Cui, Y. Yang, W. Wang, D. Guo, M. Dai, J. Guo, T. Zhang, Q. Liao, Y. Liu, Y. L. Zhao, D. L. Han, Y. Zhao, Y. G. Yang, W. Wu, Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res. 29, 725–738 (2019).
T. Stuart, A. Butler, P. Hoffman, C. Hafemeister, E. Papalexi, W. M. Mauck III, Y. Hao, M. Stoeckius, P. Smibert, R. Satija, Comprehensive integration of single-cell data. Cell 177, 1888–1902.e21 (2019).
F. A. Wolf, F. K. Hamey, M. Plass, J. Solana, J. S. Dahlin, B. Göttgens, N. Rajewsky, L. Simon, F. J. Theis, PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 59 (2019).
J. Villar, L. Ouaknin, A. Cros, E. Segura, Monocytes differentiate along two alternative pathways during sterile inflammation. EMBO Rep. 24, e56308 (2023).
A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert, M. A. Gillette, A. Paulovich, S. L. Pomeroy, T. R. Golub, E. S. Lander, J. P. Mesirov, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A. 102, 15545–15550 (2005).
V. K. Mootha, C. M. Lindgren, K. F. Eriksson, A. Subramanian, S. Sihag, J. Lehar, P. Puigserver, E. Carlsson, M. Ridderstråle, E. Laurila, N. Houstis, M. J. Daly, N. Patterson, J. P. Mesirov, T. R. Golub, P. Tamayo, B. Spiegelman, E. S. Lander, J. N. Hirschhorn, D. Altshuler, L. C. Groop, PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).
The Cancer Genome Atlas Program (TCGA) (National Cancer Institute’s Center for Cancer Genomics, 2023); www.cancer.gov/ccg/research/genome-sequencing/tcga.
V. Mysore, S. Tahir, K. Furuhashi, J. Arora, F. Rosetti, X. Cullere, P. Yazbeck, M. Sekulic, M. E. Lemieux, S. Raychaudhuri, B. H. Horwitz, T. N. Mayadas, Monocytes transition to macrophages within the inflamed vasculature via monocyte CCR2 and endothelial TNFR2. J. Exp. Med. 219, e20210562 (2022).
Y. Katzenelenbogen, F. Sheban, A. Yalin, I. Yofe, D. Svetlichnyy, D. A. Jaitin, C. Bornstein, A. Moshe, H. Keren-Shaul, M. Cohen, S. Y. Wang, B. Li, E. David, T. M. Salame, A. Weiner, I. Amit, Coupled scRNA-seq and intracellular protein activity reveal an immunosuppressive role of TREM2 in cancer. Cell 182, 872–885.e19 (2020).
A. T. Henze, M. Mazzone, The impact of hypoxia on tumor-associated macrophages. J. Clin. Invest. 126, 3672–3679 (2016).
R. Bill, P. Wirapati, M. Messemaker, W. Roh, B. Zitti, F. Duval, M. Kiss, J. C. Park, T. M. Saal, J. Hoelzl, D. Tarussio, F. Benedetti, S. Tissot, L. Kandalaft, M. Varrone, G. Ciriello, T. A. McKee, Y. Monnier, M. Mermod, E. M. Blaum, I. Gushterova, A. L. K. Gonye, N. Hacohen, G. Getz, T. R. Mempel, A. M. Klein, R. Weissleder, W. C. Faquin, P. M. Sadow, D. Lin, S. I. Pai, M. Sade-Feldman, M. J. Pittet, CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers. Science 381, 515–524 (2023).
A. Sebestyen, L. Kopper, T. Danko, J. Timar, Hypoxia signaling in cancer: From basics to clinical practice. Pathol. Oncol. Res. 27, 1609802 (2021).
C. Bleriot, G. Dunsmore, D. Alonso-Curbelo, F. Ginhoux, A temporal perspective for tumor-associated macrophage identities and functions. Cancer Cell 42, 747–758 (2024).
C. Bleriot, T. Dupuis, G. Jouvion, G. Eberl, O. Disson, M. Lecuit, Liver-resident macrophage necroptosis orchestrates type 1 microbicidal inflammation and type-2-mediated tissue repair during bacterial infection. Immunity 42, 145–158 (2015).
D. Vanneste, Q. Bai, S. Hasan, W. Peng, D. Pirottin, J. Schyns, P. Maréchal, C. Ruscitti, M. Meunier, Z. Liu, C. Legrand, L. Fievez, F. Ginhoux, C. Radermecker, F. Bureau, T. Marichal, MafB-restricted local monocyte proliferation precedes lung interstitial macrophage differentiation. Nat. Immunol. 24, 827–840 (2023).
H. L. Penny, J. L. Sieow, S. Y. Gun, M. C. Lau, B. Lee, J. Tan, C. Phua, F. Toh, Y. Nga, W. H. Yeap, B. Janela, D. Kumar, H. Chen, J. Yeong, J. A. Kenkel, A. Pang, D. Lim, H. C. Toh, T. L. K. Hon, C. I. Johnson, H. J. Khameneh, A. Mortellaro, E. G. Engleman, O. Rotzschke, F. Ginhoux, J. P. Abastado, J. Chen, S. C. Wong, Targeting glycolysis in macrophages confers protection against pancreatic ductal adenocarcinoma. Int. J. Mol. Sci. 22, 6350 (2021).
N. M. Aiello, A. D. Rhim, B. Z. Stanger, Orthotopic injection of pancreatic cancer cells. Cold Spring Harb. Protoc. 2016, pdb.prot078360 (2016).
Y. Hao, S. Hao, E. Andersen-Nissen, W. M. Mauck III, S. Zheng, A. Butler, M. J. Lee, A. J. Wilk, C. Darby, M. Zager, P. Hoffman, M. Stoeckius, E. Papalexi, E. P. Mimitou, J. Jain, A. Srivastava, T. Stuart, L. M. Fleming, B. Yeung, A. J. Rogers, J. M. McElrath, C. A. Blish, R. Gottardo, P. Smibert, R. Satija, Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski, S. Jha, P. Batut, M. Chaisson, T. R. Gingeras, STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
A. McDavid, G. Finak, P. K. Chattopadyay, M. Dominguez, L. Lamoreaux, S. S. Ma, M. Roederer, R. Gottardo, Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics 29, 461–467 (2013).
C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, C. Chen, X. Ren, Z. Zhang, SciBet as a portable and fast single cell type identifier. Nat. Commun. 11, 1818 (2020).
Z. Gu, L. Gu, R. Eils, M. Schlesner, B. Brors, circlize implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).
Z. Du, J.-R. Lin, R. Rashid, Z. Maliga, S. Wang, J. C. Aster, B. Izar, P. K. Sorger, S. Santagata, Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat. Protoc. 14, 2900–2930 (2019).
S. Hanzelmann, R. Castelo, J. Guinney, GSVA: Gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 14, 7 (2013).
P. Bankhead, M. B. Loughrey, J. A. Fernández, Y. Dombrowski, D. G. McArt, P. D. Dunne, S. McQuaid, R. T. Gray, L. J. Murray, H. G. Coleman, J. A. James, M. Salto-Tellez, P. W. Hamilton, QuPath: Open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).
J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, A. Cardona, Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
