CHAPTER 14 Innate Immunity INTRODUCTION M any different cell types of the innate immune system have affinity for pathogens and tumor cells, and it is their quick response that constitutes the first line of defense against bacteria, viruses, parasites, and malignant transformation. Innate immunity against infections and tumors can be executed by dendritic cells, NK cells, and macrophages, and the biological result of the recognition of pathogens by these cell types is expression of costimulatory molecules, cytokines, and chemokines, In addition, macrophages and dendritic cells can internalize cells and cellular debris. One indication of the importance of innate immunity is the speed with which new discoveries have been added over the past few years, in particular at the level of identification of the receptors involved in ligand recognition on tumor cells, infected cells, and apoptotic cells. A considerable body of evidence, accumulated only recently, shows that the Toll-like receptors (TLRs) are the principle sensors of pathogens on macrophages (UNIT 14.12). For NK cells, efficient cell isolation methods and useful functional assays (UNIT 14.12) have been developed over the past 10 years. In addition, a broad range of activating and inhibitory receptors have also been identified for these cells. Nevertheless, when the innate immune system had yet to capture the attention of most immunologists, macrophages were already extensively investigated in many laboratories, and much of the knowledge about their receptors and functions is represented in the protocols dedicated to macrophages in the first part of this Chapter (UNITS 14.1-14.9). At the moment, Chapter 14 represents a chapter in transition, in which new protocols for the analysis of the innate immune response will be combined with updated protocols currently presented at other locations in earlier versions of Current Protocols in Immunology. Complement will continue to keep its own place in this series (see Chapter 13), but NK cells will gradually be introduced into Chapter 14. A commentary unit on the receptors and ligands involved in NK cell recognition is included in this chapter (UNIT 14.10). A commentary section on signaling through NK receptors (UNIT 11.9B) can be found in Chapter 11. Protocols on isolating mouse (UNIT 3.22) and human (UNIT 7.7) NK cells are provided elsewhere, and assays for measuring cytotoxic NK cell function can be found in UNIT 7.18. Protocols on other cell types that form integral parts of the innate immune system, such as neutrophils (UNIT 7.23) and dendritic cells (UNITS 3.7 & 7.32) are also presented elsewhere. Eventually, after updating, many of these units will be brought together into the present chapter. STUDIES OF MACROPHAGES AND MONOCYTES Since their first description as "big eaters" more than a hundred years ago (Metchnikoff, 1884, 1893), macrophages have been recognized as scavenger cells in both lower invertebrates and higher organisms. It is now realized that macrophages represent a ubiquitously distributed population ...