Supplemental references Arai T, Tabona P, Summerfield JA. Human mannose-binding protein gene is regulated by interleukins, dexamethasone and heat shock. Q J Med 1993; 86: 575582. Basu S, Binder RJ, Suto R, Anderson KM, Srivastava PK. Necrotic but not apoptotic cell death releases heat shock proteins, which deliver a partial maturation signal to dendritic cells and activate the NF-kappa B pathway. Int Immunol 2000; 12: 15391546. Bharadwaj D, Mold C, Markham E, Du Clos TW. Serum amyloid P component binds to Fc gamma receptors and opsonizes particles for phagocytosis. J Immunol 2001; 166: 6735-6741. Bottazzi B, Vouret-Craviari V, Bastone A, De Gioia L, Matteucci C, Peri G et al. Multimer formation and ligand recognition by the long pentraxin PTX3. Similarities and differences with the short pentraxins C-reactive protein and serum amyloid P component. J Biol Chem 1997; 272: 32817-32823. Brouckaert G, Kalai M, Krysko DV, Saelens X, Vercammen D, Ndlovu et al. Phagocytosis of necrotic cells by macrophages is phosphatidylserine dependent and does not induce inflammatory cytokine production. Mol Biol Cell 2004; 15: 10891100. Butler PJ, Tennent GA, Pepys MB. Pentraxin-chromatin interactions: serum amyloid P component specifically displaces H1-type histones and solubilizes native long chromatin. J Exp Med 1990; 172: 13-18. Caminschi I, Proietto AI, Ahmet F, Kitsoulis S, Shin Teh J, Lo JC et al. The dendritic cell subtype-restricted C-type lectin Clec9A is a target for vaccine enhancement. Blood 2008; 112: 3264-3273. Chang MK, Bergmark C, Laurila A, Horkko S, Han KH, Friedman P et al. Monoclonal antibodies against oxidized low-density lipoprotein bind to apoptotic cells and inhibit their phagocytosis by elicited macrophages: evidence that oxidationspecific epitopes mediate macrophage recognition. Proc Natl Acad Sci U S A 1999; 96: 6353-6358. Chen W, Frank ME, Jin W, Wahl SM. TGF-beta released by apoptotic T cells contributes to an immunosuppressive milieu. Immunity 2001; 14: 715-725. Culley FJ, Bodman-Smith KB, Ferguson MA, Nikolaev AV, Shantilal N, Raynes JG. C-reactive protein binds to phosphorylated carbohydrates. Glycobiology 2000; 10: 5965. Degterev A, Huang Z, Boyce M, Li Y, Jagtap P, Mizushima N et al. Chemical inhibitor of nonapoptotic cell death with therapeutic potential for ischemic brain injury. Nat Chem Biol 2005; 1: 112-119. Devitt A, Moffatt OD, Raykundalia C, Capra JD, Simmons DL, Gregory CD. Human CD14 mediates recognition and phagocytosis of apoptotic cells. Nature 1998; 392: 505-509. Devitt A, Parker KG, Ogden CA, Oldreive C, Clay MF, Melville LA et al. Persistence of apoptotic cells without autoimmune disease or inflammation in CD14-/- mice. J Cell Biol 2004; 167: 1161-1170. Devitt A, Pierce S, Oldreive C, Shingler WH, Gregory CD. CD14-dependent clearance of apoptotic cells by human macrophages: the role of phosphatidylserine. Cell Death Differ 2003; 10: 371-382. Diervo AJ, Reynolds JW. Phospholipid composition and cardiolipin synthesis in fermentative and nonfermentative marine bacteria. J Bacteriol 1975; 123: 294-301. Diez-Roux G, Lang RA. Macrophages induce apoptosis in normal cells in vivo. Development 1997; 124: 3633-3638. Duffield JS, Erwig LP, Wei X, Liew FY, Rees AJ, Savill JS. Activated macrophages direct apoptosis and suppress mitosis of mesangial cells. J Immunol 2000; 164: 21102119. Ehrenstein MR, Cook HT, Neuberger MS. Deficiency in serum immunoglobulin (Ig)M predisposes to development of IgG autoantibodies. J Exp Med 2000; 191: 1253-1258. Fadok VA, Bratton DL, Konowal A, Freed PW, Westcott JY, Henson PM. Macrophages that have ingested apoptotic cells in vitro inhibit proinflammatory cytokine production through autocrine/paracrine mechanisms involving TGF-beta, PGE2, and PAF. J Clin Invest 1998; 101: 890-898. Fries DM, Lightfoot R, Koval M, Ischiropoulos H. Autologous apoptotic cell engulfment stimulates chemokine secretion by vascular smooth muscle cells. Am J Pathol 2005; 167: 345-353. Fujita H, Takahashi S, Okabe S. Characterization of antichemotactic factor extracted from the gastric mucosa of rats. J Physiol Pharmacol 1997; 48: 761-774. Fukasawa M, Sekine F, Miura M, Nishijima M, Hanada K. Involvement of heparan sulfate proteoglycans in the binding step for phagocytosis of latex beads by Chinese hamster ovary cells. Exp Cell Res 1997; 230: 154-162. Gao Y, Herndon JM, Zhang H, Griffith TS, Ferguson TA. Antiinflammatory effects of CD95 ligand (FasL)-induced apoptosis. J Exp Med 1998; 188: 887-896. Garcia de Frutos P, Hardig Y, Dahlback B. Serum amyloid P component binding to C4b-binding protein. J Biol Chem 1995; 270: 26950-26955. Gorgani NN, Parish CR, Altin JG. Differential binding of histidine-rich glycoprotein (HRG) to human IgG subclasses and IgG molecules containing kappa and lambda light chains. J Biol Chem 1999; 274: 29633-29640. Gorgani NN, Parish CR, Easterbrook Smith SB, Altin JG. Histidine-rich glycoprotein binds to human IgG and C1q and inhibits the formation of insoluble immune complexes. Biochemistry 1997; 36: 6653-6662. Gutberlet T, Dietrich U, Bradaczek H, Pohlentz G, Leopold K, Fischer W. Cardiolipin, alpha-D-glucopyranosyl, and L-lysylcardiolipin from gram-positive bacteria: FAB MS, monofilm and X-ray powder diffraction studies. Biochim Biophys Acta 2000; 1463: 307-322. Hanayama R, Tanaka M, Miwa K, Shinohara A, Iwamatsu A, Nagata S. Identification of a factor that links apoptotic cells to phagocytes. Nature 2002; 417: 182-187. Hayashi F, Smith KD, Ozinsky A, Hawn TR, Yi EC, Goodlett DR et al. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 2001; 410: 1099-1103. Hoeppner DJ, Hengartner MO, Schnabel R. Engulfment genes cooperate with ced-3 to promote cell death in Caenorhabditis elegans. Nature 2001; 412: 202-206. Horkko S, Miller E, Branch DW, Palinski W, Witztum JL. The epitopes for some antiphospholipid antibodies are adducts of oxidized phospholipid and beta2 glycoprotein 1 (and other proteins). Proc Natl Acad Sci U S A 1997; 94: 1035610361. Hundt M, Zielinska-Skowronek M, Schmidt RE. Lack of specific receptors for Creactive protein on white blood cells. Eur J Immunol 2001; 31: 3475-3483. Huysamen C, Willment JA, Dennehy KM, Brown GD. CLEC9A is a novel activation C-type lectin-like receptor expressed on BDCA3+ dendritic cells and a subset of monocytes. J Biol Chem 2008; 283: 16693-16701. Ichimura T, Asseldonk EJ, Humphreys BD, Gunaratnam L, Duffield JS, Bonventre JV. Kidney injury molecule-1 is a phosphatidylserine receptor that confers a phagocytic phenotype on epithelial cells. J Clin Invest 2008; 118: 1657-1668. Ishii KJ, Suzuki K, Coban C, Takeshita F, Itoh Y, Matoba H et al. Genomic DNA released by dying cells induces the maturation of APCs. J Immunol 2001; 167: 26022607. Jiang H, Robey FA, Gewurz H. Localization of sites through which C-reactive protein binds and activates complement to residues 14-26 and 76-92 of the human C1q A chain. J Exp Med 1992; 175: 1373-1379. Kawasaki Y, Nakagawa A, Nagaosa K, Shiratsuchi A, Nakanishi Y. Phosphatidylserine binding of class B scavenger receptor type I, a phagocytosis receptor of testicular sertoli cells. J Biol Chem 2002; 277: 27559-27566. Kobayashi N, Karisola P, Pena-Cruz V, Dorfman DM, Jinushi M, Umetsu SE et al. TIM-1 and TIM-4 glycoproteins bind phosphatidylserine and mediate uptake of apoptotic cells. Immunity 2007; 27: 927-940. Leung LL, Nachman RL, Harpel PC. Complex formation of platelet thrombospondin with histidine-rich glycoprotein. J Clin Invest 1984; 73: 5-12. Li YP, Mold C, Du Clos TW. Sublytic complement attack exposes C-reactive protein binding sites on cell membranes. J Immunol 1994; 152: 2995-3005. Maiti SN, Balasubramanian K, Ramoth JA, Schroit AJ. Beta-2-glycoprotein 1dependent macrophage uptake of apoptotic cells. Binding to lipoprotein receptorrelated protein receptor family members. J Biol Chem 2008; 283: 3761-3766. Marin-Teva JL, Dusart I, Colin C, Gervais A, van Rooijen N, Mallat M. Microglia promote the death of developing Purkinje cells. Neuron 2004; 41: 535-547. Miyanishi M, Tada K, Koike M, Uchiyama Y, Kitamura T, Nagata S. Identification of Tim4 as a phosphatidylserine receptor. Nature 2007; 450: 435-439. Mileykovskaya E, Dowhan W. Visualization of phospholipid domains in Escherichia coli by using the cardiolipin-specific fluorescent dye 10-N-nonyl acridine orange. J Bacteriol 2000; 182: 1172-1175. Moffatt OD, Devitt A, Bell ED, Simmons DL, Gregory CD. Macrophage recognition of ICAM-3 on apoptotic leukocytes. J Immunol 1999; 162: 6800-6810. Nauta AJ, Bottazzi B, Mantovani A, Salvatori G, Kishore U, Schwaeble WJ et al. Biochemical and functional characterization of the interaction between pentraxin 3 and C1q. Eur J Immunol 2003; 33: 465-473. Oldenborg PA, Gresham HD, Lindberg FP. CD47-signal regulatory protein alpha (SIRPalpha) regulates Fcgamma and complement receptor-mediated phagocytosis. J Exp Med 2001; 193: 855-862. Oka K, Sawamura T, Kikuta K, Itokawa S, Kume N, Kita T et al. Lectin-like oxidized low-density lipoprotein receptor 1 mediates phagocytosis of aged/apoptotic cells in endothelial cells. Proc Natl Acad Sci U S A 1998; 95: 9535-9540. Ollert MW, David K, Bredehorst R, Vogel CW. Classical complement pathway activation on nucleated cells. Role of factor H in the control of deposited C3b. J Immunol 1995; 155: 4955-4962. Paidassi H, Tacnet-Delorme P, Garlatti V, Darnault C, Ghebrehiwet B, Gaboriaud C et al. C1q binds phosphatidylserine and likely acts as a multiligand-bridging molecule in apoptotic cell recognition. J Immunol 2008; 180: 2329-2338. Palinski W, Horkko S, Miller E, Steinbrecher UP, Powell HC, Curtiss LK et al. Cloning of monoclonal autoantibodies to epitopes of oxidized lipoproteins from apolipoprotein E-deficient mice. Demonstration of epitopes of oxidized low density lipoprotein in human plasma. J Clin Invest 1996; 98: 800-814. Park D, Tosello-Trampont AC, Elliott MR, Lu M, Haney LB, Ma Z et al. BAI1 is an engulfment receptor for apoptotic cells upstream of the ELMO/Dock180/Rac module. Nature 2007; 450: 430-434. Park SY, Jung MY, Kim HJ, Lee SJ, Kim SY, Lee BH et al. Rapid cell corpse clearance by stabilin-2, a membrane phosphatidylserine receptor. Cell Death Differ 2008; 15: 192-201. Park SY, Kim SY, Jung MY, Bae DJ, Kim IS. Epidermal growth factor-like domain repeat of stabilin-2 recognizes phosphatidylserine during cell corpse clearance. Mol Cell Biol 2008; 28: 5288-5298. Pepys MB, Booth SE, Tennent GA, Butler PJ, Williams DG. Binding of pentraxins to different nuclear structures: C-reactive protein binds to small nuclear ribonucleoprotein particles, serum amyloid P component binds to chromatin and nucleoli. Clin Exp Immunol 1994; 97: 152-157. Pepys MB, Butler PJ. Serum amyloid P component is the major calcium-dependent specific DNA binding protein of the serum. Biochem Biophys Res Commun 1987; 148: 308-313. Reddien PW, Cameron S, Horvitz HR. Phagocytosis promotes programmed cell death in C. elegans. Nature 2001; 412: 198-202. Saeland E, van Royen A, Hendriksen K, Vile-Weekhout H, Rijkers GT, Sanders LA et al. Human C-reactive protein does not bind to FcgammaRIIa on phagocytic cells. J Clin Invest 2001; 107: 641-643. Saevarsdottir S, Vikingsdottir T, Valdimarsson H. The potential role of mannanbinding lectin in the clearance of self-components including immune complexes. Scand J Immunol 2004; 60: 23-29. Sancho D, Mourao-Sa D, Joffre OP, Schulz O, Rogers NC, Pennington DJ et al. Tumor therapy in mice via antigen targeting to a novel, DC-restricted C-type lectin. J Clin Invest 2008; 118: 2098-2110. Shaw PX, Horkko S, Chang MK, Curtiss LK, Palinski W, Silverman GJ et al. Natural antibodies with the T15 idiotype may act in atherosclerosis, apoptotic clearance, and protective immunity. J Clin Invest 2000; 105: 1731-1740. Shi Y, Evans JE, Rock KL. Molecular identification of a danger signal that alerts the immune system to dying cells. Nature 2003; 425: 516-521. Sjoberg AP, Trouw LA, McGrath FD, Hack CE, Blom AM. Regulation of complement activation by C-reactive protein: targeting of the inhibitory activity of C4b-binding protein. J Immunol 2006; 176: 7612-7620. Smith KD, Andersen-Nissen E, Hayashi F, Strobe K, Bergman MA, Barrett SL et al. Toll-like receptor 5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility. Nat Immunol 2003; 4: 1247-1253. Tanaka M, Miyake Y, Asano K. Maintenance of self-tolerance by apoptotic cell clearance. Front Biosci 2008; 13: 6043-6049. Tsai RK, Discher DE. Inhibition of "self" engulfment through deactivation of myosinII at the phagocytic synapse between human cells. J Cell Biol 2008; 180: 989-1003. Uehara H, Shacter E. Auto-oxidation and oligomerization of protein S on the apoptotic cell surface is required for Mer tyrosine kinase-mediated phagocytosis of apoptotic cells. J Immunol 2008; 180: 2522-2530. Uwatoko S, Mannik M. The location of binding sites on C1q for DNA. J Immunol 1990; 144: 3484-3488. Williams TN, Zhang CX, Game BA, He L, Huang Y. C-reactive protein stimulates MMP-1 expression in U937 histiocytes through Fc[gamma]RII and extracellular signal-regulated kinase pathway:: an implication of CRP involvement in plaque destabilization. Arterioscler Thromb Vasc Biol 2004; 24: 61-66. Ying SC, Gewurz AT, Jiang H, Gewurz H. Human serum amyloid P component oligomers bind and activate the classical complement pathway via residues 14-26 and 76-92 of the A chain collagen-like region of C1q. J Immunol 1993; 150: 169-176. Zlatarova AS, Rouseva M, Roumenina LT, Gadjeva M, Kolev M, Dobrev I et al. Existence of different but overlapping IgG- and IgM-binding sites on the globular domain of human C1q. Biochemistry 2006; 45: 9979-9988.