Clearance of apoptotic corpses

Apoptotic corpses can be engulfed and cleared by many other cell types in addition to ‘professional’ phagocytes such as macrophage. Studies of several organisms have contributed to the understanding of apoptotic corpse engulfment. Two partially redundant engulfment pathways have been characterized that act even in non-professional phagocytes to promote corpse engulfment. This review summarizes some recent progress in signaling by these pathways, including the exposure of eat-me-signals on apoptotic cells, and insights from Drosophila on the roles of the bridging receptor Six Microns Under, the non-receptor tyrosine kinase Shark, and store-operated calcium release in the Draper/Ced-1 pathway of corpse recognition and internalization. The mechanism of apoptotic phagosome maturation is outlined, and possible connections between corpse engulfment and proliferation, cell competition, and immunity are discussed.     

Phagocytosis of apoptotic cells

Removal of apoptotic cells by phagocytes plays an important role in many biological processes, including embryological development and tissue remodelling. In addition, it has become apparent that one of the key mechanisms for the successful resolution of inflammation is the orchestrated clearance of apoptotic inflammatory cells by phagocytes (e.g., macrophages and dendritic cells) and other cells known to have phagocytic capacity (e.g., hepatocytes, endothelial cells, epithelial cells, etc.). Furthermore, phagocytosis of apoptotic cells is an active and highly regulated process that not only serves to remove potentially histotoxic cells from the inflammatory milieu, but also directs the phenotype of the phagocytic cell to be anti-inflammatory. Convincing evidence has been presented that reduced or dysregulated phagocytosis of apoptotic cells contributes to the development and propagation of inflammatory disorders. Conversely, enhanced phagocytosis of apoptotic cells may be exploited for therapeutic gain. Indeed, powerful anti-inflammatory drugs such as the glucocorticoids have been shown to augment clearance of apoptotic cells which may contribute to their therapeutic effectiveness. In this chapter, we describe methods for studying phagocytosis of apoptotic cells.     

Engulfment mechanism of apoptotic cells

Apoptotic cells are engulfed and removed by phagocytes. This ensures proper development of the organism and can modulate immune responses. Recent studies have examined molecules on apoptotic cells, such as phosphatidylserine, which may signal for engulfment through multiple receptors. Apoptotic recognition mechanisms may vary with the apoptotic and engulfing cell type, and even with the age of the corpse.     

Control of apoptotic DNA degradation

Apoptotic DNA degradation has been thought to be a cell-autonomous process. Recent evidence suggests that heterophagic recognition and engulfment of dying cells by non-apoptotic cells may be critical for the activation and/or action of apoptogenic DNases.     

Two-step engulfment of apoptotic cells

Apoptotic cells expose phosphatidylserine on their surface as an "eat me" signal, and macrophages respond by engulfing them. Although several molecules that specifically bind phosphatidylserine have been identified, the molecular mechanism that triggers engulfment remains elusive. Here, using a mouse pro-B cell line, Ba/F3, that grows in suspension, we reconstituted the engulfment of apoptotic cells. The parental Ba/F3 cells did not engulf apoptotic cells. Ba/F3 transformants expressing T cell immunoglobulin- and mucin-domain-containing molecule 4 (Tim4), a type I membrane protein that specifically binds phosphatidylserine, efficiently bound apoptotic cells in a phosphatidylserine-dependent manner but did not engulf them. However, Ba/F3 transformants expressing both Tim4 and the integrin α(v)β(3) complex bound to and engulfed apoptotic cells in the presence of milk fat globule epidermal growth factor factor VIII (MFG-E8), a secreted protein that can bind phosphatidylserine and integrin α(v)β(3). These results indicate that the engulfment of apoptotic cells proceeds in two steps: Tim4 tethers apoptotic cells, and the integrin α(v)β(3) complex mediates engulfment in coordination with MFG-E8. A similar two-step engulfment of apoptotic cells was observed with mouse resident peritoneal macrophages. Furthermore, the Tim4/integrin-mediated engulfment by the Ba/F3 cells was enhanced in cells expressing Rac1 and Rab5, suggesting that this system well reproduces the engulfment of apoptotic cells by macrophages.     

Mechanisms of apoptotic phosphatidylserine exposure

It has been a long-standing enigma which scramblase causes phosphatidylserine residues to be exposed on the surface of apoptotic cells, thereby facilitating the phagocytic recognition, engulfment and destruction of apoptotic corpses. In a recent paper in Science, Nagata and coworkers reveal that the scramblases Xkr8 and its C. elegans ortholog, CED-8, are activated by caspase cleavage in apoptotic cells.All cells are separated from the extracellular environment by the plasma membrane, a phospholipid bilayer that prevents diffusion of proteins, ions and other essential molecules into the extracellular space and constitutes the structure in which membrane proteins are embedded. In animal cells, the lipid composition of the outer and inner leaflets of the plasma membrane is not symmetrical. Phosphatidylcholine (PC) and sphingomyelin (SM) are mainly present in the outer leaflet of the plasma membrane, whereas phosphatidylserine (PS), phosphatidylinositol (PI) and phosphatidylethanolamine (PE) are restricted to the inner leaflet. This lipid asymmetry is maintained by the combined action of ATP-dependent enzymes called flippases and floppases, which specifically translocate phospholipids and other molecules from the outer to the inner membrane leaflet and from the inner to the outer membrane leaflet, respectively¹. Lipid composition asymmetry not only defines the curvature and electrochemical properties of the plasma membrane, but is also essential for the correct function of determined lipids, as for instance, PI, which only functions as a second messenger if present in the inner leaflet². Nonetheless, several physiologically relevant processes as diverse as platelet activation, neurotransmitter release, sperm capacitation or apoptosis, require dissipation of plasma membrane lipid asymmetry, a process known as scrambling. The enzymes responsible for this activity are called scramblases, and function to randomize the distribution of phospholipids between both membrane leaflets in an ATP-independent manner^2,3,4.Although plasma membrane asymmetry and the existence of flippases, floppases and scramblases have been known for decades, the identity of the specific enzymes involved in these activities has only begun to be revealed during the last few years. Very recently, the group of Shigekazu Nagata identified TMEM16F as the long sought-after calcium-dependent phospholipid scramblase³. However, to date, the identity of the scramblase(s) involved in apoptosis-related (and calcium-independent) PS exposure had remained elusive. Cell surface PS exposure is a classic feature of apoptotic cells and acts as an “eat me” signal allowing phagocytosis of post-apoptotic bodies. In a recent paper in Science, Nagata''s group identified Xk-Related Protein 8 (Xkr8) as the enzyme responsible for this activity and demonstrated an evolutionarily conserved role of this protein in apoptosis-induced lipid scrambling⁵.To identify enzymes involved in membrane lipid scrambling, Nagata''s group took advantage of their previously generated mouse Ba/F3 pro-B cell line³, which presented a high basal level of PS exposure. They then generated a cDNA library from Ba/F3 cells and overexpressed it in the parental cell line. Through sequential enrichment of cells with increased PS exposure, they were able to isolate a cDNA encoding the Xkr8 protein, which enhanced PS scrambling when overexpressed. Xkr8 overexpression (but not that of TMEM16F) was able to increase apoptosis-associated PS exposure. The authors then noticed that both impaired apoptosis-induced PS exposure and deficient post-apoptotic body clearance were correlated with low Xkr8 expression in leukemia and lymphoma cell lines, which was linked to hypermethylation of its promoter. Interestingly, these two alterations were reverted either by overexpressing Xkr8 or by restitution of endogenous Xkr8 expression after treatment with the demethylating agent 5-aza-2′-deoxycytidine (DAC), suggesting that methylation of the Xrk8 promoter may be a mechanism by which tumor cells evade their phagocytosis after apoptotic death, which may result in increased local inflammation, thus favoring tumor progression. Far from being restricted only to PS exposure, Xrk8 overexpression was able to promote scrambling of multiple lipid species during apoptosis, which was demonstrated by incorporation of fluorescent PC and SM analogues. This scrambling activity was restricted to apoptotic events, as Xkr8 overexpression had no effect on Ca²⁺-induced PS exposure. This specificity may be explained by the presence of an evolutionarily conserved caspase recognition site near Xkr8 C-terminal region, whose mutation prevented both Xkr8 cleavage by caspase-3 or -7 and PS exposure during the course of apoptosis (Figure 1). These results from human cell lines were confirmed in Xkr8^−/− mouse embryonic fibroblasts and fetal thymocytes, which were unable to expose PS upon induction of apoptosis, underscoring the broad physiological relevance of Xkr8 in the apoptotic process. Finally, the authors moved to the nematode Caenorhabditis elegans to analyze whether the role of Xpr8 as lipid scramblase is evolutionarily conserved. C. elegans harbors only one ortholog of Xk proteins, CED-8, known to participate in the phagocytic removal of apoptotic corpses⁶. To determine the role of CED-8 in PS exposure, the authors took advantage of the “floater” assay, which is based on the appearance of floating cells (“floaters”) that have detached from developing C. elegans embryos defective for apoptotic cell phagocytosis⁷. Nagata''s group discovered that ced-8 deficiency leads to the accumulation of floaters. Moreover, ced-8 deficiency synergistically enhanced the number of floaters found in other engulfment mutants, which suggests that CED-8 function is not redundant to that developed by previously known engulfment mutants. This enhancing effect of ced-8 deletion was dependent on CED-3, the C. elegans ortholog of caspase-3, confirming the aforementioned results in mammalian cells. The authors then characterized that floaters resulting from ced-8 deletion show a largely deficient PS exposure after developmental apoptosis, confirming the evolutionarily conserved role of Xk-related proteins in apoptosis-induced lipid scrambling. However, they observed that ced-8 deletion does not lead to a total impairment in apoptotic PS presentation, suggesting that additional proteins must be involved in this process. Indeed, apoptosis-inducing factor can induce PS exposure in mammalian cells in a caspase-independent fashion⁸, and the C. elegans AIF ortholog, WAF-1, physically interacts with and activates another scramblase, SCRM-1⁴.Open in a separate windowFigure 1Xrp8 acts as apoptosis-induced lipid scramblase. Under normal conditions, the combined action of multiple mechanisms, including the activity of flippases and floppases, maintains lipid asymmetry between the outer and inner leaflets of the plasma membrane. Once apoptotic program is activated, caspases-3 and -7 are able to cleave and activate Xrp8 protein, which acts as a lipid scramblase and leads to the loss of lipid asymmetry, resulting in PS exposure to the extracellular space. This acts as the “eat-me” signal that will allow phagocytosis of post-apoptotic cell corpses. PC, phosphatidylcholine; SM, sphingomyelin; PE, phosphatidylethanolamine; PS, phosphatidylserine.In summary, through a series of elegant manipulations, Nagata''s group has found the long-sought caspase-activated lipid scramblase that mediates the exposure of “eat-me” signals in post-apoptotic cell corpses. Further studies involving Xkr8 protein, including the mechanisms participating in its epigenetic repression may open new roads for the study of autoimmune diseases, such as lupus erythematosus, which is associated with failure in the post-apoptotic corpse clearance system.     

Sphingolipid-mediated apoptotic signaling pathways

Various sphingolipids are being viewed as bioactive molecules and/or second messengers. Among them, ceramide (or N-acylsphingosine) and sphingosine generally behave as pro-apoptotic mediators. Indeed, ceramide mediates the death signal initiated by numerous stress agents which either stimulate its de novo synthesis or activate sphingomyelinases that release ceramide from sphingomyelin. For instance, the early generation of ceramide promoted by TNF is mediated by a neutral sphingomyelinase the activity of which is regulated by the FAN adaptor protein, thereby controlling caspase activation and the cell death programme. In addition, the activity of this neutral sphingomyelinase is negatively modulated by caveolin, a major constituent of some membrane microdomains. The enzyme sphingosine kinase also plays a crucial role in apoptosis signalling by regulating the intracellular levels of two sphingolipids having opposite effects, namely the pro-apoptotic sphingosine and the anti-apoptotic sphingosine 1-phosphate molecule. Ceramide and sphingosine metabolism therefore appears as a pivotal regulatory pathway in the determination of cell fate.     

Mammalian initiator apoptotic caspases

Caspases are a conserved family of cysteine proteases. They play diverse roles in inflammatory responses and apoptotic pathways. Among the caspases is a subgroup whose primary function is to initiate apoptosis. Within their long prodomains, caspases-2, -9 and -12 contain a caspase activation and recruitment domain while caspases-8 and -10 bear death effector domains. Activation follows the recruitment of the procaspase molecule via the prodomain to a high molecular mass complex. Despite sharing some common features, other aspects of the biochemistry, substrate specificity, regulation and signaling mechanisms differ between initiator apoptotic caspases. Defects in expression or activity of these caspases are related to certain pathological conditions including neurodegenerative disorders, autoimmune diseases and cancer.     

Search for apoptotic nucleases in yeast: role of Tat-D nuclease in apoptotic DNA degradation

DNA fragmentation/degradation is an important step for apoptosis. However, in unicellular organisms such as yeast, this process has rarely been investigated. In the current study, we revealed eight apoptotic nuclease candidates in Saccharyomyces cerevisiae, analogous to the Caenorhabditis elegans apoptotic nucleases. One of them is Tat-D. Sequence comparison indicates that Tat-D is conserved across kingdoms, implicating that it is evolutionarily and functionally indispensable. In order to better understand the biochemical and biological functions of Tat-D, we have overexpressed, purified, and characterized the S. cerevisiae Tat-D (scTat-D). Our biochemical assays revealed that scTat-D is an endo-/exonuclease. It incises the double-stranded DNA without obvious specificity via its endonuclease activity and excises the DNA from the 3'- to 5'-end by its exonuclease activity. The enzyme activities are metal-dependent with Mg(2+) as an optimal metal ion and an optimal pH around 5. We have also identified three amino acid residues, His(185), Asp(325), and Glu(327), important for its catalysis. In addition, our study demonstrated that knock-out of TAT-D in S. cerevisiae increases the TUNEL-positive cells and cell survival in response to hydrogen hyperoxide treatment, whereas overexpression of Tat-D facilitates cell death. These results suggest a role of Tat-D in yeast apoptosis.     

Hijacking of apoptotic pathwaysby bacterial pathogens

Increasing evidence indicates that apoptosis of the host cell may constitute a defense mechanism to confine the infection by bacterial pathogens. Certain pathogens have developed elegant mechanisms to modulate the fate of the host cell, which include induction or blockage of apoptosis. These studies will promote our understanding of the pathogenesis of infectious diseases and aid the development of means for therapeutic intervention.     

Markers of apoptotic dysfunctions in schizophrenia

According to the modern concepts, alterations of apoptosis and its genetic regulation are associated with the etiopathogenesis of schizophrenia, which is observed at both the brain and peripheral blood levels. However, studies of this phenomenon are at the initial stage, and the molecular and cellular mechanisms that underlie the anomalies of the processes of apoptotic cell death in schizophrenia are unclear. In the present study, we determined the levels of apoptotic markers, annexin A5 and H-ficolin proteins, in the sera of patients with chronic and first-episode schizophrenia and healthy subjects to test the proposed relationship between schizophrenia and the rs11575945 (?1C/T) single-nucleotide substitution (functional polymorphism) of Kozak consensus sequence in the regulatory region of the annexin A5 gene. Methods of a solid-phase enzyme-linked immunosorbent assay and polymerase chain reaction with allele-specific primers were used. It was shown that the pathogenesis of schizophrenia is characterized by an increased rate of apoptosis, which is more pronounced in the case of the first-episode neuroleptic-free patients than in the case of chronic patients that receive typical neuroleptic haloperidol. It was also shown that the rs11575945 polymorphism of the annexin A5 gene is associated with schizophrenia, and its minor allele is responsible for higher levels of the annexin A5 protein in the blood and represents one of the risk factors for the development of this disease.     

Clearance of apoptotic cells by phagocytes

Phagocytic clearance of apoptotic cells may be considered to consist of four distinct steps: accumulation of phagocytes at the site where apoptotic cells are located; recognition of dying cells through a number of bridge molecules and receptors; engulfment by a unique uptake process; and processing of engulfed cells within phagocytes. Here, we will discuss these individual steps that collectively are essential for the effective removal of apoptotic cells. This will illustrate our relative lack of knowledge about the initial attraction signals, the specific mechanisms of engulfment and processing in comparison to the extensive literature on recognition mechanisms. There is now mounting evidence that clearance defects are responsible for chronic inflammatory disease and contribute to autoimmunity. Therefore, a better understanding of all aspects of the clearance process is required before it can truly be manipulated for therapeutic gain.     

Degradation of chromatin in apoptotic cells

We present here a model for the degradation of chromatin in cells undergoing apoptosis. This model rationalises all aspects of the fragmentation process that have been described to date, explaining not only the patterns of degradation seen within individual cells, but also the variability in extent of degradation seen in different cells. Although DNA fragmentation in apoptosis was initially considered to be solely internucleosomal, it is now apparent that the process is much more complex and most, if not all, cells also produce much larger DNA fragments. However, in the same way that internucleosomal DNA fragmentation is a reflection of chromatin structure, the generation of these larger fragments is a reflection of chromatin structure, too. By comparing the ionic requirements for the complete pattern of chromatin degradation in nuclei with those required for apoptosis, it is apparent that the whole process may be catalysed by two pools of Mg-activated\Ca-modulated DNase I-like enzyme activities.     

Mitochondrial regulation of apoptotic cell death

Mitochondria play a decisive role in the regulation of both apoptotic and necrotic cell death. Permeabilization of the outer mitochondrial membrane and subsequent release of intermembrane space proteins are important features of both models of cell death. The mechanisms by which these proteins are released depend presumably on cell type and the nature of stimuli. Of the mechanisms involved, mitochondrial permeability transition appears to be associated mainly with necrosis, whereas the release of caspase activating proteins during early apoptosis is regulated primarily by the Bcl-2 family of proteins. However, there is increasing evidence for interaction and co-operation between these two mechanisms. The multiple mechanisms of mitochondrial permeabilization may explain diversities in the response of mitochondria to numerous apoptotic stimuli in different types of cells.