bims-cediti Biomed News
on Cell death in innate immunity, inflammation, and tissue repair
Issue of 2026–01–11
sixteen papers selected by
Kateryna Shkarina, Universität Bonn



  1. Nat Cell Biol. 2026 Jan 06.
      Bursts of cell proliferation after infection, injury or transformation can coincide with DNA damage and spindle assembly defects. These increase the risk of cell cycle arrest in mitosis, during which many cellular processes are uniquely regulated. Ultimately, cells arrested during mitosis may die, but adaptive mechanisms also allow their escape into the next interphase. This step can have variable consequences, including chromosome missegregation, polyploidization and centrosome amplification. Escaping cells can also initiate innate immune signalling, enter senescence or engage cell death, which in turn alert the microenvironment through nucleic acid sensing mechanisms and/or the release of danger-associated molecular patterns. Here we discuss the causes and consequences of deregulated mitosis and postmitotic cell fate, highlighting the impact of DNA damage repair, the spindle assembly checkpoint and extra centrosomes on genome integrity, as well as inflammatory signalling. Finally, we attempt to reconcile conflicting observations and propose variable modes that activate innate immune responses after mitotic perturbations.
    DOI:  https://doi.org/10.1038/s41556-025-01785-9
  2. Proc Natl Acad Sci U S A. 2026 Jan 13. 123(2): e2517478123
      Nonsense-mediated decay (NMD) is an mRNA decay pathway which degrades potential harmful transcripts that contain premature termination codons. However, NMD's importance also extends to the control of isoform abundance under physiological conditions. During viral infection, NMD is inhibited through numerous mechanisms; however, NMD has been shown to have both antiviral as well as proviral activities, raising further questions into the role and control of NMD during viral infection. These observations have led us to investigate the potential involvement of NMD in dsRNA sensing as a mechanism that might explain these discrepancies. Using EIF4A2 exon 10B inclusion as an example of AS-NMD isoform accumulating during viral infection, we show that dsRNA sensing inhibits NMD. This effect is correlated with translational blockade and is driven primarily by RNaseL activation, and by PKR in the absence of RNaseL activation. Surprisingly, NMD inhibition limits the induction of IFN-β as well as interferon-stimulated genes, and this effect is upstream of IRF3 phosphorylation and translocation to the nucleus. NMD inhibition also decreases PKR and RNaseL activation as well as PIC-mediated cell death by decreasing the dsRNA content, suggesting NMD directly controls dsRNA sensing by controlling the dsRNA load. Therefore, inhibition of NMD upon dsRNA sensing provides a negative feedback loop that contributes to shaping the innate immune sensing pathways.
    Keywords:  RNaseL; dsRNA sensing; nonsense-mediated decay
    DOI:  https://doi.org/10.1073/pnas.2517478123
  3. Cell Rep. 2026 Jan 03. pii: S2211-1247(25)01455-X. [Epub ahead of print]45(1): 116683
      Increasing investigations indicate that neurotransmitters shape immune cell function; however, current results about glycine (Gly) in inflammatory macrophage responses are conflicting. Here, we found that Gly transporters support interleukin-1β (IL-1β) production in inflammatory macrophages, while Gly receptors inhibit it. Inflammatory macrophages have higher expression of Gly transporter 1 (GlyT1; also known as SLC6A9). Notably, SLC6A9 inhibition leads to extracellular accumulation of Gly and limits IL-1β production in inflammatory macrophages. Mechanically, extracellular Gly suppresses phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT1)/mammalian target of rapamycin (mTOR) signaling through the Gly receptor alpha-4 (Glrα4), thereby inhibiting activation of the NOD-like receptor 3 (NLRP3) inflammasome and IL-1β production. Furthermore, Gly supplementation or myeloid-specific SLC6A9 depletion alleviates the lipopolysaccharide (LPS)-induced inflammatory response in vivo. Collectively, our findings reveal a previously uncharacterized mechanism for the Gly-ergic system in regulating inflammatory macrophage function, providing a potential alleviating target for macrophage-associated diseases.
    Keywords:  CP: immunology; CP: metabolism; IL-1β; PI3K; SLC6A9; glycine; mTOR; macrophages
    DOI:  https://doi.org/10.1016/j.celrep.2025.116683
  4. bioRxiv. 2025 Dec 31. pii: 2025.12.30.697125. [Epub ahead of print]
      Much still remains to understand about the underlying molecular mechanisms by which the trafficking of small extracellular vesicles (sEVs) modulates innate immune responses during infection with pathogenic Gram-negative bacteria. To address this significant gap in knowledge, we used two infection models to investigate innate immune regulation by the sEVs released from cells infected with either Yersinia pestis (Yp) or Burkholderia thailandensis (Bt), designated as EXi-Yp and EXi-Bt respectively. The EXi induced differentiation of naïve human monocytes to macrophages and triggered robust pro- inflammatory cytokine release, including release of IL-6, mirroring direct bacterial infection effects. Comprehensive cell signaling analyses revealed that the EXi modulate a small set of host signaling proteins, with p38 activation being primarily responsible for the observed protective effects. EXi-induced p38 activation leads to increased IL-6 release, which in turn is responsible for decreased bacterial survival within recipient immune cells that are subsequently infected. Consistent with the in vitro results, mice administered with EXi-Yp exhibited elevated serum IL-6 levels and were protected from Yp infection. Furthermore, using our microfluidic chip platform that allows functional interrogation of EV effects under physiologically relevant conditions, we have demonstrated that EXi exchange between Yp-infected cells and naive recipient monocytes leads to differentiation of the recipient cells to macrophages. Together, our findings reveal a largely unexplored aspect of innate immunity and provide a mechanistic model in which EXi prime local and distant naïve monocytes via p38-induced differentiation and IL-6 production to protect against infection with Gram-negative bacteria.
    DOI:  https://doi.org/10.64898/2025.12.30.697125
  5. Sci Rep. 2026 Jan 09.
      The inflammasome is a multimeric intracellular complex that regulates caspase-1 activity in innate immunity, with NLRP3 serving as a central mediator of inflammatory responses. Despite extensive efforts, effective inhibitors of NLRP3 oligomerization remain limited. Here, we screened a library of small molecules and identified four candidates that disrupt homo-oligomerization of the NLRP3 pyrin domain (PYD). Among these, compound E9 exhibited superior affinity and specificity, as confirmed by split-luciferase complementation assays, microscale thermophoresis (Kd < 1 µM), molecular docking, and molecular dynamics simulations. Mechanistic analyses revealed that E9 binding induces targeted structural and dynamic remodeling of the PYD filament, dampening dominant collective motions and disrupting cooperative inter-subunit interactions. These changes reduce the filament's conformational flexibility and impair its ability to recruit ASC, thereby inhibiting inflammasome activation in THP1-ASC-GFP cells, as evidenced by suppression of speck formation. Overall, our study identifies E9 as a potent inhibitor of NLRP3 oligomerization and highlights interface-specific modulation of filament dynamics as a promising strategy for developing next-generation inflammasome-targeted therapeutics.
    Keywords:  Microscale thermophoresis; NLRP3 inflammasome; Pyrin domains; Pyroptosis; Split luciferase assay
    DOI:  https://doi.org/10.1038/s41598-026-35050-2
  6. Cell Host Microbe. 2026 Jan 06. pii: S1931-3128(25)00528-1. [Epub ahead of print]
      The NLRP6 inflammasome in intestinal epithelial cells (IECs) is a key sentinel of enteric pathogens, yet its activation mechanism remains enigmatic. Here, we identify monoubiquitination as a critical post-translational switch for NLRP6 inflammasome activation. We demonstrate that the E3 ligase UBE2O catalyzes dual-site monoubiquitination of NLRP6: at K680-687 to drive oligomerization via a conformational change, and at K115/130 within the nuclear localization signal to enforce cytoplasmic sequestration through steric hindrance. Mice harboring UBE2O deficiency or monoubiquitination-resistant NLRP6 mutations exhibit defective inflammasome activation and heightened susceptibility to rotavirus and Citrobacter rodentium infection. Furthermore, the UBE2O inhibitor arsenic trioxide suppresses NLRP6-dependent interleukin (IL)-18 secretion in acute promyelocytic leukemia (APL) patients. Thus, UBE2O-mediated dual-site monoubiquitination emerges as a central mechanism licensing NLRP6 inflammasome activation, revealing a new target for modulating intestinal immunity.
    Keywords:  NLRP6; UBE2O; conformational transition; cytoplasmic sequestration; infection; inflammasome; inflammation; monoubiquitination; oligomerization; steric hindrance
    DOI:  https://doi.org/10.1016/j.chom.2025.12.009
  7. Cell Death Differ. 2026 Jan 08.
      Sepsis, a devastating microbe-induced inflammatory response, culminates in multi-organ dysfunction, with pyroptosis mediated by the non-canonical inflammasome being a pivotal factor. The mouse Caspase-11, central to this pathway, is directly activated by cytoplasmic lipopolysaccharide (LPS). Although ubiquitination is known to tightly regulate the inflammatory response in pyroptosis, its role in modulating the non-canonical inflammasome remains enigmatic. In this study, we unveil that the E3 ubiquitin ligase Smurf1 is a critical negative regulator of the non-canonical inflammasome pathway. Smurf1 orchestrates K48-linked polyubiquitination of Caspase-11 at K245 and K247 residues, leading to its degradation via the 26S proteasome. This process is further amplified by ERK phosphorylation of Smurf1 at the S148 site. In parallel, Caspase-11 modulates Smurf1 protein content through cleavage. Notably, macrophage-specific Smurf1 deficiency exacerbates sepsis-induced mortality in mice, attributed to the hyperactivation of the non-canonical inflammasome. Conversely, targeted supplementation of Smurf1 in macrophages mitigates the high mortality and inflammatory response associated with sepsis. Thus, Smurf1 emerges as a key player in modulating the activation of the non-canonical inflammasome in response to Gram-negative bacterial infections.
    DOI:  https://doi.org/10.1038/s41418-025-01654-w
  8. bioRxiv. 2026 Jan 02. pii: 2025.12.31.697179. [Epub ahead of print]
      Bacterial sepsis remains a devastating clinical problem. Here, we describe a protective role for the recently discovered acid-sensitive, proton-activated chloride channel, PACC1 (PAC/ASOR/TMEM206), during sepsis. Initially, we found PACC1 was enriched in healthy human and mouse mononuclear phagocytes, particularly macrophages, and differentially regulated by inflammatory stimuli, suggesting PACC1 involvement in innate immunity. To further investigate, we generated de novo Pacc1 knockout ( -/- ) mice, which presented without major immunologic abnormalities at baseline. Compared to wildtype (WT), Pacc1 -/- myeloid cells showed normal phagocytic uptake of acid-insensitive Escherichia coli BioParticles , but impaired development of the acidifying phagolysosome using pH-sensitive E. coli BioParticles. Transcriptomic profiling of Pacc1 -/- macrophages revealed dysregulated phagolysosomal and cytokine networks (e.g., interferons). Because phagolysosomal bacterial clearance is essential to resolve infection, we challenged Pacc1 -/- mice with intraperitoneal gram-negative E. coli sepsis. Pacc1 -/- mice displayed increased bacterial burden, immune cell infiltration, inflammation, and lethality. Additionally, gram-positive pneumococcal pneumonia was also more severe in Pacc1 -/- mice, indicating broad anti-bacterial PACC1 impact. In contrast, phagocytosis-independent E. coli lipopolysaccharide (LPS)-induced endotoxemia yielded comparable WT and Pacc1 -/- survival, as well as similar inflammatory responses. Finally, we engineered Pacc1 -floxed ( fl/fl ) mice crossed with a myeloid lineage Cre-deleter strain to interrogate myeloid cell-intrinsic PACC1 in vivo . Consistent with a predominate role for PACC1 during phagocytosis and bacterial clearance in these cells, LysM-Cre/Pacc1 fl/fl mice exhibited impaired E. coli sepsis survival but indifferent endotoxemia phenotypes. In conclusion, PACC1 links sterilizing phagolysosomal activity with immune networks in sepsis pathobiology.
    Significance Statement: Bacterial sepsis remains a major global health burden. Here, we report an essential role for the recently discovered acid-sensitive chloride channel, PACC1 (PAC/ASOR/TMEM206), in protective host defense during bacterial infection and sepsis. PACC1 is highly expressed in human and mouse phagocytic myeloid cells, particularly macrophages, where it regulates phagocytic bacterial clearance and inflammatory responses. Using de novo generated mice, we show that global or myeloid cell-targeted deletion of PACC1 impairs development of phagolysosomal acidification, confers susceptibility to bacterial infection and excessive inflammation, and undermines host defense. These findings warrant further investigation to better understand PACC1 in sepsis pathobiology.
    DOI:  https://doi.org/10.64898/2025.12.31.697179
  9. Int Immunopharmacol. 2026 Jan 08. pii: S1567-5769(26)00022-6. [Epub ahead of print]171 116179
      Uncontrolled formation of neutrophil extracellular traps (NETs) is one of the main mechanisms leading to death in septic patients. PFKFB3, a notable enzyme of glycolysis metabolism, is involved in the inflammatory activation of granulocytes. Our previous studies demonstrated that PFKFB3-involved glycolytic metabolism supports CXCR4hi neutrophil inflammatory activation, which is a key mechanism for the inflammatory injury of the lungs induced by sepsis. However, the specific mechanism by which PFKFB3 supports NET formation in sepsis remains unclear. Here, we found that high expression of neutrophil PFKFB3 is essential for sepsis-induced NET formation. Further mechanistic studies revealed that PFKFB3 promoted sepsis-related NET formation via glycolytic reprogramming and peptidylarginine deiminase 4 (PAD4)-dependent chromatin decondensation. However, inhibiting glycolytic metabolism supported by PFKFB3 can significantly reduce PAD4-dependent NET formation and alleviate sepsis-related lung inflammatory damage. In summary, our results revealed that PFKFB3-supported glycolytic metabolism promotes sepsis-induced NET formation via PAD4-mediated chromatin decondensation. Targeting PFKFB3-supported glycolysis represents a potential strategy to alleviate sepsis-induced hyperinflammation and tissue damage.
    Keywords:  Glycolysis; NET; Neutrophil; PAD4; PFKFB3; Sepsis
    DOI:  https://doi.org/10.1016/j.intimp.2026.116179
  10. Cell Death Dis. 2026 Jan 03.
      T cell recovery is critical following damage, such as hematopoietic cell transplantation (HCT), with increased reconstitution associated with improved clinical outcomes. Endogenous thymic regeneration, a crucial process for restoring immune competence following cytoreductive therapies such as HCT conditioning, is often delayed, limiting T cell reconstitution. Fully understanding the molecular mechanisms driving regeneration is therefore crucial for uncovering therapeutic targets that can be exploited to enhance thymic function. Here, we identified that CD4+ CD8+ thymocytes rapidly and acutely undergo lytic cell death, specifically pyroptosis, following acute damage caused by ionizing radiation, and release damage-associated molecular patterns (DAMPS) into the thymic microenvironment, including ATP. Extracellular ATP stimulates the P2Y2 purinergic receptor on thymic epithelial cells (TECs)-a stromal cell crucial for supporting T cell development-resulting in the upregulation FOXN1, the master TEC transcription factor. Targeting the P2Y2 receptor with a P2Y2 agonist, UTPγS, promotes rapid regeneration of the TEC compartment in vivo following acute damage. These findings reveal a novel damage-sensing mechanism employed by the thymus where thymocytes adopt an alternative cell death mechanism which promotes thymic repair via P2Y2 signaling in TECs. This work identifies P2Y2 as a promising therapeutic target for enhancing thymus regeneration and improving immune recovery after HCT.
    DOI:  https://doi.org/10.1038/s41419-025-08345-x
  11. bioRxiv. 2025 Dec 30. pii: 2025.12.30.697096. [Epub ahead of print]
      Bax functions as a proapoptotic protein perforating the mitochondrial membrane to release mitochondrial proteins and DNA that kill the cell. Structures of full-length Bax monomer in solution and core domain dimers in solution and bound to lipid/detergent bicelles reveal how Bax proteins must be activated, unfold, refold and dimerize prior to forming oligomeric pores in the membrane. In particular, amphipathic core dimer forms part of the pore wall between the nonpolar lipid bilayer and the aqueous conduit. However, atomic resolution structures of other parts of the pore were scarce. Here, we elucidate a structure of Bax C-terminal α-helix 9 (α9) in lysolipid micelles using NMR. According to this high-resolution structure the α9 regions form an amphipathic helical dimer with an extended nonpolar interface and several uncharged polar residues on the surface. Structure-guided mutagenesis and functional assessment demonstrate that the nonpolar interactions are important for Bax dimerization in and perforation of the mitochondrial membrane. Surprisingly the polar residues are also important because they form bifurcated hydrogen bonds between helical turns to stabilize each helix and thereby the dimer. Molecular dynamics simulations of an oligomer constructed with wall-forming core and transmembrane α9 dimers linked by flexible α6-α7-α8 bridges in a mitochondrial lipid bilayer generate an atomic resolution model for a stable Bax pore capable to release cytochrome C. Thus, we made an important step toward elucidating molecular mechanisms of apoptotic Bax perforation.
    DOI:  https://doi.org/10.64898/2025.12.30.697096
  12. Nat Rev Immunol. 2026 Jan 05.
      Ubiquitination, the covalent attachment of ubiquitin to proteins and other cellular substrates, is a dynamic post-translational modification that enables cells to rapidly respond to internal and external threats. Beyond its canonical role in targeting proteins for proteasomal degradation, ubiquitination orchestrates the assembly of signalling complexes that regulate innate and adaptive immune responses, modulates inflammatory pathways and directs selective autophagy to eliminate intracellular pathogens through lysosomal degradation. To persist and replicate within the host, viruses, bacteria and parasites have evolved diverse mechanisms to evade, manipulate or exploit the host's ubiquitin and autophagy machinery. Some pathogens subvert these systems to dampen immune surveillance, whereas others co-opt them to facilitate replication or dissemination. In this Review, we examine how ubiquitin and autophagy shape host-pathogen interactions, uncover common and pathogen-specific strategies of immune evasion, and discuss emerging therapeutic approaches that aim to leverage these interconnected pathways to enhance antimicrobial immunity.
    DOI:  https://doi.org/10.1038/s41577-025-01239-1
  13. Cell Mol Immunol. 2026 Jan 06.
      Innate immunity in host cells must be rapidly activated to combat invading microbes. Upon RIG-I activation, the transcription of type I interferons is induced within one hour in virus-infected cells. Previous studies have shown that endogenous MAVS spreads signals via aggregation on the mitochondrial membrane, whereas truncated recombinant MAVS forms prion-like filaments in vitro. How MAVS transmits signals so quickly, and the molecular architecture of its membrane aggregates, remains elusive. Here, we report that activated MAVS forms fibrils encircling its resident mitochondrion or connecting neighboring mitochondria with a "ladder-like" structure, allowing the activation of dormant MAVS on encountered mitochondria. This "intermitochondrial activation" process promotes a rapid antiviral response in cells to overcome the immediate danger caused by viruses. Moreover, stuck MAVS fibrils between mitochondria have limited cytosolic protein access and thus relay signals poorly. This study demonstrated that prion-like MAVS fibrils cluster in mitochondria to ensure a rapid antiviral response.
    Keywords:  Innate immunity; MAVS; mitochondria; prion-like fibrillation; viral infection
    DOI:  https://doi.org/10.1038/s41423-025-01382-8
  14. Front Immunol. 2025 ;16 1665811
      Elimination of latently and persistently HIV-infected cells is one of the main barriers to finding a cure for HIV. We have demonstrated that cells latently/persistently infected with HIV impair interferon signaling, which makes them susceptible to selective infection and killing by the oncolytic virus (OV) MG1. Sensitizing these cells to MG1-mediated killing can be expected to make MG1 a more effective therapeutic. As small-molecule second mitochondria-derived activator of caspases (SMAC) mimetics have been shown to increase OV-mediated death in cancer models, we used the SMAC mimetics LCL-161 and birinapant alongside MG1 to enhance the killing of HIV-infected cell lines and monocyte-derived macrophages (MDMs). We show that SMAC mimetics enhance MG1-mediated death, but that this is not a result of an increase in OV infection. This cell death occurs via both caspase-dependent and caspase-independent mechanisms and is not completely dependent on tumor necrosis factor alpha (TNFα). Together, these results show that the use of SMAC mimetics alongside OVs may be a viable strategy to eradicate latently/persistently HIV-infected cells.
    Keywords:  HIV; MG1; SMAC mimetics; VSV; oncolytic viruses
    DOI:  https://doi.org/10.3389/fimmu.2025.1665811
  15. Cell Chem Biol. 2026 Jan 06. pii: S2451-9456(25)00395-2. [Epub ahead of print]
      Caspase-1 (CASP1) is best known for regulating IL-1β processing and pyroptosis; however, its role in leukemia has not been clearly defined. Here, we show that loss of CASP1 impairs leukemic cell growth, drives differentiation, and reduces leukemic burden in vivo, independent of its CASP1 protease activity. Instead, CASP1 functions as a scaffolding hub, controlling nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) signaling via its interaction with raptor (RPTOR), a component of mTORC1. Deletion of CASP1 or disruption of its CARD domain induces excessive NF-κB activity and impairs leukemic cell function. We further developed a proteolysis-targeting chimera (PROTAC) degrader that selectively depletes Pro-CASP1 and suppresses leukemic cells. These findings reveal CASP1 as a regulator of mTORC1-NF-κB signaling in leukemia and highlight its scaffolding activity as a therapeutic vulnerability.
    Keywords:  AML; CASP1; NF-κB; RAPTOR; inflammasome; mTOR
    DOI:  https://doi.org/10.1016/j.chembiol.2025.12.002
  16. Mol Cell. 2026 Jan 08. pii: S1097-2765(25)01023-8. [Epub ahead of print]
      Replication stress is a key driver of DNA damage and genome instability. Here, we report that replication stress induces an inflammatory response in the absence of DNA damage. The DNA-sensing factor interferon-γ-inducible factor 16 (IFI16) binds nascent DNA at stalled replication forks and signals via the adaptor stimulator of interferon genes (STING) to induce activation of nuclear factor κB (NF-κB) and the production of pro-inflammatory cytokines, independently of the cytosolic DNA sensor cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS). Replication stress-induced fork remodeling generates a new DNA end that is vulnerable to degradation by nucleases and is protected by a range of factors, including the tumor suppressors BRCA1 and BRCA2. IFI16 acts directly at stalled replication forks to protect nascent DNA from degradation by the nucleases MRE11, EXO1, and DNA2. Furthermore, IFI16 is required for the interferon-mediated rescue of fork protection in BRCA-deficient cells, highlighting the critical role of IFI16 in the crosstalk between innate immunity and fork protection during replication stress.
    Keywords:  BRCA1; BRCA2; DNA sensing; IFI16; IL-6; MRE11; NF-κB; STING; fork protection; inflammation; replication stress; reversed replication forks
    DOI:  https://doi.org/10.1016/j.molcel.2025.12.024