bims-cediti 2025-08-31 papers

bims-cediti

Biomed News

on Cell death in innate immunity, inflammation, and tissue repair

Issue of 2025–08–31
twelve papers selected by
Kateryna Shkarina, Universität Bonn

Nitroxoline is a novel inhibitor of NLRP3-dependent pyroptosis.
NAIP/NLRC4 inflammasome dynamics in murine enteroids are tuned by NAIP ligand concentration and epithelial cell differentiation.
FADDDED filaments coordinate complex IIa assembly during TNF-induced apoptosis.
Proton-activated chloride channel governs phagosome-mediated antibacterial immunity in peritoneal macrophages.
Dietary saturated fatty acids promote lung myeloid cell inflammasome activation and IL-1β-mediated inflammation in mice and humans.
A Potent Inhibitor of Caspase‑8 Based on the IL-18 Tetrapeptide Sequence Reveals Shared Specificities between Inflammatory and Apoptotic Initiator Caspases.
STING induces ZBP1-mediated necroptosis independently of TNFR1 and FADD.
SARM1 activation promotes axonal degeneration via a two-step phase transition.
Alternatively spliced isoforms of IRF7 differentially regulate interferon expression to tune response to viral infection.
MAVS phosphorylation acts as a cellular stress sensor that modulates antiviral immunity.
RPA1 protects DNA damage-induced PANoptosis in limb development.
PARP7 is a proteotoxic stress sensor that labels proteins for degradation.

Cell Death Discov. 2025 Aug 20. 11(1): 394

Nitroxoline is a novel inhibitor of NLRP3-dependent pyroptosis.

Christina Maeder, Roberto Baumann, Susanne Gaul, Sven Fikenzer, Michael Schaefer, Hermann Kalwa, Ulrich Laufs, Alexander Kogel.

Aberrant activity of the NLR family pyrin domain containing 3 (NLRP3) inflammasome contributes to a wide range of diseases associated with acute inflammatory responses and chronic sterile inflammation. Activation of the NLRP3 inflammasome mediates pyroptotic cell death and the release of pro-inflammatory cytokines. To date, no selective inhibitor of inflammasome activity is available for the use in humans. We conducted a medium-throughput screening of 6280 drugs or drug-like compounds and identified novel inhibitors of the NLRP3 inflammasome. Among these, nitroxoline was further characterized because the drug is approved for antibiotic treatment in humans, and we found no toxicity over a wide range of concentrations. Treatment of THP-1 monocytes with 80 μM nitroxoline markedly reduced the secretion of the pro-inflammatory cytokine Interleukin-1β (IL-1β) by 95% from 197.8 pg ml-1 to 11.0 pg ml-1. Nitroxoline reduced downstream events of inflammasome activation including caspase-1 activity (FAM-Flica+/7AAD+ cells control 57.1 ± 9.4% vs. nitroxoline 27.9 ± 15.5%) and gasdermin D cleavage (ratio cleaved/uncleaved control 8.7 ± 4.3 vs. nitroxoline 1.3 ± 1.3, p < 0.05). The data were confirmed in cultured human PBMC, where nitroxoline abrogated IL-1β secretion. Mechanistically, drug affinity-responsive target assays revealed that nitroxoline directly interacts with the NACHT domain of NLRP3, inhibiting inflammasome assembly. Nitroxoline did not affect NF-κB-dependent gene expression, as analyzed by nuclear p65 translocation and IκBα phosphorylation, and did not inhibit the NLR-family member NLRC4 or the AIM2 inflammasomes, indicating specificity for NLRP3. Nitroxoline is a novel inhibitor of the NLRP3 inflammasome, which reduces inflammasome assembly and IL-1β release. These data set the stage for testing the effects of nitroxoline on sterile inflammation in clinical studies.

DOI: https://doi.org/10.1038/s41420-025-02699-z
Cell Rep. 2025 Aug 26. pii: S2211-1247(25)00914-3. [Epub ahead of print]44(8): 116143

NAIP/NLRC4 inflammasome dynamics in murine enteroids are tuned by NAIP ligand concentration and epithelial cell differentiation.

Patrick Rosendahl Andreassen, Chantal Ernst, Marisa Pimentel Mendes, Thea Bill Andersen, Orane Guillaume-Gentil, Stefan A Fattinger, Mikael E Sellin, Wolf-Dietrich Hardt, Julia A Vorholt.

  Inflammasomes are central components of mammalian innate immunity activated upon the detection of danger signals such as pathogen ligands. This activation generally leads to pyroptosis and interleukin release, but specific responses vary between cell types. Here, we study nucleotide-binding, leucine-rich repeat (NLR) family apoptosis inhibitory protein (NAIP)/NLR CARD-containing protein 4 (NLRC4) inflammasome dynamics of intestinal epithelial cells of murine enteroids at the single-cell level. Using an apoptosis-associated speck-like protein containing a CARD (ASC)::GFP reporter and a cell-membrane-permeable NAIP/NLRC4 agonist, we observe pyroptosis with or without ASC polymerization. We use fluidic force microscopy to inject NAIP ligands into cells, revealing a dose-dependent response. High doses promote ASC polymerization, while lower doses lead to survival or NLRC4-dependent cell death in the absence of ASC polymerization. Using a fluorescence resonance energy transfer (FRET) reporter as a proxy for interleukin maturation, we reveal that single epithelial cell caspase-1 dynamics are affected by the differentiation state of cells and NAIP ligand dosing. Our results indicate an inflammasome response that is tuned at multiple levels in intestinal epithelial cells.

Keywords:  ASC; CP: Immunology; CP: Stem cell research; FluidFM; caspase-1; enteroid; inflammasome; innate immunity; intestinal organoids; pathogen; single cell

DOI:  https://doi.org/10.1016/j.celrep.2025.116143
Proc Natl Acad Sci U S A. 2025 Aug 26. 122(34): e2425802122

FADDDED filaments coordinate complex IIa assembly during TNF-induced apoptosis.

Ying Chen, Vinh Thang Huynh, Lihua Lai, Ping Liu, Tongyang Li, Yaw Bia Tan, Che Shin Chew, Amhed Missael Vargas Velazquez, Firdaus Samsudin, Jan K Marzinek, Peter J Bond, Bin Wu, Dahai Luo, Vinay Tergaonkar.

  Extrinsic apoptosis is initiated by signaling from death receptors, leading to the assembly of RIPK1, FADD, and caspase-8 complex. Subsequently, caspase-8 forms a filamentous structure through the oligomerization of its tandem death effector domain (tDED), resulting in caspase activation and cell death. Although the DED of FADD (FADDDED) is homologous to the tDEDs of caspase-8 (casp8tDED) and both oligomerize to function, the functional form of FADDDED oligomer in extrinsic apoptosis remains unclear. Here, using cryogenic-electron microscopy, we elucidate the structure of FADDDED filaments comprising three helical chains assembled through three types of iterative interactions. Mutations disrupting FADDDED filament formation impair the recruitment of RIPK1 and caspase-8, and abrogate the cell death response, suggesting that FADDDED filamentation represents an important mechanistic step in the initiation of TNF-induced extrinsic apoptosis. Contrary to the belief that the homotypic death domains of RIPK1 and FADD are solely responsible for their interaction, we here show this interaction requires FADDDED filamentation. Furthermore, cFLIP can disrupt FADDDED filaments, uncovering an additional antiapoptotic mechanism of cFLIP beyond its disruption of caspase-8 filament. Molecular dynamics simulations reveal that FADDDED filament thermodynamically favors casp8tDED monomer over FADDDED monomer, thus explaining the hierarchy and stoichiometry of FADD/caspase-8 complex assembly. These findings highlight the hitherto unappreciated roles of FADDDED filament formation in extrinsic apoptosis.

Keywords:  FADD; RIPK1; TNFR1; extrinsic apoptosis; filament

DOI:  https://doi.org/10.1073/pnas.2425802122
J Exp Med. 2025 Nov 03. pii: e20250312. [Epub ahead of print]222(11):

Proton-activated chloride channel governs phagosome-mediated antibacterial immunity in peritoneal macrophages.

Henry Yi Cheng, Jiachen Chu, Nathachit Limjunyawong, Jianan Chen, Yingzhi Ye, Kevin Hong Chen, Nicholas Koylass, Shuying Sun, Xinzhong Dong, Zhaozhu Qiu.

The success of phagosome degradation relies on the ability of phagocytes to regulate the maturation of phagosomes. However, its underlying molecular mechanisms remain poorly understood. Here, we identify the proton-activated chloride (PAC) channel as a key negative regulator of phagosome maturation. PAC deletion enhanced phagosomal acidification and protease activities, leading to augmented bacterial killing in large peritoneal macrophages (LPMs) upon Escherichia coli infection in mice. Surprisingly, phagosome degradation also stimulated STING-IRF3-IFN responses and inflammasome activation in LPMs, both of which are enhanced upon PAC deletion. The increased inflammasome activation induced the release of cleaved gasdermin D, which localized to the surface of bacteria in the peritoneum and further contributed to their killing. Finally, enhanced bacterial clearance by PAC-deficient LPMs reduced proinflammatory immune cell infiltration and peritoneal inflammation, resulting in improved survival in mice. Our study thus provides new insights into the molecular mechanism of phagosome maturation and the dynamics of host defense response following phagosome-mediated bacterial degradation in peritoneal macrophages.

DOI: https://doi.org/10.1084/jem.20250312
Sci Transl Med. 2025 Aug 27. 17(813): eadp5653

Dietary saturated fatty acids promote lung myeloid cell inflammasome activation and IL-1β-mediated inflammation in mice and humans.

Sam J McCright, Olivia Harding, Julia Chini, Nicole DeMarco, Li-Yin Hung, Christopher F Pastore, Wenyun Lu, Joshua Rabinowitz, Jorge Henao-Mejia, De'Broski R Herbert, Lisa R Young, David A Hill.

Resident tissue macrophages and monocytes (RTMs) integrate local and systemic signals to coordinate immune cell function at homeostasis and in response to inflammatory stimuli. Obesity-associated metabolic dysfunction drives the development of RTM populations that contribute to disease states in multiple tissues. However, the contribution of specific dietary components to innate immune cell activation and function, as opposed to the direct effects of obesity, is largely unknown. Here, we studied the mechanisms by which high-fat (HF) diets shape lung RTM phenotype and function at steady state and influence responses to inflammatory insults. We found that, during HF diet feeding, lung RTMs accumulate saturated long-chain fatty acids, specifically stearic acid (SA), and demonstrate features of NLRP3 inflammasome priming and activation. In vivo, increased dietary SA was sufficient to cause neutrophil-predominant lung inflammation in the steady state and exacerbate a model of innate airway inflammation, whereas increased dietary oleic acid, the monounsaturated counterpart of SA, was sufficient to reduce inflammasome activation in the steady state and attenuate airway inflammation. Depletion of interleukin-1β (IL-1β) or pharmacologic inhibition of the endonuclease inositol requiring enzyme 1α (IRE1α) protected against SA-induced exacerbated lung inflammation. Last, we identified a population of lung monocytes with hallmarks of HF diet-induced RTM activation that were present in samples from obese humans with asthma. Together, these results identify a class of dietary lipids that regulate lung RTM phenotype and function in the steady state and modulate the severity of inflammation in the lung.

DOI: https://doi.org/10.1126/scitranslmed.adp5653
ACS Bio Med Chem Au. 2025 Aug 20. 5(4): 565-581

A Potent Inhibitor of Caspase‑8 Based on the IL-18 Tetrapeptide Sequence Reveals Shared Specificities between Inflammatory and Apoptotic Initiator Caspases.

Christopher M Bourne, Nicole R Raniszewski, Ashutosh B Mahale, Madhura Kulkarni, Patrick M Exconde, Sherry Liu, Winslow Yost, Tristan J Wrong, Robert C Patio, Matilda Kardhashi, Teni Shosanya, Mirai Kambayashi, Bohdana M Discher, Igor E Brodsky, George M Burslem, Cornelius Y Taabazuing.

  Caspases are a family of cysteine proteases that act as molecular scissors to cleave substrates and regulate biological processes, such as programmed cell death and inflammation. Extensive efforts have been made to identify caspase substrates and to determine the factors that dictate specificity. We recently discovered that human inflammatory caspases (caspases-1, -4, and -5) cleave the cytokines IL-1β and IL-18 in a sequence-dependent manner. Here, we report the development of a new peptide-based probe and inhibitor derived from the tetrapeptide sequence of IL-18 (LESD). The LESD-based inhibitor showed a strong preference for caspase-8 with an IC50 of 50 nM, and was more potent in vitro than the commonly used zIETD-FMK inhibitor, which is considered the most selective and potent caspase-8 inhibitor. We further demonstrated that the LESD-based inhibitor prevents caspase-8 activation during infection in primary bone marrow-derived macrophages. In addition, we systematically characterized the selectivity and potency of known substrates and inhibitors of the apoptotic and inflammatory caspases using standardized activity units of each caspase. Our findings reveal that VX-765, a known inhibitor of caspases-1 and -4, also inhibits caspase-8 (IC50 = 1 μM). Even when specificities are shared, the caspases exhibit different efficiencies and potencies for shared substrates and inhibitors. Altogether, we report the development of new tools that will facilitate the study of caspases and their roles in biology.

Keywords:  Yersinia pseudotuberculosis; apoptosis; caspase inhibitors; caspase substrates; in vitro kinetics; inflammasomes; pyroptosis

DOI:  https://doi.org/10.1021/acsbiomedchemau.4c00146
Nature. 2025 Aug 20.

STING induces ZBP1-mediated necroptosis independently of TNFR1 and FADD.

Konstantinos Kelepouras, Julia Saggau, Debora Bonasera, Christine Kiefer, Federica Locci, Hassan Rakhsh-Khorshid, Louisa Grauvogel, Ana Beatriz Varanda, Martin Peifer, Elena Loricchio, Antonella Montinaro, Marijana Croon, Aleksandra Trifunovic, Giusi Prencipe, Antonella Insalaco, Fabrizio De Benedetti, Henning Walczak, Gianmaria Liccardi.

Conditional deletion of Caspase-8 in epidermal keratinocytes (Casp8E-KO) causes necroptosis-driven lethal dermatitis1-7. Here, we discover that Casp8 loss leads to accumulation of cytosolic DNA responsible for the activation of a cyclic-GMP-AMP synthase (cGAS)/stimulator of interferon (IFN) gene (STING)-mediated transcriptional program. Genetic and biochemical evidence indicate that STING upregulates both Z-DNA binding protein-1 (ZBP1), and mixed lineage kinase domain-like (MLKL). Combined Casp8-deficiency- and STING-activation-driven accumulation of Z-nuclei acids, activates ZBP1 and triggers formation of a ZBP1-RIPK1-RIPK3 complex independently of FADD-RIPK1-RIPK3 complex enabling necroptosis execution. Genetically, we reveal a functional overlap between STING and ZBP1 as drivers of lethal dermatitis independently of TNFR1, uncovering a novel aetiology of necroptotic inflammation. Since gain-of-function mutations in human STING cause STING-Associated Vasculopathy with onset in Infancy (SAVI), we assessed the role of STING-induced necroptosis in SAVI's aetiology. Chronic activation of STING in patients orchestrates a necroptotic transcriptional program which is confirmed in the N153S-SAVI preclinical mouse model where immune cell-driven pathology and lethality are remarkably rescued by RIPK3 co-deletion. These findings establish STING-driven ZBP1-mediated necroptosis as a central pathogenic mechanism in both Casp8-deficient inflammation and SAVI and suggest that targeting the ZBP1-RIPK3-MLKL axis holds therapeutic potential for interferonopathies characterised by excessive necroptosis.

DOI: https://doi.org/10.1038/s41586-025-09536-4
Nat Chem Biol. 2025 Aug 22.

SARM1 activation promotes axonal degeneration via a two-step phase transition.

Wenbin Zhang, Qinyi Zhou, Jun Zhang, Jiachen Wang, Qingcui Wu, Sanduo Zheng, Xiaodong Wang.

SARM1 is a key executioner of axonal degeneration, acting through NAD⁺ depletion by NADase activity of its TIR domain. Although normally autoinhibited, SARM1 becomes activated in response to axonal damage; however, the underlying mechanism remains unclear. Here, using a class of pyridine-containing compounds that trigger SARM1-dependent axon degeneration, we uncover a two-step activation process. First, NMN primes the base exchange activity of SARM1, generating covalent adducts between ADP-ribose (an NAD⁺ hydrolysis product) and the compounds. These ADP-ribose conjugates then serve as molecular glues to promote the assembly of superhelical SARM1 filaments, in which TIR domains adopt an active configuration. After reaching solubility limits, these filaments condense into stable, phase-separated assemblies with full enzymatic activity. Unexpectedly, several clinical-stage SARM1 inhibitors targeting its TIR domain also form such adducts, paradoxically promoting its activation. These findings reveal a molecular mechanism that spatially restricts SARM1 activation to damaged axons and offer new guidance for therapeutic strategies targeting SARM1.

DOI: https://doi.org/10.1038/s41589-025-02009-9
Cell Rep. 2025 Aug 19. pii: S2211-1247(25)00937-4. [Epub ahead of print]44(9): 116166

Alternatively spliced isoforms of IRF7 differentially regulate interferon expression to tune response to viral infection.

Asmita Panthi, Max B Ferretti, Olivia Howard, Swechha Mainali Pokharel, Rhiannon McCracken, Simon Boudreault, Mathieu Quesnel-Vallieres, Qin Li, Sara Cherry, Kristen W Lynch.

  Interferon regulatory factor 7 (IRF7) is a master transcriptional regulator of innate immunity. IRF7 binds as a homodimer, or heterodimer with IRF3, to promoters of type I interferons (IFN-Is) to drive their expression, which activates expression of antiviral genes. Here, we demonstrate that alternative splicing of the first intron within the coding region of human IRF7 is regulated across immune tissues and in response to immunologic stimuli. Retention of this intron generates an alternative translation start site, resulting in an N-terminally extended form of the protein (exIRF7) compared to the canonical isoform (cIRF7). We find that exIRF7 has increased dimerization relative to cIRF7, uniquely activates expression of IFN-Is in response to double-stranded RNA (dsRNA) sensing, and controls viral infection to a greater extent than cIRF7. Thus, alternative splicing of IRF7 is a previously unrecognized mechanism by which human cells tune IRF7 function and the IFN response to control immune challenge.

Keywords:  CELF2; CP: Immunology; IRF7; alternative splicing; innate immunity; interferon; intron retention; protein dimerization; transcriptional activation

DOI:  https://doi.org/10.1016/j.celrep.2025.116166
iScience. 2025 Sep 19. 28(9): 113256

MAVS phosphorylation acts as a cellular stress sensor that modulates antiviral immunity.

Dongyi Zhao, Nao Morimoto, Riho Saito, Juri Yamada, Shuntaro Abe, Hidetaka Kosako, Yukiko Gotoh, Tomohiko Okazaki.

  Upon viral infection, cytosolic RIG-I-like receptors recognize viral RNA and activate innate immune responses through the mitochondrial antiviral-signaling protein (MAVS), leading to type I interferon (IFN) production and apoptosis. Cellular stress influences immune activation, but its impact on MAVS signaling remains largely unclear. Here, we show that MAVS undergoes phosphorylation via p38 MAPK signaling, activated by the stress-activated MAPKKK ASK1. This modification enhances MAVS interaction with TRAF, a key downstream adaptor, thereby promoting type I IFN induction. Oxidative and endoplasmic reticulum stress significantly amplified type I IFN expression upon viral infection, but this effect was attenuated in cells expressing MAVS mutants lacking phosphorylation sites. These findings suggest MAVS phosphorylation as a key mechanism integrating cellular stress signals into antiviral immunity. By linking the MAPK pathway to MAVS-dependent IFN expression, we propose MAVS phosphorylation as a cellular stress sensor that modulates antiviral immunity in a context-dependent manner.

Keywords:  Biochemistry; Cell biology; Immune response

DOI:  https://doi.org/10.1016/j.isci.2025.113256
Sci Adv. 2025 Aug 22. 11(34): eadw2756

RPA1 protects DNA damage-induced PANoptosis in limb development.

Qi Yin, Shuanglin Peng, Zhong Zhang, Shuang Jiang, Xuan Li, Denghao Huang, Yang Li, Jian Zhou, Jingang Xiao, Ling Ye, Yuxin Yin, Quan Yuan.

Extensive cell proliferation during embryogenesis often compromises genome integrity, increasing the risk of developmental defects. However, the mechanisms that safeguard genome integrity during this process remain poorly understood. Using early limb development as a model, we identify that DNA damage response factors are up-regulated in proliferating mesenchymal stem cells. Conditional knockout of Rpa1, a representative DNA damage response factor, in early limb bud mesenchyme results in the near-total absence of forelimbs and severely underdeveloped hindlimbs. Mechanistically, Rpa1 deletion leads to extensive DNA damage and activates the cGAS-STING pathway, driving transcription of Zbp1. Rpa1 deletion also leads to accumulation of Z-DNA bound by ZBP1, triggering the full activation of ZBP1 and subsequent mesenchymal stem cell death through PANoptosis. Our study reveals RPA1 as a vital protector of genomic stability during limb development and underscores ZBP1-dependent PANoptosis as a key pathway for eliminating cells with excessive DNA damage during embryonic development.

DOI: https://doi.org/10.1126/sciadv.adw2756
EMBO J. 2025 Aug 20.

PARP7 is a proteotoxic stress sensor that labels proteins for degradation.

Nonso J Ikenga, Jörg Vervoorts, Bernhard Lüscher, Roko Žaja, Karla L H Feijs-Žaja.

  ADP-ribosylation is a post-translational modification that plays a critical role in cellular stress responses. We have observed that during proteotoxic stress, cellular ADP-ribosylation increases, with ADP-ribosylated proteins accumulating in cytoplasmic foci containing ubiquitin and p62. During prolonged stress, these ADP-ribosylated proteins are transported to aggresomes and subsequently degraded via autophagy. In the absence of ubiquitination, ADP-ribosylated proteins become more prevalent and less soluble, indicating that ubiquitination is indispensable for this process. Upon inhibition of PARP7, accumulation of mono(ADP-ribosyl)ated proteins in response to proteotoxic stress is impeded. PARP7 turnover is very high under normal conditions; however, the protein becomes stabilised following proteotoxic stress and thereby forms an ideal proteotoxic stress sensor. Our findings imply that, contrary to the current paradigm, not all ADP-ribosylation may occur on specific sites to regulate specific protein characteristics. Instead, it may be rather promiscuous to enable efficient protein degradation or segregation to prevent irreversible damage caused by defective proteins.

Keywords:  ADP-ribosylation; Macrodomain; PARP; Protein Degradation; Ubiquitination

DOI:  https://doi.org/10.1038/s44318-025-00545-7