bims-cediti 2025-05-25 papers

bims-cediti

Biomed News

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

Issue of 2025–05–25
eleven papers selected by
Kateryna Shkarina, Universität Bonn

HCK regulates NLRP12-mediated PANoptosis.
Regulating the balance between GSDMD-mediated pyroptosis and CHMP4B-dependent cell repair attenuates calcium oxalate kidney stone formation.
Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation.
4-octyl itaconate reduces human NLRP3 inflammasome constitutive activation with the cryopyrin-associated periodic syndrome p.R262W, p.D305N and p.T350M variants.
Microenvironmental Conditions and Serum Availability Alter Primary Human Macrophage NF-κB Inflammatory Response and Function.
Outer membrane tube formation by Francisella novicida involves extensive envelope modifications and is linked with type VI secretion and alterations to the host phagosomal membrane.
Mouse Bone Marrow Neutrophil Extracellular Trap Proteomics by Microbial Stimuli.
Caspase Domain Duplication During the Evolution of Caspase-16.
Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease.
An integrated proteomics approach identifies phosphorylation sites on viral and host proteins that regulate West Nile virus infection.
Integrated proteomics and phosphoproteomics profiling dynamic signaling networks underlying two distinct types of macrophage activation.

Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2422079122

HCK regulates NLRP12-mediated PANoptosis.

Eswar Kumar Nadendla, Priyanshu Alluri, Balamurugan Sundaram, Sivakumar Prasanth Kumar, Sangappa B Chadchan, Roman Sarkar, Thirumala-Devi Kanneganti.

  NOD-like receptors (NLRs) are a highly conserved family of cytosolic pattern recognition receptors that drive innate immune responses against pathogens, pathogen-associated molecular patterns, damage-associated molecular patterns, and homeostatic disruptions. Within the NLR family, NLRP12 was recently identified as a key regulator of PANoptosis, which is an innate immune, lytic cell death pathway initiated by innate immune sensors and driven by caspases and RIPKs through PANoptosome complexes. While NLRP12 activation is critical for maintaining homeostasis, aberrant activation has been implicated in a broad range of disorders, including cancers and metabolic, infectious, autoinflammatory, and hemolytic diseases. However, the molecular mechanisms of NLRP12 activation remain poorly understood. Here, we identified hematopoietic cell kinase (HCK) as a regulator of NLRP12-mediated PANoptosis. HCK expression was significantly upregulated in response to NLRP12-PANoptosome triggers. Moreover, Hck knockdown inhibited NLRP12-mediated PANoptosis. Computational analyses identified residues in the putative interaction interface between NLRP12 and HCK, suggesting that HCK likely binds NLRP12 in the region between its NACHT domain and pyrin domain (PYD); removal of the NLRP12 PYD abrogated this interaction in vitro. Overall, our work identifies HCK as a regulator of NLRP12-mediated PANoptosis, suggesting that it may serve as a potential therapeutic target for mitigating inflammation and pathology.

Keywords:  HCK; NLRP12; biochemistry

DOI:  https://doi.org/10.1073/pnas.2422079122
Int J Biol Sci. 2025 ;21(7): 3099-3121

Regulating the balance between GSDMD-mediated pyroptosis and CHMP4B-dependent cell repair attenuates calcium oxalate kidney stone formation.

Shushuai Yang, Yuanjiong Qi, Yue Chen, Hailong Kong, Bin Han, Zhongsheng Peng, Chenglong Xu, Bohan Wang, Liqun Chen, Shiyong Qi.

  An imbalance exists between renal tubular epithelial cells (RTECs) injury and repair in kidney stone disease, yet the underlying mechanism remains largely unclear. Here, we found that gasdermin D (GSDMD)-mediated pyroptosis occurred in both patients and mice with calcium oxalate (CaOx) nephrolithiasis, and the expression levels of NOD-like receptor protein 3 (NLRP3) and GSDMD were associated with the severity of kidney stones. Deficiency of GSDMD alleviated renal tubule damage and inflammatory response, ultimately inhibiting renal injury and crystal deposition. Additionally, we found that charged multivesicular body protein 4B (CHMP4B)-dependent cell repair was activated during pyroptosis of RTECs; however, the enhancement was insufficient to offset the damage. Importantly, Ca2+ fluxes during pyroptosis induce activation of the CHMP4B-dependent cell repair machinery. Overexpression of CHMP4B attenuates cell death and reduces the severity of kidney stones. Notably, combining the overexpression of CHMP4B with a GSDMD inhibitor demonstrates heightened efficacy in ameliorating kidney damage and crystal deposition induced by glyoxylate (Gly). Taken together, these results highlight the imbalance between GSDMD-mediated pyroptosis and CHMP4B-dependent cell repair as a driver for CaOx kidney stone formation. Our findings provide new insights and potential therapeutic targets for CaOx kidney stones.

Keywords:  calcium oxalate; cell repair; imbalance; kidney stone; pyroptosis

DOI:  https://doi.org/10.7150/ijbs.105415
Nat Cell Biol. 2025 May 22.

Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation.

Subhash B Arya, Samuel P Collie, Yang Xu, Martin Fernandez, Jonathan Z Sexton, Shyamal Mosalaganti, Pierre A Coulombe, Carole A Parent.

Acute inflammation, characterized by a rapid influx of neutrophils, is a protective response that can lead to chronic inflammatory diseases when left unresolved. We previously showed that secretion of LTB4-containing exosomes via nuclear envelope-derived multivesicular bodies is required for effective neutrophil infiltration during inflammation. Here we report that the co-secretion of these exosomes with nuclear DNA facilitates the resolution of the neutrophil infiltrate in a mouse skin model of sterile inflammation. Activated neutrophils exhibit rapid and repetitive DNA secretion as they migrate directionally using a mechanism distinct from suicidal neutrophil extracellular trap release and cell death. Packaging of DNA in the lumen of nuclear envelope-multivesicular bodies is mediated by lamin B receptor and chromatin decondensation. These findings advance our understanding of neutrophil functions during inflammation and the physiological relevance of DNA secretion.

DOI: https://doi.org/10.1038/s41556-025-01671-4
Cell Mol Life Sci. 2025 May 23. 82(1): 209

4-octyl itaconate reduces human NLRP3 inflammasome constitutive activation with the cryopyrin-associated periodic syndrome p.R262W, p.D305N and p.T350M variants.

Cristina Molina-Lopez, Laura Hurtado-Navarro, Luke A J O'Neill, Pablo Pelegrin.

  Cryopyrin-associated periodic syndrome (CAPS) is a condition characterized by dominant genetic variants in the NLRP3 gene, which lead to the formation of constitutively active inflammasomes. These inflammasomes play a crucial role in CAPS patients' inflammatory episodes, these being primarily driven by the production of interleukin (IL)-1b. Although treatment with IL-1 blockers is effective for CAPS, some patients develop refractory responses and adverse reactions to these therapies. Consequently, there is a need for novel treatments for CAPS patients. Promising candidates are the derivatives of itaconate, which have been shown to impair NLRP3 inflammasome activation and IL-1β release in blood mononuclear cells from CAPS patients. In this study, we provide insight into the inhibitory mechanisms by which the itaconate derivative 4-octyl itaconate (4-OI) acts on NLRP3 that has different gain-of-function mutations (p.R262W, p.D305N and p.T350M) associated with CAPS. Notably, 4-OI effectively blocks the basal auto-activation of the inflammasome formed by NLRP3 p.R262W, p.D305N and p.T350M variants, which in turn reduces caspase-1 activation, gasdermin D processing, and IL-18 release. Furthermore, after lipopolysaccharide priming of macrophages, 4-OI also decreases IL-1β gene expression and release. Overall, 4-OI impairs CAPS-associated inflammasome function at multiple levels, meaning that therapeutic agents based on itaconate could be a promising therapeutic approach to managing inflammatory episodes in CAPS patients carrying p.R262W, p.D305N or p.T350M variants.

Keywords:  Autoinflammatory disease; CAPS; Inflammasome; Itaconate; NLRP3

DOI:  https://doi.org/10.1007/s00018-025-05699-5
J Leukoc Biol. 2025 May 22. pii: qiaf071. [Epub ahead of print]

Microenvironmental Conditions and Serum Availability Alter Primary Human Macrophage NF-κB Inflammatory Response and Function.

Breana Channer, Marzieh Daniali, Lexi Sheldon, Katy Emanuel, Yash Agarwal, Taylor Kist, Brian J Murphy, Meng Niu, Will Dampier, Howard Fox, Peter J Gaskill.

  Macrophages are central to innate immunity and are routinely used in vitro to examine molecular mechanisms contributing to innate immune signaling. However, there is a lack of consensus within the field for optimal in vitro culturing methods, and it is not well understood whether differences in culture conditions produce incongruent outcomes. Here, we compared the effects of commonly used culture medium compositions on TLR4-mediated pro-inflammatory activity in primary human monocyte-derived macrophages (hMDM) isolated from healthy blood donors. hMDM were cultured in fetal bovine serum (FBS)-containing or FBS-free conditions in either DMEM, RPMI, or in Macrophage-Serum Free Medium (M-SFM). LPS-mediated immune response was measured through NF-κB activation and cytokine and chemokine secretion, which were muted in M-SFM cultures compared to DMEM and RPMI cultures. FBS supplementation increased total cytokine secretion in response to LPS but also showed higher baseline secretion, suggesting a pro-inflammatory phenotype. Moreover, M-SFM cultures exhibited less phagocytosis compared to DMEM and RPMI cultures. Morphologic analysis of unstimulated hMDM revealed the highest cell area and length-to-width ratio in M-SFM compared to DMEM or RPMI cultures. FBS-free and M-SFM conditions produced distinct transcriptional profiles compared to media supplemented with FBS, most notably in cell cycle pathways and lipid homeostasis, respectively. Overall, DMEM and RPMI produce comparable morphologic and functional results, albeit with some small differences, while M-SFM produces a muted inflammatory response in macrophages. These data demonstrate that in vitro microenvironment drives differential inflammatory outcomes in human macrophages and is a critical component of experimental design in this cell type.

Keywords:  Macrophage; NF-kB; TLR4; culture media; inflammation; innate immunity; morphology; myeloid cells; serum

DOI:  https://doi.org/10.1093/jleuko/qiaf071
mBio. 2025 May 19. e0106025

Outer membrane tube formation by Francisella novicida involves extensive envelope modifications and is linked with type VI secretion and alterations to the host phagosomal membrane.

Maheen Rashid, Shoichi Tachiyama, Shiwei Zhu, Hang Zhao, William D McCaig, Jingchuan Sun, Huilin Li, Jun Liu, David G Thanassi.

  Francisella tularensis is a gram-negative, intracellular pathogen that causes the zoonotic disease tularemia. Due to its ease of dissemination and high lethality, F. tularensis is classified as a tier 1 select agent with potential for misuse as a bioweapon. The mechanisms by which Francisella replicates intracellularly and interacts with the host during infection are not well understood. Francisella produces spherical outer membrane vesicles (OMVs) and novel tubular extensions of its cell surface that are also released extracellularly. These OMV and outer membrane tubes (OMTs) contain Francisella virulence factors and are produced in response to amino acid starvation and during infection of macrophages. To investigate how the OMTs are formed, we used cryogenic electron tomography to examine the model Francisella spp., Francisella novicida, during in vitro culture and within the macrophage phagosome. OMT formation involved progressive alterations of the bacterial envelope, resulting in extensions of both the inner and outer membranes. A dynamic cytoplasmic structure was present at the base of the OMT that extended into the tubes during elongation, together with cytoplasmic material. OMT produced within the macrophage phagosome was associated with changes to the phagosomal membrane, suggesting a role in phagosomal escape. Consistent with this, using confocal microscopy, we observed co-localization of the Francisella type VI secretion system with the OMT, both within bacteria and in released tubular vesicles. These findings reveal the cellular transformations that occur during membrane tubulation by Francisella and provide insights into the function of membrane-derived structures during host-pathogen interactions.
IMPORTANCE: Francisella tularensis is an intracellular bacterial pathogen that causes the zoonotic disease tularemia. Following uptake by host cells, the bacteria rapidly escape the phagosome and replicate intracellularly. In previous studies, we found that Francisella produces tubular extensions of its cell surface in response to specific cues and during macrophage infection. In the present study, we used cryogenic electron tomography to examine tube formation by the model Francisella sp., F. novicida. This analysis revealed that tube formation involves extensive bacterial envelope alterations and a dynamic cytoplasmic organelle. Furthermore, tubes produced by bacteria within infected macrophages were associated with the breakdown of the phagosomal membrane. In addition, we found that the Francisella type VI secretion system, which is essential for phagosomal escape, co-localized with the bacterial tubes. These findings reveal the cellular transformations that occur during membrane tubulation by Francisella and suggest a role for the tubes in phagosomal escape.

Keywords:  Francisella; bacterial pathogens; macrophage infection; outer membrane vesicles; type VI secretion system

DOI:  https://doi.org/10.1128/mbio.01060-25
Sci Data. 2025 May 23. 12(1): 853

Mouse Bone Marrow Neutrophil Extracellular Trap Proteomics by Microbial Stimuli.

Yijie Wang, Yujia Liu, Chunjing Du, Yue Zhang, Liuluan Zhu.

Neutrophils, the most abundant white blood cells in human circulation, play a crucial role in innate immunity. One of their key defense mechanisms is the formation of neutrophil extracellular traps (NETs), web-like structures composed of chromatin and antimicrobial proteins that help capture and neutralize pathogens. While previous studies have identified a limited set of NET-associated proteins, the comprehensive proteomic landscape of NETs induced by different stimuli remains largely unexplored. In this study, we used data-independent acquisition mass spectrometry to analyze the proteomic composition of NETs induced by five distinct stimuli: β-glucan, lipopolysaccharide, polyinosinic-polycytidylic acid sodium, resiquimod, and severe fever with thrombocytopenia syndrome bunyavirus. Across all conditions, we identified 5,868 NET-associated proteins, revealing significant stimulus-dependent differences in protein composition. Notably, differentially expressed proteins were detected in each condition, highlighting unique proteomic signatures that may reflect distinct immune responses. This dataset offers key insights into the proteomic diversity of NETs and their role in immune regulation, providing a foundation for future research on NET-mediated immunity in infectious and inflammatory diseases.

DOI: https://doi.org/10.1038/s41597-025-05181-8
J Mol Evol. 2025 May 20.

Caspase Domain Duplication During the Evolution of Caspase-16.

Leopold Eckhart, Attila Placido Sachslehner, Julia Steinbinder, Heinz Fischer.

  Caspases are cysteine-dependent aspartate-directed proteases which have critical functions in programmed cell death and inflammation. Their catalytic activity depends on a catalytic dyad of cysteine and histidine within a characteristic protein fold, the so-called caspase domain. Here, we investigated the evolution of caspase-16 (CASP16), an enigmatic member of the caspase family, for which only a partial human gene had been reported previously. The presence of CASP16 orthologs in placental mammals, marsupials and monotremes suggests that caspase-16 originated prior to the divergence of the main phylogenetic clades of mammals. Caspase-16 proteins of various species contain a carboxy-terminal caspase domain and an amino-terminal prodomain predicted to fold into a caspase domain-like structure, which is a unique feature among caspases known so far. Comparative sequence analysis indicates that the prodomain of caspase-16 has evolved by the duplication of exons encoding the caspase domain, whereby the catalytic site was lost in the amino-terminal domain and conserved in the carboxy-terminal domain of caspase-16. The murine and human orthologs of CASP16 contain frameshift mutations and therefore represent pseudogenes (CASP16P). CASP16 of the chimpanzee displays more than 98% nucleotide sequence identity with the human CASP16P gene but, like CASP16 genes of other primates, has an intact protein coding sequence. We conclude that caspase-16 structurally differs from other mammalian caspases, and the pseudogenization of CASP16 distinguishes humans from their phylogenetically closest relatives.

Keywords:  Caspase; Evolution; Protein domain; Pseudogenization; Pyroptosis

DOI:  https://doi.org/10.1007/s00239-025-10252-w
Nat Commun. 2025 May 20. 16(1): 4640

Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease.

Jordyn J VanPortfliet, Yuanjiu Lei, Muthumeena Ramanathan, Camila Guerra Martinez, Jessica Wong, Tim J Stodola, Brian R Hoffmann, Kathryn Pflug, Raquel Sitcheran, Stephen C Kneeland, Stephen A Murray, Peter J McGuire, Carolyn L Cannon, A Phillip West.

Mitochondrial diseases (MtD) represent a significant public health challenge due to their heterogenous clinical presentation, often severe and progressive symptoms, and lack of effective therapies. Environmental exposures, such bacterial and viral infection, can further compromise mitochondrial function and exacerbate the progression of MtD. However, the underlying immune alterations that enhance immunopathology in MtD remain unclear. Here we employ in vitro and in vivo approaches to clarify the molecular and cellular basis for innate immune hyperactivity in models of polymerase gamma (Polg)-related MtD. We reveal that type I interferon (IFN-I)-mediated upregulation of caspase-11 and guanylate-binding proteins (GBP) increase macrophage sensing of the opportunistic microbe Pseudomonas aeruginosa (PA) in Polg mutant mice. Furthermore, we show that excessive cytokine secretion and activation of pyroptotic cell death pathways contribute to lung inflammation and morbidity after infection with PA. Our work provides a mechanistic framework for understanding innate immune dysregulation in MtD and reveals potential targets for limiting infection- and inflammation-related complications in Polg-related MtD.

DOI: https://doi.org/10.1038/s41467-025-59907-8
Cell Rep. 2025 May 15. pii: S2211-1247(25)00499-1. [Epub ahead of print]44(5): 115728

An integrated proteomics approach identifies phosphorylation sites on viral and host proteins that regulate West Nile virus infection.

Zachary Walter, Minghua Li, Melissa Molho, Lauren Berish, Andrew Isopi, Mary O'Mara, Mark Dittmar, Chike Nwaezeapu, Alicia Richards, Martin McCullagh, Nevan J Krogan, Sara Cherry, Jeffrey R Johnson, Holly Ramage.

  Upon infection, viruses alter the proteome, creating a hospitable environment for infection. Cells respond to limit viral replication, including through protein regulation by post-translational modifications. We use mass spectrometry to define proteome alterations during West Nile virus (WNV) infection. Our studies identify upregulation of HERPUD1, which restricts WNV replication through a mechanism independent of its role in endoplasmic reticulum (ER)-associated degradation (ERAD). We also identify modifications on viral proteins, including a WNV NS3 phosphorylation site that impacts viral replication. Finally, we reveal activation of two host kinases with antiviral activity. We identify phosphorylation at S108 of AMPKβ1, a non-catalytic subunit that regulates activity of the AMPK complex. We also show activation of PAK2 by phosphorylation at S141, which restricts translation of the viral genome. This work contributes to our understanding of the interplay between host and virus while providing a resource to define the changes to the proteome that regulate viral infection.

Keywords:  CP: Microbiology; Orthoflaviviruses; West Nile virus; innate immunity; phosphorylation; post-translational modifications; viral helicase; viral translation; virus-host interactions

DOI:  https://doi.org/10.1016/j.celrep.2025.115728
Cell Immunol. 2025 May 13. pii: S0008-8749(25)00057-7. [Epub ahead of print]413 104972

Integrated proteomics and phosphoproteomics profiling dynamic signaling networks underlying two distinct types of macrophage activation.

Lihong Wu, Hang Xu, Xiaonan Zhang, Minghui Zhang, Yuting Xu, Qianyue Zhang, Huiying Tao, Changming Dong, Xinxin Zhang, Mingming Zhou, Jinbo Yang, Chunhua Lin, Qiaoling Song.

  Macrophages play a crucial role in antimicrobial host defense and those with differential maturation/differentiation status differ in inflammatory responses. Herein, GM-CSF and M-CSF primed mouse bone marrow derived macrophages (GM-BMDMs, GM and M-BMDMs, M), the well-established macrophage models in vitro, were utilized and their dynamic signaling changes in response to gram-negative bacteria component LPS treatment were analyzed using both 4D label-free proteomics and phosphoproteomics. Protein changes maintained relatively constant within or across GM and M macrophages post LPS challenge while phospho-protein exhibited more diverse and transient changes. Early induction of phospho-mediated GTPase activities, mRNA processing, and protein-mediated metabolic changes like oxidative phosphorylation (OXPHOS)/mitochondria function was identified at 1 h and maintained until 6 h post LPS treatment in GM and M while canonical TLR mediated MyD88-dependent and -independent pathways were activated at 3 and 6 h, individually at protein levels. Classical and novel phospho-sites for MyD88 and TRIF signaling pathways were also detected by phosphoproteomics. Comprehensively, the integrated protein and phospho-protein trend analysis was conducted and the core protein-phospho-protein network for the early phase actin reorganization, phagocytosis, and TLR signaling in both GM and M were presented. Taken together, these data described differences and similarities between these two types of macrophages in terms of their inflammatory responses to LPS.

Keywords:  GM-CSF; LPS challenge; M-CSF; Macrophage; Phosphoproteomics; Proteomics

DOI:  https://doi.org/10.1016/j.cellimm.2025.104972