Biology subjects

Bardoel, B. W.

Publications and source records attributed to Bardoel, B. W..

11 recordsLinked to original sources

bioRxiv2026

C1q-mediated steric hindrance limits FcγR contribution to antibody-driven phagocytosis by human neutrophils

Phagocytosis and killing of bacteria by neutrophils is a key driver of human immunity against invading infections. IgG antibodies targeting the bacterial surface can potently enhance phagocytic uptake by engaging Fc gamma receptors (Fc{gamma}Rs) on the neutrophil membrane. In addition, IgG-mediated complement activation triggers surface deposition of complement opsonins that engage complement receptors (CRs) to further enhance target cell clearance. In this paper, we reveal that complement deposition prevents engagement of Fc{gamma}Rs to the Fc-domain of surface-bound IgG molecules. When complement is present, we observe that blockade of Fc{gamma}Rs does not influence phagocytosis of both Gram-positive and -negative bacteria (using Staphylococcus aureus and Klebsiella pneumoniae as model organisms). Complement-mediated hindrance of Fc{gamma}R engagement was observed in different model conditions, for example using either pre-existing polyclonal antibodies in human serum or recombinant monoclonal antibodies (mAbs) targeting different bacterial antigens. Using Fc engineering, we found that inhibition of Fc{gamma}R binding is dependent on the ability of IgGs to form IgG hexamers. Mechanistically, we show that complement proteins, in particular C1q, directly prevents the interaction between IgG-Fc and Fc{gamma}R by steric hindrance. Together, these insights help us define the respective roles of Fc{gamma}R and CR in neutrophil phagocytosis, while also providing important fundamental insights for therapeutic antibody development.

immunology↗

bioRxiv2026

Identification of a C3b-specific nanobody that does not bind C3 and blocks alternative pathway convertases

The human complement system is a protein network in blood and other body fluids that fights invading pathogens and is involved in maintaining homeostasis. A central step in the complement cascade is the conversion of complement protein C3 to C3b by convertase enzymes. Upon cleavage of C3, the nascent C3b molecule undergoes a large conformational change which exposes new epitopes. Molecules that discriminate between C3b and C3 could provide a powerful tool to selectively bind surface-bound complement activation products while leaving the circulating precursors untouched. In this study, we developed C3b-specific nanobodies by generating phage libraries from llamas immunized with purified and surface-bound C3b. We describe UNbC3b-1 as a high-affinity binder that recognizes soluble and surface-bound C3b molecules but does not bind to C3 in its native state. A 4.2 [A] structure of the UNbC3b-1:C3b complex generated by cryogenic electron microscopy shows that UNbC3b-1 binds C3b at the interface of MG3, MG4, and MG6, overlapping with the complement receptor immunoglobulin (CRIg) binding site. Functionally, we show that UNbC3b-1 inhibits complement activity in the alternative pathway (AP), likely by preventing association between substrate C3 and the AP C3 convertase (C3bBb). Altogether, nanobody UNbC3b-1 is a valuable tool to specifically bind C3b molecules and to selectively inhibit the AP convertases of the complement system.

immunology↗

bioRxiv2025

Excessive C5 conversion prevents C9 polymerisation and subsequent MAC-dependent killing of Klebsiella pneumoniae

Membrane Attack Complex (MAC) pores are important in the human innate immune response to directly kill pathogenic Gram-negative bacteria. MAC pores assemble when complement proteins in serum are activated on bacteria and convert complement protein C5 into C5b, which together with C6, C7, C8, and multiple copies of C9 form a pore that damages the bacterial envelope. Due to rising multidrug-resistant infections with Gram-negative pathogen Klebsiella pneumoniae (Kpn), there is interest in developing complement-activating monoclonal antibodies (mAbs) that trigger MAC-dependent killing. However, some Kpn strains resist MAC-dependent killing in serum despite potent complement activation and C5 conversion, revealing a critical gap in understanding how these strains resist MAC-dependent killing. We demonstrate that Kpn strains can resist MAC-dependent killing through a paradoxical mechanism of excessively converting C5, which limits C9 polymerisation and subsequent killing. In these strains, spiking serum with supplementary C9 restored killing. Additionally, partially inhibiting C5 conversion using complement inhibitors increased C9 polymerisation and subsequent killing. This suggests that these Kpn strains are in principle sensitive to MAC-dependent killing, but an imbalance between generated C5b and available C9 in serum limits C9 polymerisation and prevents killing. We also observed this paradoxical effect with an of excess complement-activating mAbs on Kpn strains that are typically susceptible to MAC-dependent killing in serum. Excessive C5 conversion was responsible for this reduced killing, as supplementary C9 restored killing. Lastly, in neonatal plasma, where C9 is naturally limited, complement-activating mAbs induced killing of Kpn only in the presence of supplementary C9. Our study highlights that the balance between C5 conversion and available C9 is important for MAC-dependent killing of Kpn. Additionally, absence of killing in serum does not necessarily indicate that Kpn strains are MAC-resistant. These insights are important for interpreting mAb efficacy in serum bactericidal assays and in complement-deficient populations. Author SummaryAntibiotic-resistant infections caused by Klebsiella pneumoniae represent a major global health challenge. The human immune system normally combats such bacteria by activation of complement proteins, a group of molecules in the blood that can assemble the Membrane Attack Complex (MAC). The MAC forms pores that puncture the bacterial cell envelope and kill bacteria. Here, we found that potent activation of complement proteins can paraxodically prevent killing of certain K. pneumoniae strains. Excessive conversion of MAC component C5 limits the assembly of MAC pores consisting of multiple copies of C9, which are required for killing. We show that when extra C9 was added, the bacteria were killed, demonstrating that they are not truly resistant to MAC pores but escape through this imbalance. We also observed this effect in newborn samples, where natural C9 levels are lower and when testing antibody-based therapies designed to boost complement activity. These findings reveal that the absence of bacterial killing in laboratory assays does not always reflect genuine resistance, but can result from disproportional activation. Recognising this mechanism is critical for developing effective antibody therapies, protecting vulnerable patients, and addressing the growing threat of antibiotic-resistant infections.

immunology↗

bioRxiv2025

Bactericidal Membrane Attack Complex formation initiates at the new pole of E. coli

Human immune protection against bacteria critically depends on activation of the complement system. The direct bacteriolytic activity of complement molecules against Gram-negative bacteria acts via the formation of Membrane Attack Complex (MAC) pores. Bactericidal MAC pores damage the bacterial outer membrane, leading to destabilization of the inner membrane. Although it is well-established that inner membrane damage is crucial for bacterial cell death, the critical event causing MAC-mediated inner membrane damage remains elusive. Here we questioned whether the bacterial cell envelope possesses vulnerable spots for MAC pores to insert. We followed the localization of MAC pores on E. coli over time using fluorescence microscopy and elucidate that MAC deposition initiates at the new bacterial pole, which induces inner membrane damage and halts bacterial division. MAC components C8 and C9 preferentially localize at new bacterial poles, while C3b localizes randomly on the bacterial surface. This suggests that preferential MAC localization is determined by one of the initial steps of MAC formation. These findings provide valuable information about the interplay between immune components and the Gram-negative cell envelope.

microbiology↗

bioRxiv2023

Inhibition of cleavage of human complement component C5 and the R885H C5 variant by two distinct high affinity anti-C5 nanobodies

The human complement system plays a crucial role in immune defense. However, its erroneous activation contributes to many serious inflammatory diseases. Since most unwanted complement effector functions result from C5 cleavage, development of C5 inhibitors, such as clinically approved monoclonal antibody Eculizumab, are of great interest. In this study, we developed and characterized two anti-C5 nanobodies, UNbC5-1 and UNbC5-2. Using surface plasmon resonance (SPR), we determined a binding affinity of 120 pM for UNbC5-1 and 8 pM for UNbC5-2. Competition experiments determined that the two nanobodies recognize distinct epitopes on C5. Both nanobodies efficiently interfered with C5 cleavage in a human serum environment, as they prevented red blood cell lysis via membrane attack complexes (C5b-9) and the formation of chemoattractant C5a. The cryo-EM structure of UNbC5-1 and UNbC5-2 in complex with C5 revealed that the binding interfaces of UNbC5-1 and UNbC5-2 overlap with known complement inhibitors Eculizumab and RaCI3, respectively. UNbC5-1 binds to the MG7 domain of C5, facilitated by a hydrophobic core and polar interactions, and UNbC5-2 interacts with the C5d domain mostly by salt bridges and hydrogen bonds. Interestingly, UNbC5-1 potently binds and inhibits C5 R885H, a genetic variant of C5, that is not recognized by Eculizumab. Altogether, we identified and characterized two different, high affinity nanobodies against human C5. Both nanobodies could serve as diagnostic and/or research tools to detect C5 or inhibit C5 cleavage. Furthermore, the residues targeted by UNbC5-1 hold important information for therapeutic inhibition of different polymorphic variants of C5.

immunology↗

bioRxiv2022

Colistin resistance mutations in phoQ sensitize Klebsiella pneumoniae to IgM-mediated complement killing

The Gram-negative bacterium Klebsiella pneumoniae is notorious for a strong increase of infections with antibiotic resistant strains. To treat infections with antibiotic resistant K. pneumoniae, clinicians increasingly need to use the last resort antibiotic colistin. K. pneumoniae can develop colistin resistance by modifying its membranes. During infection the membranes of Gram-negative bacteria are also targeted by the human immune system via the complement system. Gram-negative bacteria have an outer and inner membrane separated by a thin cell wall. Activation of the complement system leads to the formation of the membrane attack complex (MAC), a pore that inserts into the outer membrane, and ultimately leads to lysis of the bacterium. As both colistin and the MAC interact with the outer membrane of Gram-negative bacteria, we wondered if developing colistin resistance influences MAC-mediated killing of K. pneumoniae. Using clinical isolates that developed colistin resistance, we found that the strain Kp209_CSTR became more sensitive to MAC-mediated killing compared to the wild-type strain. MAC-mediated membrane permeabilization of Kp209_CSTR required antibody dependent activation of the classical complement pathway. Strikingly, Kp209_CSTR was bound by IgM in human serum that did not recognise the wild-type strain. Depletion of Kp209_CSTR-specific antibodies from serum prevented MAC-mediated membrane permeabilization, which was restored by adding back IgM. Genomic sequence comparison revealed that Kp209_CSTR has a deletion in the phoQ gene. RNAseq analysis suggested that this mutation locks PhoQ in a constitutively active state. These results indicate that PhoQ activation in Kp209_CSTR leads to both colistin resistance and sensitivity to MAC-mediated killing. Together, our results show that developing colistin resistance can sensitize K. pneumoniae to killing by the immune system.

microbiology↗

bioRxiv2022

Polyfunctional pathogen-specific CD4+ T cells reside in the lungs and tumors of NSCLC patients

Local T cell responses are required for optimal protection of the lungs against airborne pathogens. This localized protection is mediated by various immune cells, including resident memory T cells (TRM). While human lung CD8+ TRM line the epithelium and are enriched for recognition of respiratory viruses, we found CD4+ TRM to exhibit more heterogeneous localization patterns, surrounding airways, forming clusters in the lung parenchyma, and lining the epithelium. This heterogeneity was also reflected functionally, as lung CD4+ TRM were enriched for recognition of diverse classes of respiratory pathogens. Upon stimulation, lung CD4+ TRM expressed different polyfunctional cytokine profiles depending on the pathogen recognized. CD4+ TRM responding to respiratory viruses and bacteria were biased for production of IFN-{gamma} and IL-17, respectively. Strikingly, pathogen-specific CD4+ TRM also represent a significant fraction in NSCLC tumors that remained polyfunctional despite high PD-1 expression. These findings are not only important for vaccine design, but also provide a rationale for reinvigorating anti-tumor immunity through triggering of polyfunctional pathogen-specific CD4+ tumor infiltrating lymphocytes.

immunology↗

bioRxiv2021

Soluble MAC is primarily released from MAC-resistant bacteria that potently convert complement component C5

The Membrane Attack Complex (MAC or C5b-9) is an important effector of the immune system to kill invading microbes. MAC is formed when complement enzymes on the bacterial surface convert complement component C5 into C5b. Although the MAC is a membrane-inserted complex, soluble forms of MAC (sMAC, or terminal complement complex (TCC)) are often detected in sera of patients suffering from infections. Consequently, sMAC has been proposed as a biomarker, but it remains unclear when and how it is formed during infections. Here, we studied mechanisms of MAC formation on bacteria and found that sMAC is primarily formed in human serum by bacteria resistant to MAC-dependent killing. Surprisingly, C5 was converted into C5b more potently by MAC-resistant compared to MAC-sensitive Escherichia coli strains. Both the increase in C5 conversion and sMAC generation were linked to the expression of lipopolysaccharide (LPS) O-Antigen in the bacterial outer membrane. In addition, we found that MAC precursors are released from the surface of MAC-resistant bacteria during MAC assembly. Release of MAC precursors from bacteria induced lysis of bystander human erythrocytes in the absence of other serum components. However, serum regulators vitronectin (Vn) and clusterin (Clu) can prevent this bystander lysis. Combining size exclusion chromatography with mass spectrometry profiling, we show that sMAC released from bacteria in serum is a heterogeneous mixture of complexes composed of C5b-8, up to 3 copies of C9 and multiple copies of Vn and Clu. Altogether, our data provide molecular insight into how sMAC is generated during bacterial infections. This fundamental knowledge could form the basis for exploring the use of sMAC as biomarker.

microbiology↗

bioRxiv2021

Polymerization of C9 enhances bacterial cell envelope damage and killing by membrane attack complex pores

Complement proteins can form Membrane Attack Complex (MAC) pores that directly kill Gram-negative bacteria. MAC pores assemble by stepwise binding of C5b, C6, C7, C8 and finally C9, which can polymerize into a transmembrane ring of up to 18 C9 monomers. It is still unclear if the assembly of a polymeric-C9 ring is necessary to sufficiently damage the bacterial cell envelope to kill bacteria, because a robust way to specifically prevent polymerization of C9 has been lacking. In this paper, polymerization of C9 was prevented without affecting the binding of C9 to C5b-8 by locking the first transmembrane helix domain of C9. We show that polymerization of C9 strongly enhanced bacterial cell envelope damage and killing by MAC pores for several Escherichia coli and Klebsiella strains. Moreover, we show that polymerization of C9 is impaired on complement-resistant E. coli strains that survive killing by MAC pores. Altogether, these insights are important to understand how MAC pores kill bacteria and how bacterial pathogens can resist MAC-dependent killing.

microbiology↗

bioRxiv2020

Outer membrane permeabilization by the membrane attack complex sensitizes Gram-negative bacteria to antimicrobial proteins in serum and phagocytes

Infections with Gram-negative bacteria form an increasing risk for human health, which is mainly due to the increase in antibiotic resistance. The cell envelope of Gram-negative bacteria consists of an inner membrane, a peptidoglycan layer and an outer membrane, which forms an impermeable barrier to many antibiotics and antimicrobial proteins. The complement system is an important factor of the human immune system that can efficiently kill Gram-negative bacteria via the formation of large pores in the bacterial outer membrane, called Membrane Attack Complexes (MACs). To better understand how these MAC pores damage the complex cell envelope of Gram-negative bacteria, we recently developed a fluorescent reporter system to study membrane damage in E. coli. Here, we used a similar experimental setup in combination with flow cytometry, confocal microscopy and conventional plating assays to elucidate how different components of the immune system act synergistically to effectively clear invading bacteria. We demonstrate how MAC-dependent outer membrane damage enhances the susceptibility of E. coli to further degradation of the cell envelope by lysozyme, leading to drastic changes in the morphology of these bacteria. Furthermore, we elucidate that the MAC enhances the susceptibility of E. coli to phospholipases, and to degradation and killing inside human neutrophils. Altogether, this study provides a detailed overview on how different players of the human immune system work closely together to degrade the complex cell envelope of Gram-negative bacteria. This knowledge may facilitate the development of new antimicrobials that could stimulate, or work synergistically with the immune system.

immunology↗

bioRxiv2019

Bacterial killing by complement requires direct anchoring of Membrane Attack Complex precursor C5b-7

An important effector function of the human complement system is to directly kill Gram-negative bacteria via Membrane Attack Complex (MAC) pores. MAC pores are assembled when surface-bound convertase enzymes convert C5 into C5b, which together with C6, C7, C8 and multiple copies of C9 forms a transmembrane pore that damages the bacterial cell envelope. Recently, we found that bacterial killing by MAC pores requires local conversion of C5 by surface-bound convertases. In this study we aimed to understand why local assembly of MAC pores is essential for bacterial killing. Here, we show that rapid interaction of C7 with C5b6 is required to form bactericidal MAC pores. Binding experiments with fluorescently labelled C6 show that C7 prevents release of C5b6 from the bacterial surface. Moreover, trypsin shaving experiments and atomic force microscopy revealed that this rapid interaction between C7 and C5b6 is crucial to efficiently anchor C5b-7 to the bacterial cell envelope and form complete MAC pores. Using complement-resistant clinical E. coli strains, we show that bacterial pathogens can prevent complement-dependent killing by interfering with the anchoring of C5b-7. While C5 convertase assembly was unaffected, these resistant strains blocked efficient anchoring of C5b-7 and thus prevented stable insertion of MAC pores into the bacterial cell envelope. Altogether, these findings provide basic molecular insights into how bactericidal MAC pores are assembled and how bacteria evade MAC-dependent killing.

immunology↗