Evidence for multiple modes of neutrophil serine protease recognition by the EAP family of Staphylococcal innate immune evasion proteins

The mononuclear phagocyte system obscures the accurate diagnosis of infected joint replacements

INTRODUCTION

Diagnosing infected joint replacements relies heavily on assessing the neutrophil response to bacteria. Bacteria form biofilms on joint replacements. Biofilms are sessile bacterial communities encased in a protective extracellular matrix, making them notoriously difficult to culture, remarkably tolerant to antibiotics, and able to evade phagocytosis. Phagocytized bacteria dramatically alter cytokine production and compromise macrophage antigen presentation. We hypothesize that a subset of joint replacements have a dormant infection that suppresses the neutrophil response to bacteria but can be distinguished from uninfected joint replacements by the response of the mononuclear phagocyte system (MPS) within periarticular tissue, synovial fluid, and circulating plasma.

METHODS

Single cell RNASeq transcriptomic and OLink proteomic profiling was performed on matched whole blood, synovial fluid, and periarticular tissue samples collected from 4 joint replacements with an active infection and 3 joint replacements without infection as well as 6 joint replacements with a prior infection deemed "infection-free" by the 2018 Musculoskeletal Infection Society criteria (follow-up of 26 ± 3 months).

RESULTS

The MPS and neutrophil responses differ by infected state; the cellular distribution of the MPS response in the subset of joints with dormant infections resembled actively infected joints (p = 0.843, Chi-square test) but was significantly different from uninfected joints (p < 0.001, Chi-square test) despite the absence of systemic acute phase reactants and recruitment of neutrophils (p < 0.001, t-test). When compared to no infection, the cellular composition of dormant infection was distinct. There was reduction in classically activated M1 macrophages (p < 0.001, Fischer's test) and alternatively activated M2 macrophages coupled with an increase in classical monocytes (p < 0.001, Fischer's test), myeloid dendritic cells (p < 0.001, Fischer's test), regulatory T-cells (p < 0.001, Fischer's test), natural killer cells (p = 0.009, Fischer's test), and plasmacytoid dendritic cells (p = 0.005, Fischer's test). Hierarchical cluster analysis and single-cell gene expression revealed that classically M1 and alternatively M2 activated macrophages as well as myeloid dendritic cells can independently distinguish the dormant and uninfected patient populations suggesting that a process that modulates neutrophil recruitment (C1QA, C1QB, LY86, SELL, CXCL5, CCL20, CD14, ITGAM), macrophage polarization (FOSB, JUN), immune checkpoint regulation (IFITM2, IFITM3, CST7, THBS1), and T-cell response (VISIG4, CD28, FYN, LAT2, FCGR3A, CD52) was occurring during dormant infection. Gene set variation analysis suggested that activation of the TNF (FDR < 0.01) and IL17 (FDR < 0.01) pathways may distinguish dormant infections from the active and uninfected populations, while an inactivation of neutrophil extracellular traps (NETs) may be involved in the lack of a clinical response to a dormant infection using established diagnostic criteria. Synovial inflammatory proteomics show an increase in synovial CXCL5 associated with dormant infection (p = 0.011, t-test), suggesting the establishment of a chronic inflammatory state by the MPS during a dormant infection involved in neutrophil inhibition. Plasma inflammatory proteomics also support a chronic inflammatory state (EGF, GZMN, FGF2, PTN, MMP12) during dormant infection that involves a reduction in neutrophil recruitment (CXCL5, p = 0.006, t-test), antigen presentation (LAMP3, p = 0.047, t-test), and T-cell function (CD28, p = 0.045, t-test; CD70, p = 0.002, t-test) that are also seen during the development of bacterial tolerance.

DISCUSSION

All current diagnostic criteria assume each patient can mount the same neutrophil response to an implant-associated infection. However, the state of the MPS is of critical importance to accurate diagnosis of an implant-associated infection. A reduction in neutrophil recruitment and function mediated by the MPS may allow joint replacements with a dormant infection to be mischaracterized as uninfected, thus limiting the prognostic capabilities of all current diagnostic tests.

New advances in understanding inhibition of myeloperoxidase and neutrophil serine proteases by two families of staphylococcal innate immune evasion proteins

Neutrophils are the most abundant leukocytes in humans and play an important early role in the innate immune response against microorganisms. Neutrophil phagosomes contain high concentrations of antibacterial enzymes, including myeloperoxidase (MPO) and the neutrophil serine proteases (NSPs). These antibacterial enzymes can also be released extracellularly upon degranulation or as a component of neutrophil extracellular traps (NETs). Due to host/pathogen coevolution, S. aureus expresses a diverse arsenal of innate immune evasion proteins that target many aspects of the neutrophil antibacterial response. In the last decade, two new classes of staphylococcal innate immune evasion proteins that act as potent, selective inhibitors of MPO and NSPs, respectively, have been discovered. The Staphylococcal Peroxidase INhibitor (SPIN) is a small ∼8.3 kDa α-helical bundle protein that blocks MPO activity by interfering with substrate and product exchange with the MPO active site. The Extracellular Adherence Protein (EAP) family consists of three unique proteins comprised of one or more copies of an ∼11 kDa β-grasp domain capable of high-affinity, selective, non-covalent inhibition of NSPs. This brief review article summarizes recent advances in understanding the structural and functional properties of SPIN and EAP family members and outlines some potential avenues for future investigation of these enzyme inhibitors.

S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases

Staphylococcus aureus expresses three high-affinity neutrophil serine protease (NSP) inhibitors known as the extracellular adherence protein domain (EAPs) proteins. Whereas EapH1 and EapH2 are comprised of a single EAP domain, the modular extracellular adherence protein (Eap) from S. aureus strain Mu50 consists of four EAP domains. We recently reported that EapH2 can simultaneously bind and inhibit cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant NSPs. This unusual property of EapH2 arises from independent CG and NE-binding sites that lie on opposing faces of its EAP domain. Here we used X-ray crystallography and enzyme assays to show that all four individual domains of Eap (i.e. Eap1, Eap2, Eap3, and Eap4) exhibit an EapH2-like ability to form ternary complexes with CG and NE that inhibit both enzymes simultaneously. We found that Eap1, Eap2, and Eap3 have similar functional profiles insofar as NSP inhibition is concerned but that Eap4 displays an unexpected ability to inhibit two NE enzymes simultaneously. Using X-ray crystallography, we determined that this second NE-binding site in Eap4 arises through the same region of its EAP domain that also comprises its CG-binding site. Interestingly, small angle X-ray scattering data showed that stable tail-to-tail dimers of the NE/Eap4/NE ternary complex exist in solution. This arrangement is compatible with NSP-binding at all available sites in a two-domain fragment of Eap. Together, our work implies that Eap is a polyvalent inhibitor of NSPs. It also raises the possibility that higher-order structures of NSP-bound Eap may have unique functional properties.

Staphylococcal peroxidase inhibitor (SPIN): Residue-level investigation of the helical bundle domain

Myeloperoxidase is a critical component of the antibacterial arsenal of neutrophils, whereby it consumes H2O2 as an oxidant to convert halogen and pseudohalogen anions into cytotoxic hypohalous acids. Following phagocytosis by neutrophils, the human pathogen Staphylococcus aureus secretes a potent myeloperoxidase inhibitory protein, called SPIN, as part of its immune evasion repertoire. The matured S. aureus SPIN polypeptide consists of only 73 residues yet contains two functional domains: whereas the 60 residue C-terminal helical bundle domain is responsible for MPO binding, the 13 residue N-terminal domain is required to inhibit MPO. Previous studies have informed understanding of the SPIN N-terminal domain, but comparatively little is known about the helical domain insofar as the contribution of individual residues is concerned. To address this limitation, we carried out a residue-level structure/function investigation on the helical bundle domain of S. aureus SPIN. Using sequence conservation and existing structures of SPIN bound to human MPO as a guide, we selected residues L49, E50, H51, E52, Y55, and Y75 for interrogation by site-directed mutagenesis. We found that loss of L49 or E52 reduced SPIN activity by roughly an order of magnitude, but that loss of Y55 or H51 caused progressively greater loss of inhibitory potency. Direct binding studies by SPR showed that loss of inhibitory potency in these SPIN mutants resulted from a diminished initial interaction between the inhibitor and MPO. Together, our studies provide new insights into the structure/function relationships of SPIN and identify positions Y55 and H51 as critical determinants of SPIN function.

Simultaneous inhibition of two neutrophil serine proteases by the S. aureus innate immune evasion protein EapH2

Extracellular adherence protein domain (EAP) proteins are high-affinity, selective inhibitors of neutrophil serine proteases (NSP), including cathepsin-G (CG) and neutrophil elastase (NE). Most Staphylococcus aureus isolates encode for two EAPs, EapH1 and EapH2, that contain a single functional domain and share 43% identity with one another. Although structure/function investigations from our group have shown that EapH1 uses a globally similar binding mode to inhibit CG and NE, NSP inhibition by EapH2 is incompletely understood due to a lack of NSP/EapH2 cocrystal structures. To address this limitation, we further studied NSP inhibition by EapH2 in comparison with EapH1. Like its effects on NE, we found that EapH2 is a reversible, time-dependent, and low nanomolar affinity inhibitor of CG. We characterized an EapH2 mutant which suggested that the CG binding mode of EapH2 is comparable to EapH1. To test this directly, we used NMR chemical shift perturbation to study EapH1 and EapH2 binding to CG and NE in solution. Although we found that overlapping regions of EapH1 and EapH2 were involved in CG binding, we found that altogether distinct regions of EapH1 and EapH2 experienced changes upon binding to NE. An important implication of this observation is that EapH2 might be capable of binding and inhibiting CG and NE simultaneously. We confirmed this unexpected feature by solving crystal structures of the CG/EapH2/NE complex and demonstrating their functional relevance through enzyme inhibition assays. Together, our work defines a new mechanism of simultaneous inhibition of two serine proteases by a single EAP protein.

Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family

Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure-function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10-9 M) and of NE (on the order of 10-10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.

Staphylococcus aureus and Neutrophil Extracellular Traps: The Master Manipulator Meets Its Match in Immunothrombosis

Over the past 10 years, neutrophil extracellular traps (NETs) have become widely accepted as an integral player in immunothrombosis, due to their complex interplay with both pathogens and components of the coagulation system. While the release of NETs is an attempt by neutrophils to trap pathogens and constrain infections, NETs can have bystander effects on the host by inducing uncontrolled thrombosis, inflammation, and tissue damage. From an evolutionary perspective, pathogens have adapted to bypass the host innate immune response. Staphylococcus aureus (S. aureus), in particular, proficiently overcomes NET formation using several virulence factors. Here we review mechanisms of NET formation and how these are intertwined with platelet activation, the release of endothelial von Willebrand factor, and the activation of the coagulation system. We discuss the unique ability of S. aureus to modulate NET formation and alter released NETs, which helps S. aureus to escape from the host's defense mechanisms. We then discuss how platelets and the coagulation system could play a role in NET formation in S. aureus-induced infective endocarditis, and we explain how targeting these complex cellular interactions could reveal novel therapies to treat this disease and other immunothrombotic disorders.

Local structural plasticity of the Staphylococcus aureus evasion protein EapH1 enables engagement with multiple neutrophil serine proteases

Members of the EAP family of Staphylococcus aureus immune evasion proteins potently inhibit the neutrophil serine proteases (NSPs) neutrophil elastase, cathepsin-G, and proteinase-3. Previously, we determined a 1.8 Å resolution crystal structure of the EAP family member EapH1 bound to neutrophil elastase. This structure revealed that EapH1 blocks access to the enzyme's active site by forming a noncovalent complex with this host protease. To determine how EapH1 inhibits other NSPs, we studied here the effects of EapH1 on cathepsin-G. We found that EapH1 inhibits cathepsin-G with a K_i of 9.8 ± 4.7 nm Although this K_i value is ∼466-fold weaker than the K_i for EapH1 inhibition of neutrophil elastase, the time dependence of inhibition was maintained. To define the physical basis for EapH1's inhibition of cathepsin-G, we crystallized EapH1 bound to this protease, solved the structure at 1.6 Å resolution, and refined the model to R_work and R_free values of 17.4% and 20.9%, respectively. This structure revealed a protease-binding mode for EapH1 with cathepsin-G that was globally similar to that seen in the previously determined EapH1-neutrophil elastase structure. The nature of the intermolecular interactions formed by EapH1 with cathepsin-G differed considerably from that with neutrophil elastase, however, with far greater contributions from the inhibitor backbone in the cathepsin-G-bound form. Together, these results reveal that EapH1's ability to form high-affinity interactions with multiple NSP targets is due to its remarkable level of local structural plasticity.

The Legionella pneumophila Metaeffector Lpg2505 (MesI) Regulates SidI-Mediated Translation Inhibition and Novel Glycosyl Hydrolase Activity

Legionella pneumophila, the etiological agent of Legionnaires' disease, employs an arsenal of hundreds of Dot/Icm-translocated effector proteins to facilitate replication within eukaryotic phagocytes. Several effectors, called metaeffectors, function to regulate the activity of other Dot/Icm-translocated effectors during infection. The metaeffector Lpg2505 is essential for L. pneumophila intracellular replication only when its cognate effector, SidI, is present. SidI is a cytotoxic effector that interacts with the host translation factor eEF1A and potently inhibits eukaryotic protein translation by an unknown mechanism. Here, we evaluated the impact of Lpg2505 on SidI-mediated phenotypes and investigated the mechanism of SidI function. We determined that Lpg2505 binds with nanomolar affinity to SidI and suppresses SidI-mediated inhibition of protein translation. SidI binding to eEF1A and Lpg2505 is not mutually exclusive, and the proteins bind distinct regions of SidI. We also discovered that SidI possesses GDP-dependent glycosyl hydrolase activity and that this activity is regulated by Lpg2505. We have therefore renamed Lpg2505 MesI (metaeffector of SidI). This work reveals novel enzymatic activity for SidI and provides insight into how intracellular replication of L. pneumophila is regulated by a metaeffector.

Staphylococcus aureus evasion proteins EapH1 and EapH2: Residue-level investigation of an alternative binding motif for human neutrophil elastase

The Staphylococcus aureusExtracellular Adherence Protein (Eap) and its homologs, EapH1 and EapH2, are a family of secreted proteins that potently inhibit the neutrophil serine proteases Neutrophil Elastase (hNE), Cathepsin G, and Proteinase 3. Similarly to EapH1, inhibition of hNE by EapH2 is characterized by a rapid association rate (2.9 × 10⁵ M^-1s^-1) coupled with a very slow dissociation rate (5.9 × 10^-4 s^-1), yielding an apparent inhibition constant of 2.11 nM. As with EapH1, inhibition of hNE by EapH2 is also time-dependent in character. A phenylalanine in EapH2 replaces the leucine in EapH1 that sits over the hNE catalytic serine and creates a potential steric clash. Indeed, the EapH1 L59F mutant is severely decreased in its ability to inhibit hNE (~9500-fold). When compared to the EapH1:hNE co-crystal structure, a model of the EapH2:hNE complex predicts an alternative binding motif comprised of EapH2 residues 120-127. These putative interfacing residues were individually mutated and kinetically interrogated. The EapH2 N127A mutant resulted in the largest decrease in hNE inhibition (~200-fold) and loss of the time-dependent characteristic. Surprisingly, the time-dependent characteristic was still abolished in the EapH2 T125A mutant, even though it was less perturbed in hNE inhibition (~25-fold). T125 forms an intra-molecular hydrogen bond to the carbonyl oxygen of N127 in the EapH2 crystal structure. Given these observations, we conclude (i) that EapH2 has an altogether distinct hNE binding motif than EapH1, (ii) that N127 is the main functional determinant in EapH2, and (iii) that T125 serves an ancillary role aiding in the optimal orientation of N127.

Staphylococcus aureus versus neutrophil: Scrutiny of ancient combat

Staphylococcus aureus (S.aureus) is a Gram-positive bacterium that causes many infections and diseases. This pathogen can cause many types of infections such as impetigo, toxic shock syndrome toxin (TSST1), pneumonia, endocarditis, and autoimmune diseases like lupus erythematosus and can infect other healthy individuals. In the pathogenic process, colonization is a main risk factor for invasive diseases. Various factors including the cell wall-associated factors and receptors of the epithelial cells facilitate adhesion and colonization of this pathogen. S. aureus has many enzymes, toxins, and strategies to evade from the immune system either by an enzyme that lyses cellular component or by hiding from the immune system via surface antigens like protein A and second immunoglobulin-binding protein (Sbi). The strategies of this bacterium can be divided into five groups: A: Inhibit neutrophil recruitment B: Inhibit phagocytosis C: Inhibit killing by ROS, D: Neutrophil killing, and E: Resistance to antimicrobial peptide. On the other hand, innate immune system via neutrophils, the most important polymorphonuclear leukocytes, fights against bacterial cells by neutrophil extracellular trap (NET). In this review, we try to explain the role of each factor in immune evasion.

Immune Evasion by Staphylococcus aureus

Staphylococcus aureus has become a serious threat to human health. In addition to having increased antibiotic resistance, the bacterium is a master at adapting to its host by evading almost every facet of the immune system, the so-called immune evasion proteins. Many of these immune evasion proteins target neutrophils, the most important immune cells in clearing S. aureus infections. The neutrophil attacks pathogens via a plethora of strategies. Therefore, it is no surprise that S. aureus has evolved numerous immune evasion strategies at almost every level imaginable. In this review we discuss step by step the aspects of neutrophil-mediated killing of S. aureus, such as neutrophil activation, migration to the site of infection, bacterial opsonization, phagocytosis, and subsequent neutrophil-mediated killing. After each section we discuss how S. aureus evasion molecules are able to resist the neutrophil attack of these different steps. To date, around 40 immune evasion molecules of S. aureus are known, but its repertoire is still expanding due to the discovery of new evasion proteins and the addition of new functions to already identified evasion proteins. Interestingly, because the different parts of neutrophil attack are redundant, the evasion molecules display redundant functions as well. Knowing how and with which proteins S. aureus is evading the immune system is important in understanding the pathophysiology of this pathogen. This knowledge is crucial for the development of therapeutic approaches that aim to clear staphylococcal infections.

Heterogeneous early immune responses to the S. aureus EapH2 antigen induced by gastrointestinal tract colonisation impact the response to subsequent vaccination

INTRODUCTION

S. aureus is a pathogen to which individuals are exposed shortly after birth, with immune responses to S. aureus increasing during childhood. There is marked heterogeneity between the anti- S. aureus immune responses of different humans, the basis of which is not fully understood.

METHODS

To investigate development of anti-S. aureus immune responses, we studied S. aureus colonised mice under controlled conditions. Mice were either acquired colonised from breeding colonies, or experimentally colonised by exposure to a cage environment which had been sprayed with a S. aureus suspension. Colonisation was monitored by sequential stool sampling, and immunoglobulin levels against both whole fixed S. aureus and individual S. aureus antigens quantified. The immunological impact of colonisation on subsequent vaccination was investigated.

RESULTS

Colonised BALB/c and BL/6 mice develop serum anti- S. aureus cell surface IgG1 antibodies. Responses were proportional to the cumulative S. aureus bioburden in the mice, and were higher in BALB/c mice, which have higher colonisation levels, than in C57BL/6 animals. We observed marked variation in the induction of anti-cell surface antibodies, even in genetically identical mice experimentally colonised with the same S. aureus clone. Heterogeneity was also evident when monitoring immune responses to the secreted S. aureus protein EapH2. Approximately 50% of colonised mice developed anti-EapH2 responses (responders); in other mice, responses were not significantly different to those in uncolonised mice (non-responders). Following vaccination with a replication deficient adenovirus expressing EapH2, less anti-EapH2 antibody was generated in non-responder than responder animals.

CONCLUSIONS

In genetically identical mice, S. aureus colonisation results in all-or-nothing antibody responses against some antigens, including EapH2. For antigens involved in colonisation success by microbes, apparently stochastic early immune responses may impact both vaccine responses and the establishment of an animal-specific microbiome.

Investigation of Human Neutrophil Elastase Inhibition by Staphylococcus aureus EapH1: The Key Role Played by Arginine 89

Staphylococcus aureus secretes a family of potent, noncovalent inhibitory proteins that selectively target the neutrophil serine proteases neutrophil elastase, cathepsin-G, and proteinase-3. A majority of our understanding of these so-called EAP domain proteins has come from structure/function studies on EapH1 and its effects on human neutrophil elastase (hNE). Inspection of the EapH1/hNE cocrystal structure suggested that EapH1 residues R89, E94, and K95 are positioned near the EapH1/hNE interface and might contribute to the potent inhibition of hNE by EapH1. In this study, we used site directed mutagenesis, kinetic evaluation, and surface plasmon resonance to probe the individual contributions of R89, E94, and K95 to EapH1 function. We found that the wild-type EapH1/hNE complex is characterized by a fast association rate (2.0 × 10⁶ M^-1 s^-1) and a very slow dissociation rate (4.3 × 10^-5 s^-1), yielding an apparent inhibition constant of 21 pM. The slow dissociation rate of EapH1 from hNE resulted in a time-dependent inhibition pattern. Although conservative mutants E94Q and K95M, as well as the E94Q/K95M double mutant, had on- and off-rates comparable to wild-type EapH1, mutation of R89 to methionine resulted in a 15,000-fold decrease in inhibition (321 nM) and loss of the time-dependent inhibition characteristic. The double mutants R89M/E94Q and R89M/K95M, as well as the triple mutant R89M/E94Q/K95M were similarly perturbed. Mutation of R89 to lysine restored a portion of the inhibition of hNE (27 nM). Given these observations, we conclude that R89 is a primary contributor to EapH1 function vis-à-vis time-dependent inhibition of hNE.

Vaccination with the Staphylococcus aureus secreted proteins EapH1 and EapH2 impacts both S. aureus carriage and invasive disease

INTRODUCTION

There is a need for an efficacious vaccine reducing infections due to Staphylococcus aureus, a common cause of community and hospital infection. Infecting organisms originate from S. aureus populations colonising the nares and bowel. Antimicrobials are widely used to transiently reduce S. aureus colonisation prior to surgery, a practice which is selecting for resistant S. aureus isolates. S. aureus secretes multiple proteins, including the protease inhibitors extracellular adhesion protein homologue 1 and 2 (EapH1 and EapH2).

METHODS

Mice were vaccinated intramuscularly or intranasally with Adenovirus serotype 5 and Modified Vaccinia Ankara viral vectors expressing EapH1 and EapH2 proteins, or with control viruses. Using murine S. aureus colonisation models, we monitored S. aureus colonisation by sequential stool sampling. Monitoring of S. aureus invasive disease after intravenous challenge was performed using bacterial load and abscess numbers in the kidney.

RESULTS

Intramuscular vaccination with Adenovirus serotype 5 and Modified Vaccinia Ankara viral vectors expressing EapH1 and EapH2 proteins significantly reduces bacterial recovery in the murine renal abscess model of infection, but the magnitude of the effect is small. A single intranasal vaccination with an adenoviral vaccine expressing these proteins reduced S. aureus gastrointestinal (GI) tract colonisation.

CONCLUSION

Vaccination against EapH1 / EapH2 proteins may offer an antibiotic independent way to reduce S. aureus colonisation, as well as contributing to protection against S. aureus invasive disease.