Biology subjects

Schmidt, F. I.

Publications and source records attributed to Schmidt, F. I..

10 recordsLinked to original sources

bioRxiv2026

Human NLRC4 can act as a direct sensor for cytosolic flagellin

Innate immune cells sense pathogenic bacteria like Legionella pneumophila through patterns such as the protein flagellin, a critical component of the bacterial motility apparatus. Recognition of cytosolic flagellin in mouse immune cells is well understood and mediated by the receptors, neuronal apoptosis inhibitory protein (Naip) 5 or Naip6, which activate the Nlrc4 inflammasome multi-protein complex for initiating cell death or interleukin-1 family cytokine release. However, the role of human NAIP as a cytosolic flagellin sensor remains controversial. Using a multipronged approach, we demonstrate that in a reconstituted cell system human NLRC4 engaged Legionella FlaA flagellin directly (i.e. without the need for hNAIP), whereas human NAIP did not interact with FlaA. Ectopic cytosolic FlaA expression also induced NLRC4 oligomerization, a prerequisite for inflammasome activation, in the absence of NAIP. Unexpectedly, the presence of NAIP diminished the binding of NLRC4 to flagellins and subsequent interleukin-1{beta} release. Interestingly, in resting THP-1 cells, NAIP stably interacted with NLRC4, and during infection or stimulation with FlaA pro-inflammatory responses in THP-1 cells were predominantly NLRC4-dependent. Our data highlight NLRC4 as a putative direct sensor of cytosolic flagellins in the human system and NAIP as a potential negative regulator of flagellin sensing.

immunology↗

bioRxiv2025

Lipid nanoparticle delivered intrabodies for inhibiting necroptosis and pyroptosis

Intrabodies are intracellularly expressed high-affinity protein binders such as nanobodies and monobodies that offer an alternative approach to small molecules. However, the maturation of intrabody technology into new therapeutic modalities has been limited by the availability of a clinically relevant delivery system enabling sufficiently high levels of protein to be expressed in the cytosol. Here, we use lipid nanoparticle (LNP) systems based on clinically approved formulations for the efficient intracellular delivery of mRNAs encoding for intrabodies targeting mixed lineage kinase domain-like pseudokinase (MLKL) and apoptosis-associated speck-like protein containing a CARD (ASC), key mediators of the necrotic cell death modalities, necroptosis and pyroptosis, respectively. LNP delivery of intrabody mRNA resulted in robust protein expression, with a MLKL binding intrabody preventing MLKL membrane translocation and protecting against necroptotic cell death. Similarly, LNP delivery of a bivalent intrabody targeting the inflammasome adaptor protein ASC protected against NLRP3 and AIM2 inflammasome-driven responses, including caspase-1 and IL-1{beta} activation and gasdermin D-driven pyroptotic killing. These findings establish that LNPs harbouring anti-necrotic intrabody mRNAs allow for sufficient intracellular expression to neutralize necrotic cell death signalling and provide a general, clinically relevant, strategy for delivering therapeutic intrabodies into cells.

bioengineering↗

bioRxiv2025

A novel reporter to visualize and quantify endogenous inflammasomes and caspase-1 recruitment

Inflammasomes are signaling complexes that coordinate inflammation by inducing rapid cytokine secretion and that protect against invading pathogens by initiating death of infected cells. Yet, current methods do not allow us to specifically monitor inflammasome activation in real-time at endogenous protein levels. To overcome this shortcoming, we developed and characterized a novel fluorescent reporter that visualizes inflammasome assembly and reports on the recruitment of the effector protein caspase-1 without impairing downstream signaling. The reporter permits the analysis of inflammasome assembly over time as well as precise quantification of cells with assembled inflammasomes. We have successfully applied the reporter in lentivirus-transduced human and murine cell lines and primary cells but have also applied recombinant viruses that encode the reporter in their genome to detect inflammasome responses in primary cells. Mouse intestinal enteroids expressing the reporter allowed us to visualize how Salmonella infection triggers NAIP/NLRC4 inflammasome assembly, cell death, and expulsion in complex tissues. Lastly, we apply the new tool to gain mechanistic insights and prove that caspase-1 activation on inflammasomes relies on the assembly of filaments of caspase-1CARD, which can be terminated by the CARD-only protein CARD17 to shut down cytokine secretion. We anticipate broad application of the reporter in fundamental and applied research, as it permits the quantitative assessment of inflammasome assembly at both high temporal and spatial resolution or in high throughput.

immunology↗

bioRxiv2023

hnRNPM and ELAVL1 control type I interferon induction by promoting IRF3 phosphorylation downstream of both cGAS and RIG-I

RIG-I and cGAS are crucial sensors of viral nucleic acids and induce type I IFNs via TBK1/IKK and IRF3. Here, we have identified hnRNPM as a novel positive regulator of IRF3 phosphorylation and type I IFN induction downstream of both cGAS and RIG-I. Combining interactome analysis and genome editing, we further identified ELAVL1 as an immune-relevant interactor of hnRNPM. Depletion of hnRNPM or ELAVL1 impaired type I IFN induction by HSV-1 and SeV. In addition, we found that hnRNPM and ELAVL1 interact with TBK1 and NF-kB p65. Confocal microscopy revealed cytosolic and perinuclear interactions between hnRNPM, ELAVL1, and TBK1. To our knowledge, hnRNPM and ELAVL1 represent the first non-redundant signaling components merging the cGAS-STING and RIG-I-MAVS pathways, thus representing a novel platform that fuels antiviral defense.

immunology↗

bioRxiv2023

Antagonistic nanobodies reveal mechanism of GSDMD pore formation and unexpected therapeutic potential

Activation of various inflammasomes converges on the cleavage of gasdermin D (GSDMD) by pro-inflammatory caspases, followed by oligomerization of the N-terminal domain (GSDMDNT) and the assembly of pores penetrating target membranes. Yet, it remained unclear what triggers the conformational changes that allow membrane insertion, as methods to study pore formation in living cells were limited. We raised nanobodies specific for human GSDMD and found two nanobodies that prevent pyroptosis and IL-1{beta} release when expressed in the cytosol of human macrophages. Nanobody binding to GSDMDNT blocked its oligomerization, while inflammasome assembly and GSDMD processing itself were not affected. The nanobody-stabilized monomers of GSDMDNT partitioned into the plasma membrane, suggesting that pore formation is initiated by insertion of monomers, followed by oligomerization in the target membrane. When GSDMD pore formation was inhibited, cells still underwent caspase-1-dependent apoptosis, likely due to the substantially augmented caspase-1 activity. This hints at a novel layer of regulation of caspase-1 activity by GSDMD pores. Moreover, we revealed the unexpected therapeutic potential of antagonistic GSDMD nanobodies, as recombinant nanobodies added to the medium prevented cell death by pyroptosis, likely by entering through GSDMD pores and curtailing the assembly of additional pores. GSDMD nanobodies may thus be suitable to treat the ever-growing list of diseases caused by activation of the (non-) canonical inflammasomes.

immunology↗

bioRxiv2023

Pyroptosis inhibiting nanobodies block Gasdermin D pore formation

Gasdermin D (GSDMD) is a key mediator of pyroptosis, a pro-inflammatory form of cell death occurring downstream of inflammasome activation as part of the innate immune defence. Upon cleavage by inflammatory caspases, the N-terminal domain of GSDMD forms pores in the plasma membrane resulting in cytokine release and eventually cell death. Targeting GSDMD is an attractive way to dampen inflammation. In this study, six GSDMD targeting nanobodies were characterized in terms of their binding affinity, stability, and effect on GSDMD pore formation. Three of the nanobodies inhibited GSDMD pore formation in a liposome leakage assay, although caspase cleavage was not perturbed. We determined the crystal structure of human GSDMD in complex with two nanobodies at 1.9 [A] resolution, providing detailed insights into the GSDMD-nanobody interactions and epitope binding. The pore formation is sterically blocked by one of the nanobodies that binds to the oligomerization interface of the N-terminal domain in the multi-subunit assembly. Our biochemical and structural findings provide new tools for studying inflammasome biology and build a framework for the design of novel GSDMD targeting drugs.

biochemistry↗

bioRxiv2022

P38 kinases mediate NLRP1 inflammasome activation after ribotoxic stress response and virus infection

Inflammasomes integrate cytosolic evidence of infection or damage to mount inflammatory responses. The inflammasome sensor NLRP1 is expressed in human keratinocytes and coordinates inflammation in the skin. We found that diverse stress signals converge on the activation of p38 kinases to initiate human NLRP1 inflammasome assembly: UV irradiation and microbial molecules that initiate the ribotoxic stress response critically relied on the MAP3 kinase ZAK to activate p38 and ultimately human NLRP1. Infection with insect-transmitted alphaviruses, including Semliki Forest, Ross River, and Chikungunya virus, also activated NLRP1 in a p38-dependent manner. In the absence on ZAK, inflammasome assembly was maintained, although at reduced levels, indicating contribution of other upstream kinases. NLRP1 activation by direct nanobody-mediated ubiquitination was independent of p38 activity. Stimulation of p38 by overexpression of MAP2 kinases MKK3 or MKK6 is sufficient for NLRP1 activation, and NLRP1 is directly phosphorylated by p38. Taken together, we define p38 activation as a unifying signaling hub that controls NLRP1 inflammasome activation by integrating a variety of cellular stress signals relevant to the skin.

immunology↗

bioRxiv2021

Clostridium difficile Toxin B activates the NLRP3 inflammasome in human macrophages, demonstrating a novel regulatory mechanism for the Pyrin inflammasome

Pyrin is a cytosolic immune sensor that forms an inflammasome when bacterial virulence factors inhibit RhoA, triggering the release of inflammatory cytokines, including IL-1{beta}. Gain of function mutations in the MEFV gene encoding Pyrin cause auto-inflammatory disorders, such as familial Mediterranean fever (FMF) and Pyrin associated auto-inflammation with Neutrophilic Dermatosis (PAAND). To precisely define the role of Pyrin in detecting pathogen virulence factors in relevant human immune cells, we investigated how the Pyrin inflammasome response was initiated and regulated in monocyte-derived macrophages (hMDM) compared to human monocytes. Unlike monocytes and murine macrophages, we determined that hMDM failed to activate Pyrin in response to known Pyrin activators Clostridioides difficile (C. difficile) toxins A or B (TcdA or TcdB). In contrast, TcdB activated the NLRP3 inflammasome in hMDM. Notably, we ascertained that the Pyrin inflammasome response could be re-enabled in hMDM by prolonged priming with either LPS or type I or II interferons, and required an increase in Pyrin expression. These data demonstrate an unexpected redundancy in detecting these toxins by inflammasome sensors.

immunology↗

bioRxiv2020

Nanobody-directed targeting of optogenetic tools reveals differential regulation of cilia length

Compartmentalization of cellular signaling forms the molecular basis of cellular behavior. The primary cilium constitutes a subcellular compartment that orchestrates signal transduction independent from the cell body. Ciliary dysfunction causes severe diseases, termed ciliopathies. Analyzing ciliary signaling and function has been challenging due to the lack of tools to temporarily manipulate and analyze ciliary signaling. Here, we describe a nanobodybased targeting approach for optogenetic tools that is applicable in vitro and in vivo and allows to specifically analyze ciliary signaling and function. Thereby, we overcome the loss of protein function observed after direct fusion to a ciliary targeting sequence. We functionally localized modifiers of cAMP signaling, i.e. the photo-activated adenylate cyclase bPAC and the light-activated phosphodiesterase LAPD, as well as the cAMP biosensor mlCNBD-FRET to the cilium. Using this approach, we studied the contribution of spatial cAMP signaling in controlling cilia length. Combining optogenetics with nanobody-based targeting will pave the way to the molecular understanding of ciliary function in health and disease.

cell biology↗

bioRxiv2020

ASC oligomer favor caspase-1CARD domain recruitment after intracellular potassium efflux

Signaling through the inflammasome is important for the inflammatory response. Low concentrations of intracellular K+ are associated with the specific oligomerization and activation of the NLRP3 inflammasome, a type of inflammasome involved in sterile inflammation. Subsequent to NLRP3 oligomerization, ASC protein binds and form oligomeric filaments culminating in large protein complexes named ASC specks. ASC specks are also initiated from different inflammasome scaffolds, as AIM2, NLRC4 or Pyrin. ASC oligomers induce the recruitment of caspase-1 through interactions between their respective caspase activation and recruitment domains (CARD), and favoring its activation. So far ASC oligomerization and caspase-1 activation are considered as a K+-independent process. Here we found that ASC oligomers change their structure upon low intracellular K+ independently of NLRP3 and allow the ASCCARD domain to be more accessible for the recruitment of pro-caspase-1CARD domain. Therefore, conditions that decrease intracellular K+ not only drive NLRP3 responses, but also enhance the recruitment of pro-caspase-1 by ASC specks formed by different inflammasomes, indicating that intracellular K+ homeostasis is a key regulatory step for inflammasome regulation.

immunology↗