bims-cediti 2025-08-10 papers

bims-cediti

Biomed News

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

Issue of 2025–08–10
ten papers selected by
Kateryna Shkarina, Universität Bonn

Ofirnoflast: a first-in-class NEK7-targeted inhibitor of the NLRP3 inflammasome.
10 things you wish you knew about inflammatory caspases: a holistic review of their biochemistry, activation, and signalling.
Harnessing Immunogenic Cell Death to Boost the Impact of Radiation Therapy.
RNA N-glycosylation enables immune evasion and homeostatic efferocytosis.
A threshold level of JNK activates damage-responsive enhancers via JAK/STAT to promote tissue regeneration.
Phosphatidic acid production on the vacuole harboring Legionella pneumophila is a signal for recognition of interferon-induced GTPases.
Integrated real-time imaging of executioner caspase dynamics, apoptosis-induced proliferation, and immunogenic cell death using a stable fluorescent reporter platform.
A two-step mechanism for RIG-I activation by influenza virus mvRNAs.
A noncanonical cytoplasmic role for BUB1 in restraining DNA damage-induced dsRNA accumulation and sensing within stress granules.
Terminal Loop Sequences in Viral Double-Stranded RNAs Modulate RIG-I Signaling.

J Drug Target. 2025 Aug 08. 1-13

Ofirnoflast: a first-in-class NEK7-targeted inhibitor of the NLRP3 inflammasome.

Alexis Mollard, Devan Bursey, William Burnett, Taylor Avei, Benjamin Bearss, Ramesh Subbiah, Viduth K Chaugule, Naga Srinivas Tripuraneni, Shipra Bijpuria, Russ Teichert, Chadwick Davis, Margit Janat-Amsbury, Jared Bearss, David Bearss.

  Ofirnoflast is a first-in-class, orally bioavailable NEK7 inhibitor currently undergoing Phase 2 clinical evaluation. It disrupts NLRP3 inflammasome assembly by targeting NEK7's scaffolding function-blocking complex formation independently of NLRP3 activation status, upstream of caspase activation, pyroptosis, and inflammatory cytokine release. This mechanism offers a novel therapeutic approach for chronic inflammation. Unlike NSAIDs, corticosteroids, cytokine-neutralising biologics, and NLRP3-directed small molecules-which are frequently limited by off-target effects, immunosuppression, or incomplete efficacy-ofirnoflast provides a targeted approach with fewer anticipated liabilities. We demonstrate that ofirnoflast engages an allosteric site adjacent to NEK7's ATP-binding pocket, inducing conformational shifts that impair its scaffolding function. In THP-1 macrophages and iPSC-derived microglia, ofirnoflast suppresses ASC specks, IL-1β release, and pyroptotic cell death. Biophysical assays and molecular dynamics simulations confirm that ofirnoflast stabilises NEK7 in a unique conformation and suggest a type-2 kinase-inhibitor binding mode. In vivo, ofirnoflast exhibits oral bioavailability, achieving systemic exposures well above cellular potency thresholds. In a DSS-induced colitis model, treatment significantly reduces cytokine levels and improves phsyiological outcomes. Collectively, these findings validate NEK7 as a druggable checkpoint for NLRP3 inflammasome control and position Ofirnoflast as a mechanistically distinct, clinically advanced candidate for treating inflammation driven by aberrant inflammasome activation.

Keywords:  IL-1β; NEK7; NLRP3; inflammasome; inflammation

DOI:  https://doi.org/10.1080/1061186X.2025.2542856
J Biol Chem. 2025 Aug 02. pii: S0021-9258(25)02408-1. [Epub ahead of print] 110557

10 things you wish you knew about inflammatory caspases: a holistic review of their biochemistry, activation, and signalling.

Sebastian Grant, Dave Boucher.

Caspases are a family of cysteine proteases conserved across all multicellular life which play critical functions that range from cell death, inflammation and cellular differentiation. Caspases cleave a subset of protein substrates after aspartic acid residues, which subsequently leads to defining cellular consequences. Inflammatory caspases are a subfamily of caspases which are activated by signalling platforms known as inflammasomes, which are assembled upon sensing of diverse sterile and microbial stimuli. Upon their activation, inflammatory caspases generate a potent inflammatory response that is critical to control infections and maintain homeostasis, but can also drive numerous disease pathologies. A robust understanding of inflammatory caspase activation, substrate selectivity and wider functions is critical to aid the development of therapeutics which can fine-tune their activity for the treatment of disease. In this review, we provide a holistic overview of inflammatory caspase activation, activity, and signalling, highlighting the biochemical features controlling these elements.

DOI: https://doi.org/10.1016/j.jbc.2025.110557
Cancer J. 2025 Jul-Aug 01;31(4):pii: e0780. [Epub ahead of print]31(4):

Harnessing Immunogenic Cell Death to Boost the Impact of Radiation Therapy.

Jonathan Mannion, Pascal Meier.

  Harnessing radiotherapy (RT) to effectively eliminate cancer cells has been a cornerstone of clinical oncology for decades. Beyond its well-established cytotoxic effects, RT triggers a diverse array of tumor cell death modalities, including apoptosis, necrosis, mitotic catastrophe, and, under specific conditions, immunogenic forms such as necroptosis and pyroptosis. Although apoptosis serves as a homeostatic and immunologically silent process that removes over 200 billion cells daily in our body, lytic forms of regulated cell death, such as necroptosis and pyroptosis, have evolved to detect and combat pathogens, thereby acting as potent danger signals that alert and mobilise immune responses. Here, we review emerging pathogen-mimicry approaches to rewire RT-induced cell death towards more immunogenic cell death modalities, aiming to transform RT from a primarily tumor-debulking modality into a driver of durable anti-tumor immunity.

Keywords:  Immunogenic cell death; RIP kinases; apoptosis; ferroptosis; immunotherapy; necroptosis; pyroptosis; radiotherapy

DOI:  https://doi.org/10.1097/PPO.0000000000000780
Nature. 2025 Aug 06.

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis.

Vincent R Graziano, Jennifer Porat, Marie Dominique Ah Kioon, Ivana Mejdrová, Alyssa J Matz, Charlotta G Lebedenko, Peiyuan Chai, John V Pluvinage, Rafael Ricci-Azevedo, Andrew G Harrison, Skylar S Wright, Xinzheng Wang, Madison S Strine, Penghua Wang, Michael R Wilson, Sivapriya Kailasan Vanaja, Beiyan Zhou, Franck J Barrat, Thomas Carell, Ryan A Flynn, Vijay A Rathinam.

Glycosylation is central to the localization and function of biomolecules1. We recently discovered that small RNAs undergo N-glycosylation2 at the modified RNA base 3-(3-amino-3-carboxypropyl) uridine (acp3U)3. However, the functional significance of N-glycosylation of RNAs is unknown. Here we show that the N-glycans on glycoRNAs prevent innate immune sensing of endogenous small RNAs. We found that de-N-glycosylation of cell-culture-derived and circulating human and mouse glycoRNA elicited potent inflammatory responses including the production of type I interferons in a Toll-like receptor 3- and Toll-like receptor 7-dependent manner. Furthermore, we show that N-glycans on cell surface RNAs prevent apoptotic cells from triggering endosomal RNA sensors in efferocytes, thus facilitating the non-inflammatory clearance of dead cells. Mechanistically, N-glycans conceal the hypermodified uracil base acp3U, which we identified as immunostimulatory when exposed in RNA. Consistent with this, genetic deletion of an enzyme (DTWD2) that synthesizes acp3U abrogated innate immune activation by de-N-glycosylated small RNAs and apoptotic cells. Furthermore, synthetic acp3U-containing RNAs are sufficient to trigger innate immune responses. Thus, our study has uncovered a natural mechanism by which N-glycans block RNAs from inducing acp3U-dependent innate immune activation, demonstrating how glycoRNAs exist on the cell surface and in the endosomal network without inducing autoinflammatory responses.

DOI: https://doi.org/10.1038/s41586-025-09310-6
Development. 2025 Aug 07. pii: dev.204632. [Epub ahead of print]

A threshold level of JNK activates damage-responsive enhancers via JAK/STAT to promote tissue regeneration.

John W Quinn, Mariah C Lee, Chloe Van Hazel, Melissa A Wilson, Robin E Harris.

  Tissue regeneration requires precise activation and coordination of genes, many of which are reused from development. While key factors have been identified, how their expression is initiated and spatially regulated after injury remains unclear. The stress-activated MAP kinase JNK is a conserved driver of regeneration and promotes expression of genes involved in proliferation, growth, and cell fate changes in Drosophila. However, how JNK selectively activates its targets in damaged tissue is not well understood. We previously identified Damage-Responsive, Maturity-Silenced (DRMS) enhancers as JNK-activated elements critical for regeneration. Here, we show that cell death is dispensable for the activation of these enhancers, which only depends on JNK and its immediate downstream effectors. One of these is JAK/STAT, which acts as a direct, additional input necessary to expand enhancer activity into the wound periphery where JNK alone is insufficient. Furthermore, we demonstrate that a threshold level of JNK is required to initiate enhancer activation. Together, our findings reveal how JNK and JAK/STAT signaling cooperate to drive spatially and temporally regulated gene expression through damage-responsive enhancers, ensuring proper regenerative outcomes.

Keywords:  Drosophila; Enhancer; Gene regulation; JAK/STAT; JNK; Regeneration

DOI:  https://doi.org/10.1242/dev.204632
Proc Natl Acad Sci U S A. 2025 Aug 12. 122(32): e2420096122

Phosphatidic acid production on the vacuole harboring Legionella pneumophila is a signal for recognition of interferon-induced GTPases.

Hiromu Oide, Tomoko Kubori, Hiroki Nagai, Takashi Nozawa, Ichiro Nakagawa, Miwa Sasai, Masahiro Yamamoto, Kohei Arasaki.

  The interferon (IFN)-inducible GTPases play a crucial role in cell autonomous immunity against intracellular pathogens. Particularly, these GTPases directly recognize the host membrane-derived vacuole containing pathogens and subsequently destroy it. Although it has been revealed that these GTPases target the membrane of Legionella pneumophila (L. pneumophila)-containing vacuole (LCV), molecular mechanism has been totally uncleared. Here, we show that mouse guanylate-binding protein 2 (mGBP2) is specifically recruited to the LCV and subsequently ruptures it. Furthermore, we also show that mGBP2 recognizes phosphatidic acid (PA) produced by the Legionella effector Lpg2552 and fails to target the vacuole harboring Lpg2552-depleted L. pneumophila. Consistently, this strain successfully grows in cells expressing mGBP2. We additionally identified lysine 585 (K585) of mGBP2 is required for the binding to PA and K585-mutated mGBP2 fails to recognize LCV. Interestingly, this lysine residue is only conserved in GBP1 among human GBPs and the conserved lysine residue is important for PA recognition and subsequent LCV distribution. Importantly, L. pneumophila lacking Lpg2552 exhibits high resistance against IFN stimulation in THP-1-derived human macrophage.

Keywords:  GBP; Legionella pneumophila; Lpg2552; cell autonomous immunity; phosphatidic acid

DOI:  https://doi.org/10.1073/pnas.2420096122
Cell Death Discov. 2025 Aug 06. 11(1): 368

Integrated real-time imaging of executioner caspase dynamics, apoptosis-induced proliferation, and immunogenic cell death using a stable fluorescent reporter platform.

Selen Selcen, Lena Wieland, Tiago De Oliveira, Michael Ghadimi, Lena-Christin Conradi, Günter Schneider, Leonie Witte, Matthias Wirth.

Regulated cell death plays a central role in tissue homeostasis, disease progression, and therapeutic responses. However, tools to study these processes with high spatiotemporal resolution in physiologically relevant systems remain limited. Here, we present a fluorescent reporter cell system that enables real-time visualization of caspase-3/-7 activity via a DEVD-based biosensor, alongside a constitutive fluorescent marker for assessing successful transduction and cell presence. We generated stable cell lines expressing this reporter and adapted them to both 2D and 3D culture systems, including organoids. This platform allowed dynamic tracking of apoptotic events and viability loss at single-cell resolution. Using a proliferation dye, we also detected apoptosis-induced proliferation in neighboring cells. Furthermore, the system enabled simultaneous detection of immunogenic cell death via an endpoint measurement of surface calreticulin exposure by flow cytometry, supporting its application in studying immunogenic signaling. By measuring and integrating multiple cell death readouts by live-cell imaging, our system is well-suited for high-content screening and mechanistic dissection of different modes of cell death. When combined with complementary markers of pyroptosis and necroptosis, this platform may also be extended to investigate more complex, integrated forms of cell death.

DOI: https://doi.org/10.1038/s41420-025-02662-y
Sci Adv. 2025 Aug 08. 11(32): eadw8034

A two-step mechanism for RIG-I activation by influenza virus mvRNAs.

Emmanuelle Pitré, Karishma Bisht, Kaleigh A Remick, Amir Ghorbani, Jonathan W Yewdell, Elizaveta Elshina, Aartjan J W Te Velthuis.

Influenza A virus (IAV) noncanonical RNAs are bound by retinoic acid-inducible gene I (RIG-I). However, innate immune activation is infrequent and it is not understood why noncanonical IAV RNAs activate RIG-I in a sequence- or RNA structure-dependent manner. We hypothesized that multiple events need to occur before IAV RNA synthesis activates RIG-I and investigated whether RIG-I activation is stimulated by the noncanonical or aberrant transcription of mini viral RNAs (mvRNA), an RNA that is overexpressed in highly pathogenic IAV infections. We find that mvRNAs can cause noncanonical transcription termination through a truncated 5' polyadenylation signal or a 5' transient RNA structure that interrupts polyadenylation. The resulting capped complementary RNAs stimulate the release of an mvRNA and complement RIG-I activation in trans. Overall, our findings indicate that sequential rounds of noncanonical or aberrant viral replication and transcription are needed for innate immune signaling by IAV RNA synthesis.

DOI: https://doi.org/10.1126/sciadv.adw8034
Sci Immunol. 2025 Aug 08. 10(110): eadq2055

A noncanonical cytoplasmic role for BUB1 in restraining DNA damage-induced dsRNA accumulation and sensing within stress granules.

Mengjie Hu, Dong Pan, Meng Jiao, Xuhui Bao, Xinjian Liu, Fang Li, Chuan-Yuan Li.

Budding uninhibited by benzimidazoles 1 (BUB1) is a nuclear serine/threonine protein kinase that ensures proper chromosome segregation before mitosis. We report that BUB1 plays an unexpected cytoplasmic role in restraining DNA damage-induced accumulation of cytoplasmic dsRNA and the ensuing immune response. Tumors deficient in BUB1 were sensitive to radiotherapy in a CD8 T cell-dependent manner. We found increased immune cell infiltration accompanied by elevated type I interferon production from irradiated BUB1-deficient cells caused by enhanced cytoplasmic dsRNA accumulation and activation of the MDA5/MAVS dsRNA-sensing pathway. Mechanistically, we found that after radiation exposure, BUB1 underwent nucleus-to-cytoplasm migration, where it bound and phosphorylated the poly(A)-binding protein PABPC1, which was degraded together with its associated messenger RNAs stored in the stress granules, thereby preventing dsRNA accumulation and activation of the innate immune response.

DOI: https://doi.org/10.1126/sciimmunol.adq2055
bioRxiv. 2025 Aug 02. pii: 2025.08.02.668285. [Epub ahead of print]

Terminal Loop Sequences in Viral Double-Stranded RNAs Modulate RIG-I Signaling.

Matthew Hackbart, Patrick Wang, Victoria Gnazzo, Carolina B Lopez.

Detection of foreign RNAs is a crucial activation step for innate immunity pathways in response to viral infections. Retinoic acid-inducible gene I (RIG-I) is a cytoplasmic RNA sensor that triggers type I and III interferon (IFN) expression and activates the antiviral response. The activating ligand for RIG-I has been shown to be 5'-triphosphated blunt-ended double stranded(ds) RNA, but questions remain on the molecular mechanisms for RIG-I activation during viral infections. Here we show that immune-activating copy-back viral genomes (cbVGs) contain RNA stem loops away from the 5' end of the RNA that enhance RIG-I signaling and IFN expression. Importantly, the sequence of the terminal loops of the activating motifs impacts the strength of IFN expression. Additionally, we show that synthetic versions of these cbVG-derived stem loops trigger innate immune responses in mice demonstrating their potential as immunostimulants in vivo.

DOI: https://doi.org/10.1101/2025.08.02.668285