Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A cardioimmunologist’s toolkit: genetic tools to dissect immune cells in cardiac disease

Abstract

Cardioimmunology is a field that encompasses the immune cells and pathways that modulate cardiac function in homeostasis and regulate the temporal balance between tissue injury and repair in disease. Over the past two decades, genetic fate mapping and high-dimensional sequencing techniques have defined increasing functional heterogeneity of innate and adaptive immune cell populations in the heart and other organs, revealing a complexity not previously appreciated and challenging established frameworks for the immune system. Given these rapid advances, understanding how to use these tools has become crucial. However, cardiovascular biologists without immunological expertise might not be aware of the strengths and caveats of immune-related tools and how they can be applied to examine the pathogenesis of myocardial diseases. In this Review, we guide readers through case-based examples to demonstrate how tool selection can affect data quality and interpretation and we provide critical analysis of the experimental tools that are currently available, focusing on their use in models of ischaemic heart injury and heart failure. The goal is to increase the use of relevant immunological tools and strategies among cardiovascular researchers to improve the precision, translatability and consistency of future studies of immune cells in cardiac disease.

Key points

  • Various tissue-resident interstitial immune cell populations live in the heart and promote homeostatic functions.

  • Resident cardiac immune cells are not homogeneous and often contain subpopulations with different lifecycles dictated by a balance between in situ proliferation, cell death and replacement by circulating precursors.

  • Unique lifecycles often predict unique origins, transcriptional signatures and functions; understanding how to target these levels of heterogeneity can reveal novel mechanisms of disease pathogenesis.

  • We present a detailed case study summarizing the latest advances in cardioimmunology to provide context and explanation to guide readers without an immunological background through novel targeting and cell tracking approaches.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: The M1/M2 paradigm conflates macrophage heterogeneity.
Fig. 2: Reciprocal bone marrow chimeras to assess intrinsic or extrinsic effects of immune cells.
Fig. 3: Probing immune cell transcriptomic data sets.
Fig. 4: Isolation of immune cell subsets and characterization of gene expression.

References

  1. Abbafati, C. et al. Global burden of 87 risk factors in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet 396, 1223–1249 (2020).

    Article  Google Scholar 

  2. Adamo, L., Rocha-Resende, C., Prabhu, S. D. & Mann, D. L. Reappraising the role of inflammation in heart failure. Nat. Rev. Cardiol. 17, 269–285 (2020).

    PubMed  Article  Google Scholar 

  3. Epelman, S., Liu, P. P. & Mann, D. L. Role of innate and adaptive immune mechanisms in cardiac injury and repair. Nat. Rev. Immunol. 15, 117–129 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  4. Skelly, D. A. et al. Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart. Cell Rep. 22, 600–610 (2018).

    CAS  PubMed  Article  Google Scholar 

  5. Jin, K. et al. Single-cell RNA sequencing reveals the temporal diversity and dynamics of cardiac immunity after myocardial infarction. Small Methods 6, e2100752 (2022).

    PubMed  Article  CAS  Google Scholar 

  6. Villani, A. C. et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356, eaah4573 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  7. Suffiotti, M., Carmona, S. J., Jandus, C. & Gfeller, D. Identification of innate lymphoid cells in single-cell RNA-Seq data. Immunogenetics 69, 439–450 (2017).

    CAS  PubMed  Article  Google Scholar 

  8. Martini, E. et al. Single-cell sequencing of mouse heart immune infiltrate in pressure overload-driven heart failure reveals extent of immune activation. Circulation 140, 2089–2107 (2019).

    CAS  PubMed  Article  Google Scholar 

  9. Schlitzer, A. et al. Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat. Immunol. 16, 718–728 (2015).

    CAS  PubMed  Article  Google Scholar 

  10. Mills, C. D., Kincaid, K., Alt, J. M., Heilman, M. J. & Hill, A. M. M-1/M-2 macrophages and the Th1/Th2 paradigm. J. Immunol. 164, 6166–6173 (2000).

    CAS  PubMed  Article  Google Scholar 

  11. Mantovani, A., Sozzani, S., Locati, M., Allavena, P. & Sica, A. Macrophage polarization: tumor-associated macrophages as a paradigm for polarized M2 mononuclear phagocytes. Trends Immunol. 23, 549–555 (2002).

    CAS  PubMed  Article  Google Scholar 

  12. Nahrendorf, M. & Swirski, F. K. Abandoning M1/M2 for a network model of macrophage function. Circ. Res. 119, 414–417 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. Martinez, F. O. & Gordon, S. The M1 and M2 paradigm of macrophage activation: time for reassessment. F1000Prime Rep. 6, 13 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  14. Zaman, R., Hamidzada, H. & Epelman, S. Exploring cardiac macrophage heterogeneity in the healthy and diseased myocardium. Curr. Opin. Immunol. 68, 54–63 (2021).

    CAS  PubMed  Article  Google Scholar 

  15. Raggi, F. et al. Regulation of human macrophage M1-M2 polarization balance by hypoxia and the triggering receptor expressed on myeloid cells-1. Front. Immunol. 8, 1097 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  16. Xu, Z. J. et al. The M2 macrophage marker CD206: a novel prognostic indicator for acute myeloid leukemia. Oncoimmunology 9, 1683347 (2020).

    PubMed  Article  Google Scholar 

  17. Kim, Y., Nurakhayev, S., Nurkesh, A., Zharkinbekov, Z. & Saparov, A. Macrophage polarization in cardiac tissue repair following myocardial infarction. Int. J. Mol. Sci. 22, 2715 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. Ruytinx, P., Proost, P., Van Damme, J. & Struyf, S. Chemokine-induced macrophage polarization in inflammatory conditions. Front. Immunol. 9, 1930 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  19. Dick, S. A. et al. Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction. Nat. Immunol. 20, 29–39 (2019).

    CAS  PubMed  Article  Google Scholar 

  20. Dick, S. A. et al. Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles. Sci. Immunol. 7, eabf7777 (2022).

    CAS  PubMed  Article  Google Scholar 

  21. Zaman, R. et al. Selective loss of resident macrophage-derived insulin-like growth factor-1 abolishes adaptive cardiac growth to stress. Immunity 54, 2057–2071.e6 (2021).

    CAS  PubMed  Article  Google Scholar 

  22. Bajpai, G. et al. Tissue resident CCR2- and CCR2+ cardiac macrophages differentially orchestrate monocyte recruitment and fate specification following myocardial injury. Circ. Res. 124, 263–278 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. Bajpai, G. et al. The human heart contains distinct macrophage subsets with divergent origins and functions. Nat. Med. 24, 1234–1245 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. Jin, K., Yang, P. & Guo, R. Single-cell RNA sequencing reveals the temporal diversity and dynamics of cardiac immunity after myocardial infarction. Small Methods https://doi.org/10.1002/smtd.202100752 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Ni, S.-H. et al. Single-cell transcriptomic analyses of cardiac immune cells reveal that Rel-driven CD72-positive macrophages induce cardiomyocyte injury. Cardiovasc. Res. https://doi.org/10.1093/cvr/cvab193 (2021).

    Article  PubMed  Google Scholar 

  26. Calcagno, D. M. et al. The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-acivated macrophages. Sci. Immunol. 5, eaaz1974 (2021).

    Article  CAS  Google Scholar 

  27. King, K. R. et al. IRF3 and type i interferons fuel a fatal response to myocardial infarction. Nat. Med. 23, 1481–1487 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  29. Lavin, Y. et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 159, 1312–1326 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. Gosselin, D. et al. An environment-dependent transcriptional network specifies human microglia identity. Science 356, 1248–1259 (2017).

    CAS  Article  Google Scholar 

  31. Sakai, M. et al. Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain kupffer cell identity. Immunity 51, 655–670.e8 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  32. Sajti, E. et al. Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung. Nat. Immunol. 21, 221–231 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  33. Schneider, C. et al. Tissue-resident group 2 innate lymphoid cells differentiate by layered ontogeny and in situ perinatal priming. Immunity 50, 1425–1438.e5 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. Ballesteros, I. et al. Co-option of neutrophil fates by tissue environments. Cell 183, 1282–1297.e18 (2020).

    CAS  PubMed  Article  Google Scholar 

  35. Poss, K. D., Wilson, L. G. & Keating, M. T. Heart regeneration in zebrafish. Science 298, 2188–2190 (2002).

    CAS  PubMed  Article  Google Scholar 

  36. Laube, F., Heister, M., Scholz, C., Borchardt, T. & Braun, T. Re-programming of newt cardiomyocytes is induced by tissue regeneration. J. Cell Sci. 119, 4719–4729 (2006).

    CAS  PubMed  Article  Google Scholar 

  37. Godwin, J. W., Pinto, A. R. & Rosenthal, N. A. Macrophages are required for adult salamander limb regeneration. Proc. Natl Acad. Sci. USA 110, 9415–9420 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. Aurora, A. B. et al. Macrophages are required for neonatal heart regeneration. J. Clin. Invest. 124, 1382–1392 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. Lavine, K. J. et al. Distinct macrophage lineages contribute to disparate patterns of cardiac recovery and remodeling in the neonatal and adult heart. Proc. Natl Acad. Sci. USA 111, 16029–16034 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. Pinto, A. R. et al. An abundant tissue macrophage population in the adult murine heart with a distinct alternatively-activated macrophage profile. PLoS One 7, e36814 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. Swirski, F. K. & Nahrendorf, M. Leukocyte behavior in atherosclerosis, myocardial infarction, and heart failure. Science 339, 161–166 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. Chakarov, S. et al. Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches. Science 363, eaau0964 (2019).

    CAS  PubMed  Article  Google Scholar 

  43. Litviňuková, M. et al. Cells of the adult human heart. Nature 588, 466–472 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  44. Epelman, S., Lavine, K. J. & Randolph, G. J. Origin and functions of tissue macrophages. Immunity 41, 21–35 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  45. Li, Q. & Barres, B. A. Microglia and macrophages in brain homeostasis and disease. Nat. Rev. Immunol. 18, 225–242 (2018).

    CAS  PubMed  Article  Google Scholar 

  46. Borges Da Silva, H. et al. Splenic macrophage subsets and their function during blood-borne infections. Front. Immunol. 6, 480 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  47. Nicolás-Ávila, J. A. et al. A network of macrophages supports mitochondrial homeostasis in the heart. Cell 183, 94–109.e23 (2020).

    PubMed  Article  CAS  Google Scholar 

  48. Hulsmans, M. et al. Macrophages facilitate electrical conduction in the heart. Cell 169, 510–522.e20 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. Leid, J. et al. Primitive embryonic macrophages are required for coronary development and maturation. Circ. Res. 118, 1498–1511 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. Cahill, T. J. et al. Tissue-resident macrophages regulate lymphatic vessel growth and patterning in the developing heart. Development 148, dev194563 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. Liu, Z. et al. Fate mapping via Ms4a3-expression history traces monocyte-derived. Cells Cell 178, 1509–1525.e19 (2019).

    CAS  PubMed  Article  Google Scholar 

  52. Clemente-Casares, X. et al. A CD103+ conventional dendritic cell surveillance system prevents development of overt heart failure during subclinical viral myocarditis. Immunity 47, 974–989.e8 (2017).

    CAS  PubMed  Article  Google Scholar 

  53. Choi, J. H. et al. Identification of antigen-presenting dendritic cells in mouse aorta and cardiac valves. J. Exp. Med. 206, 497–505 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  54. Forte, E. et al. Cross-priming dendritic cells exacerbate immunopathology after ischemic tissue damage in the heart. Circulation 143, 821–836 (2021).

    CAS  PubMed  Article  Google Scholar 

  55. Loschko, J. et al. Inducible targeting of cDCs and their subsets in vivo. J. Immunol. Methods 434, 32–38 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. Frangogiannis, N. G. et al. Resident cardiac mast cells degranulate and release preformed TNF-α, initiating the cytokine cascade in experimental canine myocardial ischemia/reperfusion. Circulation 98, 699–710 (1998).

    CAS  PubMed  Article  Google Scholar 

  57. Adamo, L. et al. Myocardial B cells are a subset of circulating lymphocytes with delayed transit through the heart. JCI Insight 5, e134700 (2020).

    PubMed Central  Article  Google Scholar 

  58. Zouggari, Y. et al. B lymphocytes trigger monocyte mobilization and impair heart function after acute myocardial infarction. Nat. Med. 19, 1273–1280 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. Xia, N. et al. A unique population of regulatory T cells in heart potentiates cardiac protection from myocardial infarction. Circulation 142, 1956–1973 (2020).

    CAS  PubMed  Article  Google Scholar 

  60. Saxena, A. et al. Regulatory T cells are recruited in the infarcted mouse myocardium and may modulate fibroblast phenotype and function. Am. J. Physiol. Heart Circ. Physiol. 307, H1233–H1242 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. Deng, Y. et al. Unique phenotypes of heart resident type 2 innate lymphoid cells. Front. Immunol. 11, 802 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  62. Yu, X. et al. Innate lymphoid cells promote recovery of ventricular function after myocardial infarction. J. Am. Coll. Cardiol. 78, 1127–1142 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  63. Bracamonte-Baran, W. et al. Non-cytotoxic cardiac innate lymphoid cells are a resident and quiescent type 2-commited population. Front. Immunol. 10, 634 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. Choi, H. S. et al. Innate lymphoid cells play a pathogenic role in pericarditis. Cell Rep. 30, 2989–3003.e6 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. Tucker, N. R. et al. Transcriptional and cellular diversity of the human heart. Circulation 142, 466–482 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. Deniset, J. F. et al. Gata6+ pericardial cavity macrophages relocate to the injured heart and prevent cardiac fibrosis. Immunity 51, 131–140.e5 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  67. Epelman, S. et al. Embryonic and adult-derived resident cardiac macrophages are maintained through distinct mechanisms at steady state and during inflammation. Immunity 40, 91–104 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  68. Dreyer, W. J. et al. Kinetics of C5a release in cardiac lymph of dogs experiencing coronary artery ischemia-reperfusion injury. Circ. Res. 71, 1518–1524 (1992).

    CAS  PubMed  Article  Google Scholar 

  69. Newburger, P. E. & Dale, D. C. Evaluation and management of patients with isolated neutropenia. Semin. Hematol. 50, 198–206 (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  70. Hilgendorf, I. et al. Ly-6 chigh monocytes depend on nr4a1 to balance both inflammatory and reparative phases in the infarcted myocardium. Circ. Res. 114, 1611–1622 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. Frangogiannis, N. G. et al. Critical role of monocyte chemoattractant protein-1/CC chemokine ligand 2 in the pathogenesis of ischemic cardiomyopathy. Circulation 115, 584–592 (2007).

    CAS  PubMed  Article  Google Scholar 

  72. Jakubzick, C. et al. Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes. Immunity 39, 599–610 (2013).

    CAS  PubMed  Article  Google Scholar 

  73. Nahrendorf, M. et al. The healing myocardium sequentially mobilizes two monocyte subsets with divergent and complementary functions. J. Exp. Med. 204, 3037–3047 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. Sas, A. R. et al. A new neutrophil subset promotes CNS neuron survival and axon regeneration. Nat. Immunol. 21, 1496–1505 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  75. Horckmans, M. et al. Neutrophils orchestrate post-myocardial infarction healing by polarizing macrophages towards a reparative phenotype. Eur. Heart J. 38, 187–197 (2017).

    CAS  PubMed  Google Scholar 

  76. Hofmann, U. et al. Activation of CD4+ T lymphocytes improves wound healing and survival after experimental myocardial infarction in mice. Circulation 125, 1652–1663 (2012).

    CAS  PubMed  Article  Google Scholar 

  77. Curato, C. et al. Identification of noncytotoxic and IL-10-producing CD8+ AT2R+ T cell population in response to ischemic heart injury. J. Immunol. 185, 6286–6293 (2010).

    CAS  PubMed  Article  Google Scholar 

  78. Spits, H. & Cupedo, T. Innate lymphoid cells: Emerging insights in development, lineage relationships, and function. Annu. Rev. Immunol. 30, 647–675 (2012).

    CAS  PubMed  Article  Google Scholar 

  79. Spits, H. et al. Innate lymphoid cells-a proposal for uniform nomenclature. Nat. Rev. Immunol. 13, 145–149 (2013).

    CAS  PubMed  Article  Google Scholar 

  80. Bouchentouf, M. et al. Induction of cardiac angiogenesis requires killer cell lectin-like receptor 1 and α4β7 integrin expression by NK Cells. J. Immunol. 185, 7014–7025 (2010).

    CAS  PubMed  Article  Google Scholar 

  81. Dick, S. A., Zaman, R. & Epelman, S. Using high-dimensional approaches to probe monocytes and macrophages in cardiovascular disease. Front. Immunol. 10, 2146 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  82. Rizzo, G. et al. Single-cell transcriptomic profiling maps monocyte/macrophage transitions after myocardial infarction in mice. bioRxiv https://doi.org/10.1101/2020.04.14.040451 (2020).

    Article  Google Scholar 

  83. Farbehi, N. et al. Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury. eLife 8, e43882 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  84. Dick, S. A. & Epelman, S. Chronic heart failure and inflammation. Circ. Res. 119, 159–176 (2016).

    CAS  PubMed  Article  Google Scholar 

  85. Frangogiannis, N. G. The extracellular matrix in myocardial injury, repair, and remodeling. J. Clin. Invest. 127, 1600–1612 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  86. Ismahil, M. A. et al. Remodeling of the mononuclear phagocyte network underlies chronic inflammation and disease progression in heart failure critical importance of the cardiosplenic axis. Circ. Res. 114, 266–282 (2014).

    CAS  PubMed  Article  Google Scholar 

  87. Nahrendorf, M. & Swirski, F. K. Monocyte and macrophage heterogeneity in the heart. Circ. Res. 112, 1624–1633 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. Sager, H. B. et al. Proliferation and recruitment contribute to myocardial macrophage expansion in chronic heart failure. Circ. Res. 119, 853–864 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  89. Nevers, T. et al. Left ventricular T-cell recruitment contributes to the pathogenesis of heart failure. Circ. Heart Fail. 8, 776–787 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  90. Alvarez-Argote, S. & O’meara, C. C. The evolving roles of cardiac macrophages in homeostasis, regeneration, and repair. Int. J. Mol. Sci. 22, 7923 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  91. Simões, F. C. et al. Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nat. Commun. 11, 600 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  92. Dehn, S. & Thorp, E. B. Myeloid receptor CD36 is required for early phagocytosis of myocardial infarcts and induction of Nr4a1-dependent mechanisms of cardiac repair. FASEB J. 32, 254–264 (2018).

    CAS  PubMed  Article  Google Scholar 

  93. Wan, E. et al. Enhanced efferocytosis of apoptotic cardiomyocytes through MER tyrosine kinase links acute inflammation resolution to cardiac repair after infarction. Psychiatry Interpers. Biol. Process. 162, 214–220 (2009).

    Google Scholar 

  94. Zhang, S. et al. Efferocytosis fuels requirements of fatty acid oxidation and the electron transport chain to polarize macrophages for tissue repair. Cell Metab. 29, 443–456.e5 (2019).

    CAS  PubMed  Article  Google Scholar 

  95. Xiao, Y. Q. et al. Transcriptional and translational regulation of TGF-β production in response to apoptotic cells. J. Immunol. 181, 3575–3585 (2008).

    CAS  PubMed  Article  Google Scholar 

  96. Porrello, E. R. et al. Transient regenerative potential of the neonatal mouse heart. Science 331, 1078–1080 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  97. Ali, S. R. et al. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. Proc. Natl Acad. Sci. USA 111, 8850–8855 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. Bergmann, O. et al. Dynamics of cell generation and turnover in the human heart. Cell 161, 1566–1575 (2015).

    CAS  PubMed  Article  Google Scholar 

  99. Bishop, S. P., Zhou, Y., Nakada, Y. & Zhang, J. Changes in cardiomyocyte cell cycle and hypertrophic growth during fetal to adult in mammals. J. Am. Heart Assoc. 10, e017839 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  100. Mollova, M. et al. Cardiomyocyte proliferation contributes to heart growth in young humans. Proc. Natl Acad. Sci. USA 110, 1446–1451 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  101. Kamran, P. et al. Parabiosis in mice: a detailed protocol. J. Vis. Exp. 80, 50556 (2013).

    Google Scholar 

  102. Conese, M., Carbone, A., Beccia, E. & Angiolillo, A. The fountain of youth: a tale of parabiosis, stem cells, and rejuvenation. Open Med. 12, 376–383 (2017).

    CAS  Article  Google Scholar 

  103. Leuschner, F. et al. Rapid monocyte kinetics in acute myocardial infarction are sustained by extramedullary monocytopoiesis. J. Exp. Med. 209, 123–137 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  104. Bizou, M. et al. Cardiac macrophage subsets differentially regulate lymphatic network remodeling during pressure overload. Sci. Rep. 11, 16801 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  105. Wong, N. R. et al. Resident cardiac macrophages mediate adaptive myocardial remodeling. Immunity 54, 2072–2088.e7 (2021).

    CAS  PubMed  Article  Google Scholar 

  106. Kim, J. S. et al. A binary cre transgenic approach dissects microglia and CNS Border-associated macrophages. Immunity 54, 176–190.e7 (2021).

    CAS  PubMed  Article  Google Scholar 

  107. Casanova‑Acebes, M. et al. Neutrophils instruct homeostatic and pathological states in naive tissues. J. Exp. Med. 215, 2778–2795 (2018).

    Article  CAS  Google Scholar 

  108. Puhl, S. L. & Steffens, S. Neutrophils in post-myocardial infarction inflammation: damage vs. resolution? Front. Cardiovasc. Med. 6, 25 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  109. Wang, Y. et al. Wnt5a-mediated neutrophil recruitment has an obligatory role in pressure overload-induced cardiac dysfunction. Circulation 140, 487–499 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  110. Schloss, M. J. et al. The time-of-day of myocardial infarction onset affects healing through oscillations in cardiac neutrophil recruitment. EMBO Mol. Med. 8, 937–948 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  111. Adrover, J. M. et al. A neutrophil timer coordinates immune defense and vascular protection. Immunity 50, 390–402.e10 (2019).

    CAS  PubMed  Article  Google Scholar 

  112. Adrover, J. M. et al. Programmed ‘disarming’ of the neutrophil proteome reduces the magnitude of inflammation. Nat. Immunol. 21, 135–144 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  113. Kitchen, G. B. et al. The clock gene Bmal1 inhibits macrophage motility, phagocytosis, and impairs defense against pneumonia. Proc. Natl Acad. Sci. USA 117, 1543–1551 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  114. Keller, M. et al. A circadian clock in macrophages controls inflammatory immune responses. Proc. Natl Acad. Sci. USA 106, 21407–21412 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  115. Timmons, G. A., O’Siorain, J. R., Kennedy, O. D., Curtis, A. M. & Early, J. O. Innate rhythms: clocks at the center of monocyte and macrophage function. Front. Immunol. 11, 1743 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  116. Yoshida, Y. et al. Alteration of circadian machinery in monocytes underlies chronic kidney disease-associated cardiac inflammation and fibrosis. Nat. Commun. 12, 2783 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  117. Nguyen, K. D. Circadian gene bmal1 regulates diurnal oscillations of Ly6C. Science 341, 1483–1488 (2013).

    CAS  PubMed  Article  Google Scholar 

  118. Ma, Y. et al. Temporal neutrophil polarization following myocardial infarction. Cardiovasc. Res. 110, 51–61 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  119. Vafadarnejad, E. et al. Dynamics of cardiac neutrophil diversity in murine myocardial infarction. Circ. Res. 127, E232–E249 (2020).

    CAS  PubMed  Article  Google Scholar 

  120. Sicklinger, F. et al. Basophils balance healing after myocardial infarction via IL-4/IL-13. J. Clin. Invest. 131, e136778 (2021).

    CAS  PubMed Central  Article  Google Scholar 

  121. Liu, J. et al. Eosinophils improve cardiac function after myocardial infarction. Nat. Commun. 11, 6396 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  122. Dress, R. J. et al. Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage. Nat. Immunol. 20, 852–864 (2019).

    CAS  PubMed  Article  Google Scholar 

  123. Merad, M., Sathe, P., Helft, J., Miller, J. & Mortha, A. The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu. Rev. Immunol. 31, 563–604 (2013).

    CAS  PubMed  Article  Google Scholar 

  124. Tagliani, E. et al. Coordinate regulation of tissue macrophage and dendritic cell population dynamics by CSF-1. J. Exp. Med. 208, 1901–1916 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  125. Swiecki, M. & Colonna, M. The multifaceted biology of plasmacytoid dendritic cells. Nat. Rev. Immunol. 15, 471–485 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  126. Alculumbre, S. G. et al. Diversification of human plasmacytoid predendritic cells in response to a single stimulus article. Nat. Immunol. 19, 63–75 (2018).

    CAS  PubMed  Article  Google Scholar 

  127. Scott, C. L. et al. The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2. J. Exp. Med. 213, 897–911 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  128. Bauer, J. et al. Cutting edge: IFN-β expression in the spleen is restricted to a subpopulation of plasmacytoid dendritic cells exhibiting a specific immune modulatory transcriptome signature. J. Immunol. 196, 4447–4451 (2016).

    CAS  PubMed  Article  Google Scholar 

  129. Guilliams, M. et al. Unsupervised high-dimensional analysis aligns dendritic cells across tissues and species. Immunity 45, 669–684 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  130. Van der Borght, K. et al. Myocardial infarction primes autoreactive T cells through activation of dendritic cells. Cell Rep. 18, 3005–3017 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  131. Plantinga, M. et al. Conventional and monocyte-derived CD11b+ dendritic cells initiate and maintain T helper 2 cell-mediated immunity to house dust mite allergen. Immunity 38, 322–335 (2013).

    CAS  PubMed  Article  Google Scholar 

  132. Menezes, S. et al. The heterogeneity of Ly6Chi monocytes controls their differentiation into iNOS+ macrophages or monocyte-derived dendritic cells. Immunity 45, 1205–1218 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  133. Bosteels, C. et al. Inflammatory type 2 cDCs acquire features of cDC1s and macrophages to orchestrate immunity to respiratory virus infection. Immunity 52, 1039–1056.e9 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  134. Lee, J. S. et al. Conventional dendritic cells impair recovery after myocardial infarction. J. Immunol. 201, 1784–1798 (2018).

    CAS  PubMed  Article  Google Scholar 

  135. Ferris, S. T. et al. cDC1 prime and are licensed by CD4+ T cells to induce anti-tumour immunity. Nature 584, 624–629 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  136. Kim, S. et al. High amount of transcription factor IRF8 engages AP1-IRF composite elements in enhancers to direct type 1 conventional dendritic cell identity. Immunity 53, 759–774.e9 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  137. Murphy, T. L. et al. Transcriptional control of dendritic cell development. Annu. Rev. Immunol. 34, 93–119 (2016).

    CAS  PubMed  Article  Google Scholar 

  138. Schraml, B. U. et al. XGenetic tracing via DNGR-1 expression history defines dendritic cells as a hematopoietic lineage. Cell 154, 843–858 (2013).

    CAS  PubMed  Article  Google Scholar 

  139. Lanier, L. L. Shades of grey-the blurring view of innate and adaptive immunity. Nat. Rev. Immunol. 13, 73–74 (2013).

    CAS  PubMed  Article  Google Scholar 

  140. Eberl, G., Colonna, M., Santo, J. P. D. & McKenzie, A. N. J. Innate lymphoid cells: a new paradigm in immunology. Science 348, aaa6566 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  141. Walker, J. A., Barlow, J. L. & McKenzie, A. N. J. Innate lymphoid cells-how did we miss them? Nat. Rev. Immunol. 13, 75–87 (2013).

    CAS  PubMed  Article  Google Scholar 

  142. Robinette, M. L. et al. Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nat. Immunol. 16, 306–317 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  143. Chea, S. et al. Single-cell gene expression analyses reveal heterogeneous responsiveness of fetal innate lymphoid progenitors to notch signaling. Cell Rep. 14, 1500–1516 (2016).

    CAS  PubMed  Article  Google Scholar 

  144. Shih, H. Y. et al. Developmental acquisition of regulomes underlies innate lymphoid cell functionality. Cell 165, 1120–1133 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  145. Cording, S. et al. Mouse models for the study of fate and function of innate lymphoid cells. Eur. J. Immunol. 48, 1271–1280 (2018).

    CAS  PubMed  Article  Google Scholar 

  146. Ramos, G. C. et al. Myocardial aging as a T-cell-mediated phenomenon. Proc. Natl Acad. Sci. USA 114, E2420–E2429 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  147. Blanton, R. M., Carrillo-Salinas, F. J. & Alcaide, P. T-cell recruitment to the heart: friendly guests or unwelcome visitors? Am. J. Physiol. Heart Circ. Physiol. 317, H124–H140 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  148. Weirather, J. et al. Foxp3+ CD4+ T cells improve healing after myocardial infarction by modulating monocyte/macrophage differentiation. Circ. Res. 115, 55–67 (2014).

    CAS  PubMed  Article  Google Scholar 

  149. Sharir, R. et al. Experimental myocardial infarction induces altered regulatory T cell hemostasis, and adoptive transfer attenuates subsequent remodeling. PLoS One 9, e113653 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  150. Tang, T. T. et al. Regulatory T cells ameliorate cardiac remodeling after myocardial infarction. Basic Res. Cardiol. 107, 232 (2012).

    PubMed  Article  Google Scholar 

  151. Bansal, S. S. et al. Dysfunctional and proinflammatory regulatory T-lymphocytes are essential for adverse cardiac remodeling in ischemic cardiomyopathy. Circulation 139, 206–221 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  152. Bansal, S. S. et al. Activated T lymphocytes are essential drivers of pathological remodeling in ischemic heart failure. Circ. Heart Fail. 10, e003688 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  153. Laroumanie, F. et al. CD4+ T cells promote the transition from hypertrophy to heart failure during chronic pressure overload. Circulation 129, 2111–2124 (2014).

    CAS  PubMed  Article  Google Scholar 

  154. Ngwenyama, N. et al. CXCR3 regulates CD4+ T cell cardiotropism in pressure overload–induced cardiac dysfunction. JCI Insight 4, e125527 (2019).

    PubMed Central  Article  Google Scholar 

  155. Yndestad, A. et al. Enhanced expression of inflammatory cytokines and activation markers in T-cells from patients with chronic heart failure. Cardiovasc. Res. 60, 141–146 (2003).

    CAS  PubMed  Article  Google Scholar 

  156. Tang, T. et al. Defective circulating CD4+CD25+Foxp3+CD127lo regulatory T-cells in patients with chronic heart failure. Cell. Physiol. Biochem. 25, 451–458 (2010).

    CAS  PubMed  Article  Google Scholar 

  157. Ngwenyama, N. et al. Isolevuglandin-modified cardiac proteins drive CD4+ T-cell activation in the heart and promote cardiac dysfunction. Circulation 143, 1242–1255 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  158. Cho, Y. B., Lee, I. G., Joo, Y. H., Hong, S. H. & Seo, Y. J. TCR transgenic mice: a valuable tool for studying viral immunopathogenesis mechanisms. Int. J. Mol. Sci. 21, 9690 (2020).

    CAS  PubMed Central  Article  Google Scholar 

  159. Palmiter, R. D. & Brinster, R. L. Germ-line transformation of mice. Annu. Rev. Genet. 20, 465–499 (1986).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  160. Kouskoff, V., Signorelli, K., Benoist, C. & Mathis, D. Cassette vectors directing expression of T cell receptor genes in transgenic mice. J. Immunol. Methods 180, 273–280 (1995).

    CAS  PubMed  Article  Google Scholar 

  161. Holst, J. et al. Generation of T-cell receptor retrogenic mice. Nat. Protoc. 1, 406–417 (2006).

    CAS  PubMed  Article  Google Scholar 

  162. Legut, M., Dolton, G., Mian, A. A., Ottmann, O. G. & Sewell, A. K. CRISPR-mediated TCR replacement generates superior anticancer transgenic T cells. Blood 131, 311–322 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  163. Lv, H. J. & Lipes, M. A. Role of impaired central tolerance to α-myosin in inflammatory heart disease. Trends Cardiovasc. Med. 22, 113–117 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  164. Gil-Cruz, C. et al. Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy. Science 366, 881–886 (2019).

    CAS  PubMed  Article  Google Scholar 

  165. Rurik, J. G. et al. CAR T cells produced in vivo to treat cardiac injury. Science 375, 91–96 (2022).

    CAS  PubMed  Article  Google Scholar 

  166. Rocha-Resende, C. et al. Developmental changes in myocardial B cells mirror changes in B cells associated with different organs. JCI Insight 5, e139377 (2020).

    PubMed Central  Article  Google Scholar 

  167. García-Rivas, G. et al. The role of B cells in heart failure and implications for future immunomodulatory treatment strategies. ESC Heart Fail. 7, 1387–1399 (2020).

    PubMed  PubMed Central  Article  Google Scholar 

  168. Sansonetti, M., Waleczek, F. J. G., Jung, M., Thum, T. & Perbellini, F. Resident cardiac macrophages: crucial modulators of cardiac (patho)physiology. Basic Res. Cardiol. 115, 77 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  169. Csepregi, J. Z. et al. Myeloid-specific deletion of Mcl-1 yields severely neutropenic mice that survive and breed in homozygous form. J. Immunol. 201, 3793–3803 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  170. Voehringer, D. Recent advances in understanding basophil functions in vivo. F1000Research 6, 1464 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  171. Sullivan, B. M. et al. Genetic analysis of basophil function in vivo. Nat. Immunol. 12, 527–535 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  172. Voehringer, D. Protective and pathological roles of mast cells and basophils. Nat. Rev. Immunol. 13, 362–375 (2013).

    CAS  PubMed  Article  Google Scholar 

  173. Weller, P. F. & Spencer, L. A. Functions of tissue-resident eosinophils. Nat. Rev. Immunol. 17, 746–760 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  174. Rose, C. E. et al. Murine lung eosinophil activation and chemokine production in allergic airway inflammation. Cell. Mol. Immunol. 7, 361–374 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  175. Doyle, A. D. et al. Homologous recombination into the eosinophil peroxidase locus generates a strain of mice expressing Cre recombinase exclusively in eosinophils. J. Leukoc. Biol. 94, 17–24 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  176. Van Der Borght, K. et al. Myocarditis elicits dendritic cell and monocyte infiltration in the heart and self-antigen presentation by conventional type 2 dendritic cells. Front. Immunol. 9, 2714 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  177. Klose, C. S. N. & Artis, D. Innate lymphoid cells as regulators of immunity, inflammation and tissue homeostasis. Nat. Immunol. 17, 765–774 (2016).

    CAS  PubMed  Article  Google Scholar 

  178. Mazzurana, L. et al. Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing. Cell Res. 31, 554–568 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  179. Hobeika, E., Dautzenberg, M., Levit-Zerdoun, E., Pelanda, R. & Reth, M. Conditional selection of B cells in mice with an inducible B cell development. Front. Immunol. 9, 1806 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  180. Adamo, L. et al. Modulation of subsets of cardiac B lymphocytes improves cardiac function after acute injury. JCI Insight 3, e120137 (2018).

    PubMed Central  Article  Google Scholar 

  181. Forte, E. et al. Dynamic interstitial cell response during myocardial infarction predicts resilience to rupture in genetically diverse mice. Cell Rep. 30, 3149–3163.e6 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  182. Hua, X. et al. Single-cell RNA sequencing to dissect the immunological network of autoimmune myocarditis. Circulation 142, 384–400 (2020).

    CAS  PubMed  Article  Google Scholar 

  183. Koenig, A. L. et al. Single cell transcriptomics reveals cell-type-specific diversification in human heart failure. Nat. Cardiovasc. Res. 1, 263–280 (2022).

    Article  Google Scholar 

  184. Georgiades, P. et al. vavCre transgenic mice: a tool for mutagenesis in hematopoietic and endothelial lineages. Genesis 34, 251–256 (2002).

    CAS  PubMed  Article  Google Scholar 

  185. Clausen, B. E., Burkhardt, C., Reith, W., Renkawitz, R. & Förster, I. Conditional gene targeting in macrophages and granulocytes using LysMcre mice. Transgenic Res. 8, 265–277 (1999).

    CAS  PubMed  Article  Google Scholar 

  186. Yona, S. et al. Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity 38, 79–91 (2013).

    CAS  PubMed  Article  Google Scholar 

  187. Heung, L. J. & Hohl, T. M. Inflammatory monocytes are detrimental to the host immune response during acute infection with cryptococcus neoformans. PLoS Pathog. 15, e1007627 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  188. Hasenberg, A. et al. Catchup: a mouse model for imaging-based tracking and modulation of neutrophil granulocytes. Nat. Methods 12, 445–452 (2015).

    CAS  PubMed  Article  Google Scholar 

  189. Scholten, J. et al. Mast cell-specific Cre/loxP-mediated recombination in vivo. Transgenic Res. 17, 307–315 (2008).

    CAS  PubMed  Article  Google Scholar 

  190. McCormack, M. P., Forster, A., Drynan, L., Pannell, R. & Rabbitts, T. H. The LMO2 T-cell oncogene is activated via chromosomal translocations or retroviral insertion during gene therapy but has no mandatory role in normal T-cell development. Mol. Cell. Biol. 23, 9003–9013 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  191. Böiers, C. et al. Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells. Cell Stem Cell 13, 535–548 (2020).

    Article  CAS  Google Scholar 

  192. Maekawa, Y. et al. Notch2 integrates signaling by the transcription factors RBP-J and CREB1 to promote T cell cytotoxicity. Nat. Immunol. 9, 1140–1147 (2008).

    CAS  PubMed  Article  Google Scholar 

  193. Grajales-Reyes, G. E. et al. Batf3 maintains autoactivation of Irf8 for commitment of a CD8α+ conventional DC clonogenic progenitor. Nat. Immunol. 16, 708–717 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  194. Canli, Ö. et al. Myeloid cell-derived reactive oxygen species induce epithelial mutagenesis. Cancer Cell 32, 869–883.e5 (2017).

    CAS  PubMed  Article  Google Scholar 

  195. Schulz, C. et al. A lineage of myeloid cells independent of myb and hematopoietic stem cells. Science 335, 86–90 (2012).

    Article  CAS  Google Scholar 

  196. Croxford, A. L. et al. The cytokine GM-CSF drives the inflammatory signature of CCR2+ monocytes and licenses autoimmunity. Immunity 43, 502–514 (2015).

    CAS  PubMed  Article  Google Scholar 

  197. Aghajani, K., Keerthivasan, S., Yu, Y. & Gounari, F. Generation of CD4CreERT2 transgenic mice to study development of peripheral CD4-T-cells. Genesis 50, 908–913 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  198. Yasuda, T. et al. Studying Epstein-Barr virus pathologies and immune surveillance by reconstructing EBV infection in mice. Cold Spring Harb. Symp. Quant. Biol. 78, 259–263 (2013).

    PubMed  Article  Google Scholar 

  199. Yasuda, T. et al. Generation and characterization of CD19-iCre mice as a tool for efficient and specific conditional gene targeting in B cells. Sci. Rep. 11, 5524 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  200. Pimeisl, I. M. et al. Generation and characterization of a tamoxifen-inducible EomesCreER mouse line. Genesis 51, 725–733 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  201. Krause, D. S. et al. Multi-organ, multi-lineage engraftment by a single bone marrow-derived stem cell. Cell 105, 369–377 (2001).

    CAS  PubMed  Article  Google Scholar 

  202. Machein, M. R. & Plate, K. H. Bone marrow chimera experiments to determine the contribution of hematopoietic stem cells to cerebral angiogenesis. Methods Mol. Biol. 1135, 275–288 (2014).

    CAS  PubMed  Article  Google Scholar 

  203. Ochi, K., Morita, M., Wilkinson, A. C., Iwama, A. & Yamazaki, S. Non-conditioned bone marrow chimeric mouse generation using culture-based enrichment of hematopoietic stem and progenitor cells. Nat. Commun. 12, 3568 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  204. Bianco, P., Riminucci, M., Gronthos, S. & Robey, P. S. Bone marrow stromal stem cells: nature, biology, and poential applications. Stem Cell 19, 180–192 (2001).

    CAS  Article  Google Scholar 

  205. Ferreira, F. M. et al. Bone marrow chimeras — a vital tool in basic and translational research. J. Mol. Med. 97, 889–896 (2019).

    CAS  PubMed  Article  Google Scholar 

  206. Lacombe, F. et al. Flow cytometry CD45 gating for immunophenotyping of acute myeloid leukemia. Leukemia 11, 1878–1886 (1997).

    CAS  PubMed  Article  Google Scholar 

  207. Muzumdar, M. D., Tasic, B., Miyamichi, K., Li, N. & Luo, L. A global double-fluorescent cre reporter mouse. Genesis 45, 593–605 (2007).

    CAS  PubMed  Article  Google Scholar 

  208. Jaiswal, S. et al. Clonal hematopoiesis and risk of atherosclerotic cardiovascular disease. N. Engl. J. Med. 377, 111–121 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  209. Fuster, J. J. et al. Clonal hematopoiesis associated with TET2 deficiency accelerates atherosclerosis development in mice. Science 355, 842–847 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  210. Sano, S. et al. JAK2V617F-mediated clonal hematopoiesis accelerates pathological remodeling in murine heart failure. JACC Basic Transl. Sci. 4, 684–697 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  211. Sano, S. et al. Tet2-mediated clonal hematopoiesis accelerates heart failure through a mechanism involving the IL-1β/NLRP3 inflammasome. J. Am. Coll. Cardiol. 71, 875–886 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  212. Sano, S. et al. CRISPR-mediated gene editing to assess the roles of TET2 and DNMT3A in clonal hematopoiesis and cardiovascular disease. Circ. Res. 123, 335–341 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  213. Cao, X. et al. Irradiation induces bone injury by damaging bone marrow microenvironment for stem cells. Proc. Natl Acad. Sci. USA 108, 1609–1614 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  214. Lumniczky, K., Szatmári, T. & Sáfrány, G. Ionizing radiation-induced immune and inflammatory reactions in the brain. Front. Immunol. 8, 517 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  215. Peake, K. et al. Busulfan as a myelosuppressive agent for generating stable high-level bone marrow chimerism in mice. J. Vis. Exp. 98, e52553 (2015).

    Google Scholar 

  216. Youshani, A. S. et al. Non-myeloablative busulfan chimeric mouse models are less pro-inflammatory than head-shielded irradiation for studying immune cell interactions in brain tumours. J. Neuroinflammation 16, 25 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  217. Ladel, L. et al. Inherent engraftment differences between CD45.1 and CD45.2 HSCs are caused by differential expression of Cxcr4. Exp. Hematol. 53, S87 (2017).

    Article  Google Scholar 

  218. Jang, Y. et al. Cutting edge: check your mice — a point mutation in the Ncr1 locus identified in CD45.1 congenic mice with consequences in mouse susceptibility to infection. J. Immunol. 200, 1982–1987 (2018).

    CAS  PubMed  Article  Google Scholar 

  219. Luecken, M. D. & Theis, F. J. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol. Syst. Biol. 15, e8746 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  220. Clarke, Z. A. et al. Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. Nat. Protoc. 16, 2749–2764 (2021).

    CAS  PubMed  Article  Google Scholar 

  221. Müller, A. C. et al. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Nat. Protoc. 22, 924–934 (2019).

    Google Scholar 

  222. Saelens, W., Cannoodt, R., Todorov, H. & Saeys, Y. A comparison of single-cell trajectory inference methods. Nat. Biotechnol. 37, 547–554 (2019).

    CAS  PubMed  Article  Google Scholar 

  223. Lin, H. H. et al. The macrophage F4/80 receptor is required for the induction of antigen-specific efferent regulatory T cells in peripheral tolerance. J. Exp. Med. 201, 1615–1625 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  224. McGarry, M. P. & Stewart, C. C. Murine eosinophil granulocyte bind the murine macrophage-monocyte specific monoclonal antibody F4/80. J. Leukoc. Biol. 50, 471–478 (1991).

    CAS  PubMed  Article  Google Scholar 

  225. Misharin, A. V., Morales-Nebreda, L., Mutlu, G. M., Budinger, G. R. S. & Perlman, H. Flow cytometric analysis of macrophages and dendritic cell subsets in the mouse lung. Am. J. Respir. Cell Mol. Biol. 49, 503–510 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  226. dos Anjos Cassado, A. F4/80 as a major macrophage marker: the case of the peritoneum and spleen. Results Probl. Cell Differ. 62, 161–179 (2017).

    PubMed  Article  CAS  Google Scholar 

  227. Hamann, J. et al. EMR1, the human homolog of F4/80, is an eosinophil-specific receptor. Eur. J. Immunol. 37, 2797–2802 (2007).

    CAS  PubMed  Article  Google Scholar 

  228. Gautiar, E. L. et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat. Immunol. 13, 1118–1128 (2012).

    Article  CAS  Google Scholar 

  229. Finsterbusch, M. et al. Patrolling monocytes promote intravascular neutrophil activation and glomerular injury in the acutely inflamed glomerulus. Proc. Natl Acad. Sci. USA 113, E5172–E5181 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  230. Buscher, K., Marcovecchio, P., Hedrick, C. C. & Ley, K. Patrolling mechanics of non-classical monocytes in vascular inflammation. Front. Cardiovasc. Med. 4, 80 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  231. Weisheit, C. et al. Ly6Clow and not Ly6Chigh macrophages accumulate first in the heart in a model of murine pressure-overload. PLoS One 9, e112710 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  232. Abremski, K. & Hoess, R. Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J. Biol. Chem. 259, 1509–1514 (1984).

    CAS  PubMed  Article  Google Scholar 

  233. Kim, H., Kim, M., Im, S.-K. & Fang, S. Mouse Cre-LoxP system: general principles to determine tissue-specific roles of target genes. Lab. Anim. Res. 34, 147 (2018).

    PubMed  PubMed Central  Article  Google Scholar 

  234. Legué, E. & Joyner, A. L. Genetic fate mapping using site-specific recombinases. Methods Enzymol. 477, 153–181 (2010).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  235. Buch, T. et al. A Cre-inducible diphtheria toxin receptor mediates cell lineage ablation after toxin administration. Nat. Methods 2, 419–426 (2005).

    CAS  PubMed  Article  Google Scholar 

  236. DeBerge, M. et al. Macrophage AXL receptor tyrosine kinase inflames the heart after reperfused myocardial infarction. J. Clin. Invest. 131, e139576 (2021).

    CAS  PubMed Central  Article  Google Scholar 

  237. Liu, M. et al. Macrophage MST1/2 disruption impairs post-infarction cardiac repair via LTB4. Circ. Res. 129, 909–926 (2021).

    CAS  PubMed  Article  Google Scholar 

  238. Chen, B. et al. Macrophage Smad3 protects the infarcted heart, stimulating phagocytosis and regulating inflammation. Circ. Res. 125, 55–70 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  239. Wong, A. & Epelman, S. Tissue-reparative benefits of MST1/2 inhibition: separating the wheat from the chaff. Circ. Res. 129, 927–929 (2021).

    CAS  PubMed  Article  Google Scholar 

  240. Peterson, J. C., Kelder, T. P., Goumans, M. J. T. H., Jongbloed, M. R. M. & Deruiter, M. C. The role of cell tracing and fate mapping experiments in cardiac outflow tract development, new opportunities through emerging technologies. J. Cardiovasc. Dev. Dis. 8, 47 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  241. Indra, A. K. et al. Temporally-controlled site-specific mutagenesis in the basal layer of the epidermis: comparison of the recombinase activity of the tamoxifen-inducible Cre-ER(T) and Cre-ER(T2) recombinases. Nucleic Acids Res. 27, 4324–4327 (1999).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  242. Feil, S., Krauss, J., Thunemann, M. & Feil, R. Genetic inducible fate mapping in adult mice using tamoxifen-dependent Cre recombinases. Methods Mol. Biol. 1194, 113–139 (2014).

    PubMed  Article  CAS  Google Scholar 

  243. Álvarez-Aznar, A. et al. Tamoxifen-independent recombination of reporter genes limits lineage tracing and mosaic analysis using CreERT2 lines. Transgenic Res. 29, 53–68 (2020).

    PubMed  Article  CAS  Google Scholar 

  244. Rojo, R., Sauter, K. A., Lefevre, L., Hume, D. A. & Pridans, C. Maternal tamoxifen treatment expands the macrophage population of early mouse embryos. bioRxiv https://doi.org/10.1101/296749 (2018).

    Article  Google Scholar 

  245. Becher, B., Waisman, A. & Lu, L. F. Conditional gene-targeting in mice: problems and solutions. Immunity 48, 835–836 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  246. Becher, B., Waisman, A. & Lu, L. F. Cre-lox: target sensitivity matters. Immunity 51, 595 (2019).

    CAS  PubMed  Article  Google Scholar 

  247. Bian, Z. et al. Deciphering human macrophage development at single-cell resolution. Nature 582, 571–576 (2020).

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgements

The authors receive support from the Canadian Institutes of Health Research (S.E. PJT364831, AW. FRN 413754), Heart and Stroke Foundation (S.E.), Ted Rogers Centre for Heart Research (S.E., H.H.) and Peter Munk Cardiac Centre (S.E.).

Author information

Authors and Affiliations

Authors

Contributions

A.W. and H.H. researched data for the article. All the authors contributed to the discussion of content, wrote the article and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Slava Epelman.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Cardiology thanks Sumanth Prabhu, Susanne Sattler and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

Epelman lab transcriptomics data sets: https://www.epelmanlab.com/resources

Human heart cell atlas: https://www.heartcellatlas.org/

ImmGen Consortium: https://www.immgen.org

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Wong, A., Hamidzada, H. & Epelman, S. A cardioimmunologist’s toolkit: genetic tools to dissect immune cells in cardiac disease. Nat Rev Cardiol 19, 395–413 (2022). https://doi.org/10.1038/s41569-022-00701-0

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41569-022-00701-0

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing